Molecular/Cytogenetics Flashcards

Question

STK11/LKB1 gene.

Answer 1

The STK11/LKB1 gene, also called just the STK11 gene, encodes a member of the serine/threonine kinase, and regulates cell polarity and functions as a tumor suppressor. It is located on chromosome 19p13.3. The protein kinase encoded by the gene is Serine/threonine kinase 11 (STK11), AKA liver kinase B1 (LKB1), AKA renal carcinoma antigen (NY-REN-19). Germline mutations in this gene have been associated with Peutz-Jeghers syndrome, an autosomal dominant disorder characterized by the growth of polyps in the GI tract, pigmented macules on the skin and mouth, and other neoplasms. Recent studies have uncovered a large number of somatic mutations of the LKB1 gene that are present in lung, cervical, breast, intestinal, testicular, pancreatic and skin cancer.

Answer 2

Molecular findings in FD, and especially those for MAS, suggest it is caused by a somatic mutation early in embryonic life that causes a gene mosaicism. The earlier the mutation occurs, the more widespread the effects will be. The gene is located on 20q13, an area that codes for the alpha subunit on G-protein receptors. This mutation is also present in various endocrine tumors as well as FD. The G-proteins begin a cascade that ultimately leads to activation of the enzyme adenylyl cyclase that produces cAMP. In MAS, there is a missense mutation that causes the substitution of arginine in position 201 of the Gs-alpha gene. Normally, there is an almost immediate deactivation of adenylyl cyclase and a breakdown of the cAMP. In MAS, that does not occur. Overproduction of cAMP leads to increased amounts of activity that affect each tissue differently based on its designated function.

Answer 3

Whereas autosomal-dominant hyperimmunoglobulin E syndrome is caused by mutations in STAT3, DOCK8 and TYK2 mutations are implicated in the comparatively rare autosomal-recessive forms of the disease.

Answer 4

Pyrosequencing is a method of DNA sequencing (determining the order of nucleotides in DNA) based on the "sequencing by synthesis" principle. It differs from Sanger sequencing, in that it relies on the detection of pyrophosphate release on nucleotide incorporation, rather than chain termination with dideoxynucleotides. The technique was developed in Stockholm in 1996. The desired DNA sequence is able to be determined by light emitted upon incorporation of the next complementary nucleotide by the fact that only one out of four of the possible A/T/C/G nucleotides are added and available at a time so that only one letter can be incorporated on the single stranded template (which is the sequence to be determined). The intensity of the light determines if there are more than one of these "letters" in a row. The previous nucleotide letter (one out of four possible dNTP) is degraded before the next nucleotide letter is added for synthesis: allowing for the possible revealing of the next nucleotide(s) via the resulting intensity of light (if the nucleotide added was the next complementary letter in the sequence). This process is repeated with each of the four letters until the DNA sequence of the single stranded template is determined.

Answer 5

First, compared to Sanger sequencing, pyrosequencing has has higher sensitivity. Sanger sequencing needs greater than 20 % of tumor load in a specimen to render a reliable result, while pyrosequencing can render a reliable result with 5 % tumor load. Second, pyrosequencing is faster than Sanger sequencing. Third, pyrosequencing is more cost effective. One of the disadvantages of pyrosequencing is that it can only sequence a short length of nucleotide sequence. Currently, a limitation of the method is that the lengths of individual reads of DNA sequence are in the neighborhood of 300-500 nucleotides, shorter than the 800-1000 obtainable with chain termination methods (e.g. Sanger sequencing). This can make the process of genome assembly more difficult, particularly for sequences containing a large amount of repetitive DNA. As of 2007, pyrosequencing is most commonly used for resequencing or sequencing of genomes for which the sequence of a close relative is already available. The other disadvantage is that pyrosequencing data analysis sometimes can be complex and challenging, and some date analysis is done by a manual process.

Answer 6

Fabry disease (also known as Fabry's disease, Anderson-Fabry disease, angiokeratoma corporis diffusum, and alpha-galactosidase A deficiency) is a rare X-linked lysosomal, which can cause a wide range of systemic symptoms. It is a form of sphingolipidosis, as it involves dysfunctional metabolism of sphingolipids. The disease is named after one of its discoverers, Johannes Fabry (June 1, 1860–June 29, 1930).

Answer 7

Lymphangioleiomyomatosis (or lymphangiomyomatosis) (LAM) occurs almost exclusively in reproductive age women and consists of a proliferation of immature myoid cells which are currently thought to derive from perivascular epitheliod cells (PEC). LAM may involve the lungs and axial thoraco-abdominal lymphatic system including both lymph nodes and the thoracic duct. Supraclavicular and inguinal nodes may rarely be involved. In most cases, the pulmonary manifestations dominate but LAM may occasionally present exclusively in the abdomen. Abdominal LAM may mimic ovarian carcinoma radiographically and patients may present with pain, often due to hemorrhage. LAM may occur in association with tuberous sclerosis (TS) or in isolation (sporadic LAM), although in either form the LAM cells may be associated with mutations of the TS genes, TSC-1 or TSC-2. Whether LAM is sporadic or associated with TS, the histologic appearance is the same but lymph node involvement is more frequent in patients without TS.

Answer 8

Synovial sarcoma is a spindle cell tumor arising in soft tissue which displays variable epithelial differentiation including glandular formation. It also has a specific genetic alteration, a chromosomal translocation t(X;18), that results in a fusion between the SS18 (SYT) gene on chromosome 18 and one of the SSX genes on the X chromosome, creating SS18-SSX1, SS18-SSX2, or SS18-SSX4 chimeric genes.

Answer 9

TLE1 is one of four transducin-like enhancer of split (TLE) genes that encode human transcriptional repressors. It is an important protein in the Wnt/Beta-catenin pathway, a signaling pathway that is strongly associated with SS. Strong nuclear TLE1 expression is a robust IHC biomarker for SS, particularly in those cases that do not exhibit biphasic histology, and helps distinguish this tumor from other spindle cell tumors. In an appropriate clinical background and morphology, strong nuclear TLE1 expression in a CD34-negative spindle cell tumor containing scattered CK-positive cells can be regarded as diagnostic of SS.

Answer 10

Clear cell sarcoma of soft tissue is a rare tumor that affects the extremities in young adults and shows melanocytic differentiation. This tumor is usually associated with tendons or aponeuroses and presents as a slow growing mass. Microscopically, the tumor grows in a uniform, nested to fascicular pattern with thin fibrous septa. Tumor cells are polygonal to spindle-shaped with abundant clear or eosinophilic cytoplasm and prominent nucleoli. Multinucleated giant cells are present in half of cases, and intracellular melanin can occasionally be seen. Clear cell sarcoma is positive for S100 protein, HMB45, and other melanocytic markers and shows a reciprocal translocation, t(12;22)(q13;q12), that results in EWS/ATF1 gene fusion.

Answer 11

Antigen KI-67, also known as Ki-67 or MKI67 is a protein that in humans is encoded by the MKI67 gene. It is a nuclear protein that is associated with and may be necessary for cellular proliferation. Furthermore it is associated with ribosomal RNA transcription. Inactivation of antigen KI-67 leads to inhibition of ribosomal RNA synthesis. The Ki-67 protein (also known as MKI67) is a cellular marker for proliferation. It is strictly associated with cell proliferation. During interphase, the Ki-67 antigen can be exclusively detected within the cell nucleus, whereas in mitosis most of the protein is relocated to the surface of the chromosomes. Ki-67 protein is present during all active phases of the cell cycle (G1, S, G2, and mitosis), but is absent from resting cells (G0). Ki-67 is an excellent marker to determine the growth fraction of a given cell population. The fraction of Ki-67-positive tumor cells (the Ki-67 labeling index) is often correlated with the clinical course of cancer. Ki67 and MIB-1 monoclonal antibodies are directed against different epitopes of the same proliferation-related antigen. The Ki-67 protein was originally defined by the prototype monoclonal antibody Ki-67; The name is derived from the city of origin (Kiel, Germany) and the number of the original clone in the 96-well plate.Whereas Ki67 works only on frozen sections, MIB1 may be used also on fixed sections. MIB-1 is used in clinical applications to determine the Ki-67 labeling index. One of its primary advantages over the original Ki-67 antibody (and the reason why it has essentially supplanted the original antibody for clinical use) is that it can be used on formalin-fixed paraffin-embedded sections, after heat-mediated antigen retrieval.

Answer 12

Basically, podoplanin is the protein, and D2-40 is the antibody against that protein. Podoplanin is a mucin-type transmembrane glycoprotein that is expressed in lymphatic endothelial cells (and several other cell types). The mouse monoclonal antibody D2-40 was originally raised against an oncofetal antigen, M2A antigen, which is an O-linked sialoglycoprotein with a simple mucin-type carbohydrate epitope associated with germ cell neoplasms, but then this antibody clone was found to be reactive with other antigens/cell types as well. D2-40: = anti-podoplanin.

Answer 13

Normal/extensitve metabolizers: *1*1. Intermediate metabolizers: *1*2. Poor/hypo-metabolizers: *2*2. Ultra/hypermetabolizers: *1*17 or *17*17. Also, *2*17 may be considered indeterminate.

Answer 14

Clopidogrel is converted by CYP2C9 to active form in the liver, and prasugrel is converted by CYP3A4 and CYP2B6 to active form in the liver. Ticagrelor is already in active form.

Answer 15

SPNs occur mostly in females (~90%) with a mean age of presentation of 28-35. In males, the mean age at presentation tends to be 5-10 years older than that of females. This neoplasm has been shown to consistently harbor mutations in exon 3 of the beta-catenin gene, which leads to upregulation of known oncogenes such as cyclin D1. The cell of origin for SPN is unknown. Currently, no grading or staging schemes for SPN exist; if malignant features, such as invasion into adjacent structures, metastases, or malignant histology are present, the staging of these "solid pseudopapillary carcinomas" follows that of other exocrine pancreatic carcinomas.

Answer 16

SPN stains positive for alpha-1 antitrypsin, PR, vimentin, alpha-1 antichymotrypsin, CD10, CD56, NSE, beta-catenin and cyclin D1. Alpha-1 antitrypsin will generally also stain the intracytoplasmic hyaline globules that are also typically PAS-positive. Vimentin and NSE stain in a diffuse manner. PR staining is present in both male and female patients. Nuclear staining of beta-catenin is seen due to mutations in the beta-catenin gene which leads to unusual nuclear accumulation of beta-catenin, and since beta-catenin mutations lead to cyclin D1 upregulation, cyclin D1 is usually positive in SPN. SPNs stain variably for cytokeratins and synaptophysin. Only in rare instances are positive staining results seen for S100, pancreatic enzymes (trypsin, amylase, chymotrypsin, etc.), or pancreatic hormones (insulin, glucagon, and somatostatin). Most report chromogranin to be negative in SPN. SPNs characteristically lose E-cadherin expression. CD99 has a characteristic paranuclear dotlike pattern.

Answer 17

Unlike partial hydatidiform mole, mesenchymal dysplasia shows no trophoblast hyperplasia, stromal trophoblastic inclusions, or scalloping of the villous surface. The fetus associated with partial molar pregnancy is often small and malformed, unlike the more normal fetus associated with mesenchymal dysplasia. DNA ploidy may also help in distinguishing these entities, as partial hydatidiform molar pregnancy is typically triploid, whereas mesenchymal dysplasia is typically diploid.

Answer 18

Myxoid liposarcoma and round cell liposarcoma were historically considered separate subtypes of liposarcoma. The frequent transition areas between myxoid liposarcoma and round cell areas in the same tumor, along with the shared t(12;16)(q13;p11) chromosomal translocation, support a single classification as myxoid/round cell liposarcoma. The translocation results in fusion of the FUS (TLS) and CHOP (DDIT3) genes on chromosomes 16 and 12, respectively. Myxoid/round cell liposarcoma accounts for approximately 30–35% of liposarcomas. These tumors occur almost exclusively in adults, usually in the third to eighth decade with a male preponderance (male: female ratio of 3:1). Myxoid/round cell liposarcoma is somewhat unusual among soft tissue tumors in that it often metastasizes to unusual sites such as the soft tissue of the trunk or axilla before metastasizing to the lung.

Answer 19

In small biopsy specimens or cases with few, if any, lipoblasts, the detection of the t(12;16) translocation may be extremely helpful in the differential diagnosis. Fresh tissue placed in RPMI may be used for complete karyotyping. Fluorescence in situ hybridization (FISH) for chromosome 12 (CHOP (DDIT3), 12q13) and reverse transcriptase polymerase chain reaction (RT-PCR) for the FUS-CHOP (TLS/DDIT3) fusion transcripts may be performed on formalin-fixed paraffin-embedded tissue. Immunohistochemistry is of limited utility.

Answer 20

The four genes that are involved in encoding proteins that participate in DNA mismatch repair are: MLH1 (3p21), MSH2 (2p22-p21), MSH6 (2p16), and PMS2 (7p22). Tumors in patients with Lynch syndrome have a germline mutation of one allele of a DNA MMR gene and a somatic mutation in the other allele. The presence of two inactivating mutations results in defective DNA mismatch repair. If the MSI or DNA MMR IHC results show evidence of defective DNA MMR, then the patient may be evaluated further for Lynch syndrome by assessing a peripheral blood sample for germline mutations for one of the four DNA MMR genes.

Answer 21

Pattern #1: MLH1+, PMS2+, MSH2+, MSH6+; MSI phenotype is MSS or MSI-L; clinical interpretation is most likely sporadic CRC (Lynch syndrome very unlikely). Pattern #2: MLH1-, PMS2-, MSH2+, MSH6+; MSI phenotype is MSI-H; clinical interpretation is LS or sporadic CRC; etiology is germline hMLH1 mutation or hMLH1 promoter hypermethylation. Pattern #3: MLH1+, PMS2+, MSH2-, MSH6-; MSI phenotype is MSI-H; clinical interpretation is LS; etiology is germline hMSH2 mutation. Pattern #4: MLH1+, PMS2+, MSH2+, MSH6-; MSI phenotype is MSI-H; clinical interpretation is LS; etiology is germline hMSH6 mutation. Pattern #5: MLH1+, PMS2-, MSH2+, MSH6+; MSI phenotype is MSI-H; clinical interpretation is LS; etiology is germline PMS2 mutation.

Answer 22

Somatic BRAF mutations are generally not seen in tumors from those with Lynch syndrome. In patients with a BRAF mutation, LS can be ruled out in most cases.

Answer 23

FISH studies for cyclin D1 are very important in making a definitive diagnosis of MCL. Translocation t(11;14)(q13;q32) is the chromosomal rearrangement juxtaposing the cyclin D1 gene locus (CCND1) on chromosome 11q13 with the immunoglobulin heavy chain locus (IGH) located on chromosome 14q32, placing CCND1 under control of IGH enhancer sequences, and leading to over-expression of cyclin D1 protein. In addition to cyclin D1 immunoreactivity, MCL tumor cells are positive for pan-B-cell markers, CD19 and CD20. Surface immunoglobulin and IgM are also positive, with or without associated IgD positivity. Tumor cells also show CD5 immunoreactivity, and are negative or only weakly positive for CD23, a marker helpful in distinguishing between chronic lymphocytic leukemia/small lymphocytic lymphoma, which is typically positive for CD23.

Answer 24

Cytogenetically, hibernomas are often associated with rearrangements of chromosomal bands 11q13-21; however, other benign lipomatous tumors may also display such abnormalities. By IHC, hibernomas are variably positive for S100 protein and spindle cell components are positive for CD34.

Answer 25

Luminal A, luminal B, triple negative/basal-like, and HER2 type. Other less common molecular subtypes have also been described, including normal breast-like, apocrine molecular subtype, luminal ER-/AR+, and claudin-low type. Luminal A subtype (40-60% prevalence) is ER+ and/or PR+, HER2-, low Ki67. Luminal B subtype (10-20% prevalence) is ER+ and/or PR+, HER2+ (or HER2- with high Ki67). Triple negative/basal-like subtype (10-20% prevalence) is ER-, PR-, HER2-, CK5/6+ and/or HER1+. HER2 type (10-15% prevalence) is ER-, PR-, HER2+.

Answer 26

Deletion of 13q14 (>50% of cases). Other frequent findings are trisomy 12 (15-20%), del(11q), del(14q), and del(17p).

Answer 27

A subset of mantle cell lymphoma (MCL) with a tendency for peripheral blood involvement tend to have cytogenetic aberrations involving 8, 17, and 21 (in addition to the requisite t(11;14)).

Answer 28

They are a family of retrovirus-associated DNA sequences (myc) originally isolated from an avian myelocytomatosis virus (myc for MYeloCytomatosis). The proto-oncogene myc (c-myc) codes for a nuclear protein which is involved in nucleic acid metabolism and in mediating the cellular response to growth factors. Truncation of the first exon, which appears to regulate c-myc expression, is crucial for tumorigenicity. The human c-myc gene is located at 8q24.

Answer 29

Liposarcoma. Mouse Double Minute 2 homolog (MDM2) is a protein that is a negative regulator of p53 encoded by the MDM2 gene. DNA Damage Inducible Transcript 3, AKA C/EBP homologous protein (CHOP), is a transcription factor encoded by the DDIT3 gene.

Answer 30

Approximately 90% of Wilms tumors are sporadic, while a minority are associated with syndromes and/or mutations in the tumor suppressor genes WT1 (chromosome 11p13) or WT2 (chromosome 11p15).

Answer 31

A t(12;16)(q13;p11) chromosomal translocation, resulting in fusion of the FUS (TLS) and CHOP (DDIT3) genes on chromosomes 16 and 12, respectively.

Answer 32

Myxoid liposarcoma and round cell liposarcoma were historically considered separate subtypes of liposarcoma. The frequent transition areas between myxoid liposarcoma and round cell areas in the same tumor, along with the shared t(12;16)(q13;p11) chromosomal translocation, support a single classification as myxoid/round cell liposarcoma. The translocation results in fusion of the FUS (TLS) and CHOP (DDIT3) genes on chromosomes 16 and 12, respectively. Myxoid/round cell liposarcoma is the most common subtype of liposarcoma, accounting for approximately 30–35% of liposarcomas. These tumors occur almost exclusively in adults, usually in the third to eighth decade with a male preponderance (male: female ratio of 3:1). Myxoid/round cell liposarcoma is somewhat unusual among soft tissue tumors in that it often metastasizes to unusual sites such as the soft tissue of the trunk or axilla before metastasizing to the lung. Lymph node metastases are also more common in myxoid liposarcoma than many other soft tissue malignancies.

Answer 33

Nonmolecular methods: Microscopic observation direct susceptibility assay (MODS assay). Light-emitting diode microscopy. MDR-XDRTB Colour Test. Colorimetric assays. Phage amplification assays. Molecular methods: Line probe assays. Automated nucleic acid amplification tests. Loop-mediated isothermal amplification. Oligonucleotide microarray.

Answer 34

INI1/BAF47 deletions are detected in ~70% of atypical teratoid/rhabdoid tumors; however, loss of the corresponding INI1 protein is even more common than the genetic alteration. Loss of INI1 nuclear immunoreactivity in tumor cells is used as a surrogate for genetic testing to demonstrate biallelic inactivation of the gene.

Answer 35

Isocitrate dehydrogenase (IDH1/IDH2) mutations have been detected in the majority of diffuse gliomas, with the notable exception of primary (de novo) GBM, and appear to play a fundamental and early role in oncogenesis. The most common mutation is in the IDH1 gene (R132H), and is recognized by monoclonal antibody IDH-1. Diagnostically, the IHC stain shows greatest promise for its potential to distinguish low-grade diffuse glioma from gliosis. Prognostically, the presence of this mutation is favorable, as such tumors appear to show greater response to therapy.

Answer 36

FOR BLOOD: LAP (NAP) score low. B12 increased. FOR MARROW: Cytogenetic analysis: t(9;22) or variant (more than 95% of cases). Molecular: BCR-ABL1+ by FISH or PCR (100% of cases). Most cases: major BCR-ABL1, (e13 or14/a2 or 3), p210 protein. Rare cases: minor BCR-ABL1, (e1/a2 or 3), p190 protein. Rare cases: mu BCR-ABL1, (e19/a2 or 3), p230 protein.

Answer 37

Cherubism is an inherited disease characterized by progressive, painless, symmetrical expansion of the jaws, resulting in a cherubic facial appearance. M:F = 2:1, with 100% penetrance in males and 50-70% penetrance in females. Mutations in the SH3BP2 gene have been identified in about 80 percent of people with cherubism. In most of the remaining cases, the genetic cause of the condition is unknown. There are germline point mutations in the SH3BP2 gene on chromosome 4p16.3.

Answer 38

Postzygotic, somatic, activating missense mutations in GNAS1 gene coding for alpha subunit of stimulatory G protein are a consistent finding (~3/4 of cases). The GNAS1 gene is on chromosome 20q13.2-13.3. The abnormal G1 protein stimulates cAMP, and the osteoblastic cells expressing this mutation have a higher rate of DNA synthesis than normal cells. This abnormal growth leads to the formation of a disorganized fibrotic bone matrix with primitive bone formation, and lack of maturation to lamellar bone. Mineralization is also abnormal. There is a failure of the bone to align in response to mechanical stress. The extent of disease is related to the stage at which the postzygotic mutation in Gsα has occurred, whether during embryonic development or postnatally.

Answer 39

Fibrous dysplasia.

Answer 40

ING family of tumor suppressor gene has high frequency loss of heterozygosity (ING5 locus LOH correlated to solid tumor type). Notch signaling molecules may be associated with specific tumor phenotypes. Dysregulation of a number of genes involved in normal tooth development may play a role: FOS oncogene most overexpressed gene; underexpressed genes include SHH, TRAF3, DCC, CDH12, TDGF1, TGFB1.

Answer 41

The genes PRSS-1 (cationic trypsinogen), PSTI (pancreatic secretory trypsin inhibitor), and CFTR (cystic fibrosis transmembrane conductance regulator) have all been implicated as causes of recurrent pancreatitis.

Answer 42

AKA odontogenic keratocyst AKA odontogenic keratocystoma AKA primordial cyst. Micro: Epithelial lining (6-8 cells thick; lacks rete ridges and epithelium is often detached from fibrous wall, creating cleft; basal layer shows palisading and hyperchromicity; parakeratotic epithelial cells; wavy or corrugated surface keratinization; keratineceous debris in lumen) and fibrous connective tissue (may be detached from overlying epithelium). When inflamed, epithelium is altered and rete ridges are noted. Epithelial hyaline bodies (Rushton bodies) may be seen. By IHC, high Ki-67 confirms proliferation, and TP53 is overexpressed. By molecular genetics, there are mutations in the PTCH gene (chromosome 9q22.3-q31), a tumor suppressor gene, with loss of function. The mutation results in overexpression of BCL-1 and TP53. DDx: Orthokeratinized odontogenic cyst. Dentigerous cyst. Periapical cyst.

Answer 43

Multiple odontogenic keratocysts are associated with Gorlin syndrome (nevoid basal cell carcinoma syndrome). Mutations in PTCH gene (chromosome 9q22.3-q31), a tumor suppressor gene, with loss of function.

Answer 44

4 major cytogenetic abnormalities, with rearrangements involving: 8q12 (39%), 12q13-15 (8%), sporadic clonal rearrangements of other genes (23%), normal karyotype (30%). Currently identified 5 PLAG1 (8q12) and HMGA2 (12q13-15) -containing fusion genes are tumor specific.

Answer 45

Micro: Papillary and cystic lesion composed of epithelial and lymphoid components. Epithelial component lining the papillary projections composed of double layer of granular eosinophilic cells (referred to as oncocytic epithelia). Inner or luminal cells: Nonciliated, tall columnar cells with nuclei aligned toward luminal aspect. Outer or basal cells: Round, cuboidal, or polygonal cells with vesicular nuclei. Lymphoid component predominantly composed of mature lymphocytes containing lymphoid follicles with germinal centers. Epithelioid and lymphoid components are sharply demarcated from one another. Other inflammatory cells may be seen, including plasma cells, histiocytes, mast cells, and occasional multinucleated (Langhans-type) giant cells. Lumens of cysts may contain thick secretions, cholesterol crystals, cellular debris, or corpora amylacea-like laminated bodies. Squamous metaplasia and focal necrosis may be seen in association with secondary inflammation. Due to presence of oncocytic cells, WT is subject to degenerative alterations occuring spontaneously or following manipulation. Metaplastic or infarcted variant of WT accounts for

Answer 46

t(11;19) translocation and CRTC1 (AKA MECT1, TORC1, or WAMTP1)/MAML2 fusion transcript.

Answer 47

Cystic spaces: often filled with mucin, occ papillary projections present. Epidermoid cells: nests or scattered; polygonal cells. Intermediate cells: large polygonal epidermoid cells; small basal cells; often in nests or sheets. Mucous cells: intracytoplasmic mucin; large or ovoid; vacuolated or clear cytoplasm; in groups or individual cells. Clear cells: usually

Answer 48

Micro: Infiltrative (PNI commonly seen; infiltrative edges into fat, skeletal muscle, soft tissue). Combinations of patterns usually present, although one predominates. Patterns: cribriform, tubular, and solid. Cytologic features: small to medium cells with eosinophilic to clear cytoplasm; nuclei are oval to sharply angulated with coarse, basophilic chromatin and occasional small nucleoli; mitotic figures are rare except for in the solid pattern. HC: Alcian blue and PAS highlight basement membrane material of pseudolumina. IHC: May have limited practical use, as tumors in DDx often react similarly. DDx: PLGA, PA, basal cell adenocarcinoma, basal cell adenoma, epithelial-myoepithelial carcinoma, CExPA, basaloid SCC, cylindroma, sialoblastoma, NEC. Cytogenetics: No particular gene profile identified. 30% have translocations involving 6q and 9p (MYB-NFIB translocation). ~50% have loss of chromosome 12q12. LOH at 6q23-25 is associated with poorer prognosis. Alteration of p53 is associated wtih tumor recurrence and progression to solid type.

Answer 49

Micro: Tumor extension into normal tissue is common, although "apparent" encapsulation is present. Although one pattern and cell type dominate, combination and spectrum is common. Patterns: solid/lobular > microcystic > papillary-cystic > follicular. Several cell types are present: serous acinar cells > intercalated duct type cells > vacuolated cells > nonspecific glandular cells > clear cells. Lymphoid infiltrate, sometimes prominent with germinal center formation, can be seen. Stromal fibrosis or desmoplasia is uncommon. HG transformation (dedifferentiation) into HG carcinoma (including small cell carcinoma) is rare and heralds poor prognosis. HC: PAS+, diastase-resistant zymogen granules (reaction can be patchy and limited). Neg or only focally pos granules with mucicarmine. IHC: Immunoprofile is nonspecific and unpredictable, so seldom of diagnostic value. Cytogenetics: No consistent or specific structural chromosomal alterations. DDx: normal salivary gland, papillary cystadenocarcinoma, mucoepidermoid carcinoma, metastatic thyroid carcinoma, clear cell tumors (epithelial-myoepithelial CA, clear cell adenoCA, clear cell oncocytoma, met RCC), PLGA.

Answer 50

Micro: Infiltrative growth, architectural diversity, and cytologic uniformity, set in characteristic matrix. Infiltrative growth: Unencapsulated, but usually well circumscribed. Encased, entombed, incarcerated, or completely surrounded minor salivary glands. Invades into soft tissues, especially fat. Bone invasion can be seen. Significant PNI. Patterns of growth: Striking variety of growth patterns. Low power gives "eye of the storm," "streaming" or "whorled" appearance. Characteristic concentric layering of cells around central nidus, creating targetoid tableau. Periphery often shows linear, single-file cell infiltration. Arranged in lobules, theques, glandular profiles, tubules, trabeculae, and cribriform nests. Papillae, if identified, are focal and not dominant pattern. Cellular features: Uniformly bland round to polygonal or fusiform tumor cells. Small to medium, with indistinct cellular borders. Ample pale to eosinophilic cytoplasm. Round to oval nuclei with open, vesicular nuclear chromatin. Inconspicuous to small nucleoli. Matrix material: Slate gray-blue stroma usually only focal. Hyalinized, slightly eosinophilic stroma separates cells. Inconspicuous mitoses. Tyrosine-like crystals are identified in <5%. Rare metaplastic changes: squamous, sebaceous, mucous, clear, oncocytic. IHC: Variable expression of epithelial and myoepithelial markers. Cytogenetics: Chromosome 12 abnormalities are most common: p or q arms (12q22 and 12p12.3).

Answer 51

Micro: Variably sized, rounded, solid or cystic nodules of tumor cells that resemble intraductal or infiltrating ductal carcinoma of the breast. Small nodules are filled with neoplastic cells. Larger cystic nodules with irregular shape. Comedonecrosis is conspicuous. PNI and LVI frequent. Marked, dense, desmoplastic (hyalinized) fibrosis is conspicuous. Lymphoplasmacytic inflammator cell infiltrate is frequently present. Cells are arranged in cribriform, band-like solid, and papillary patterns. Small tumor nests infiltrate between larger nodules. Epithelial cells have moderate to marked pleomorphism, are cuboidal to polygonal, with ample eosinophilic granular, oncocytic cytoplasm. Nuclei are round, centrally located, with large, prominent nucleoli and hyperchromatic chromatin. Mitotic figures, including atypical forms, are usually easily identified. Uncommonly, psammoma bodies and areas of squamous differentiation seen. Variants: sarcomatoid, micropapillary, mucin-rich, osteoclast-type giant cell, low-grade SDC (controversial entity). HC: Nonreactive with mucicarmine and Alcian blue. IHC: Pos for epithelial markers, androgen receptor, HER-2/neu. Cytogenetics: Frequent LOH involving 9p21, 6q, 16q, 17p, and 17q regions.

Answer 52

IMP3 protein is a member of the insulin-like growth factor II mRNA-binding proteins that consist of IMP1, IMP2, and IMP3. The IMP3 gene is located on band 7p11.2 and is identical to the KH domain–containing protein overexpressed in cancer (KOC) protein. IMP3 is an oncofetal protein involved in embryogenesis. Recent studies have shown that IMP3 is an important cancer-specific gene that is associated with many aggressive and advanced cancers and is specifically expressed in malignant tumors but is not found in benign tissues. Moreover, IMP3 promotes tumor cell proliferation, adhesion, invasion, and metastasis. IMP3 is an important prognostic biomarker for localized RCC (predicts metastasis and prognosis) and superficial urothelial carcinoma (predicts aggressive superficial UCs).

Answer 53

Xp11.2 translocation renal cell carcinoma is a subtype of renal cancer defined by a breakpoint at Xp11.2 with gene fusions between the transcription factor E3 (TFE3) gene and 6 other genes. The most common fusion partners are the papillary renal cell carcinoma (PRCC, 1q21) gene and alveolar soft part sarcoma chromosome region, candidate 1 (ASPSCR1, 17q25) gene. The same ASPSCR1-TFE3 gene fusion is seen in alveolar soft part sarcoma, a rare pediatric tumor. Another renal translocation carcinoma exhibits the t(6;11)(p21;q12) translocation with a gene fusion between the alpha gene and the transcription factor EB (TFEB) gene. Both TFEB and TFE3 are members of the MiTF/TFE family of transcription factors.

Answer 54

UroVysion is a multitarget multicolor FISH assay that examines 4 chromosomal abnormalities that commonly occur in UC. The assay is done on exfoliated urothelial cells using centromeric fluorescent denatured chromosome enumeration probes for chromosomes 3, 7, and 17, as well as a locus-specific identifier probe for 9p21. Normal cells are diploid or possess 2 copies of each chromosome. The types of genetic abnormalities observed by FISH include gains (3 or more copies) of one or more chromosomes, monosomy (1 copy), or deletions (no copies). The abnormalities that have been found to be associated with UC are polysomy (including tetrasomy), trisomy, and 9p21 deletion. The FDA-approved criteria for a positive FISH result are (1) 4 or more cells with polysomy (3 or more copies of 2 or more chromosomes), or (2) 9p21 deletion in 12 or more cells. A minimum of 25 morphologically abnormal cells need to be scanned.

Answer 55

Direct detection of the mutations of thyroid cancer is feasible because only about 7 genes are mutated in the vast majority of thyroid cancers. The mutations in these genes are almost always mutually exclusive. The various mutations correlate closely with tumor type: Mutations in B-RAF, RET and TRK are restricted to papillary thyroid carcinomas, N-RAS is strongly associated with the follicular variant of papillary thyroid carcinoma, PAX8/PPARgamma is largely restricted to follicular neoplasms, and H-RAS and K-RAS (less common) are more likely in follicular neoplasms than papillary thyroid carcinomas.

Answer 56

Though only 7 genes appear involved in initiation of the vast majority of thyroid cancers of follicular origin, testing is complicated by the presence of multiple potential point mutations in RAS and B-RAF genes, and many different translocations of RET and TRK (at least 11 and 5, respectively). Testing for point mutations (eg, B-RAF, N-RAS, H-RAS, and K-RAS) requires only a small amplicon size, an assay that works on the relatively poor substrates of FFPE material. Detecting translocations is much more challenging. The translocations of RET and TRK are mostly intrachromosomal, making them relatively difficult to detect by FISH. Studies using FISH to detect RET translocations have found alternating positive and negative areas within morphologically malignant cells of papillary thyroid carcinoma—a finding that may reflect insensitivity of the FISH technique rather than the implausible alternative of multiple independent RET translocations. Polymerase chain reaction–based detection of the translocations is also difficult because the translocations can take place over a large distance. Use of messenger RNA as the basic substrate makes the translocations easier to detect, because relatively long introns are spliced out of the messenger RNAs, though working with RNA requires special attention to the method of preservation.

Answer 57

As of 2013, molecular genetic, biochemical, and cytogenetic tests for approximately 2300 inherited genetic diseases are offered in clinical laboratories for diagnosing disease, screening carriers, predicting clinical disease susceptibility, assessing risk, and prognosticating on the course of disease.

Answer 58

Animal studies are relatively expensive and require considerable time and effort. Therefore, numerous in vitro assays have been developed for CSC identification, which include: The colony forming cell assay/colony assay (assesses the ability of progenitor cells, in a semisolid media or methylcellulose-based culture media, to proliferate and differentiate into colonies in response to cytokine stimulation). The microsphere assay/sphere assay (assesses the ability of neural stem cells from mammalian adult brain subventricular neural cells to grow in serum-free medium in nonadherent conditions, forming sphere-shaped cell aggregates). The “side population” (SP) assay by Hoechst labeling (measures upregulation of P-glycoprotein by CSCs, which leads to active transport of some dyes, such as Hoechst or rhodamine, out of the cells). Staining for CSC surface antigens (such as ABCG2 and other markers). The aldehyde dehydrogenase (ALDH) activity assay (high levels of ALDH activity have recently been identified as a characteristic of CSCs, and the Aldefluor flow cytometric assay has been widely used for isolation and study of CSCs). Label-retaining cell assay using PKH (Paul Karl Horan) dyes (identifies CSCs by demonstrating their asymmetric division).

Answer 59

The low-grade myofibroblastic proliferations of the urinary bladder are rare lesions affecting males more often than they do females. The most-common signs and symptoms are hematuria and dysuria. Histopathologically, they are spindle cell proliferations in a loose myxoid stroma, even though compact proliferations or hypocellular fibrous patterns can be found. Typically, there are varying amounts of acute, chronic, or mixed inflammatory infiltrates. Necrosis is rare to absent. Muscularis propria infiltration is common, while perivesical soft tissue invasion is uncommon. IHC is nonspecific, except for ALK-1 positivity (20%–89%). FISH has demonstrated clonal genetic aberrations involving the ALK gene in 50% to 60% of cases. After surgery, only 6% of patients experience local recurrence, without metastases or deaths from the disease. Malignant transformation has been reported exceptionally. These myofibroblastic proliferations are probably part of a continuum with, at one end, benign pseudosarcomatous proliferations and, at the opposite end, more-aggressive lesions.

Answer 60

Epstein-Barr virus infection can be demonstrated by in situ hybridization for EBV-encoded small RNA (EBER); immunohistochemical studies for EBV latent membrane protein 1 are negative. Molecular studies demonstrate clonal immunoglobulin gene rearrangements and somatic hypermutation, indicating that the cell of origin is a postgerminal center B cell. PCR can demonstrate presence of the viral genome. Cytogenetic studies have not demonstrated any recurrent chromosomal abnormalities.

Answer 61

Currently, nucleic acid amplification tests are used most often for diagnosis of viral infections of the central nervous system. Other diagnostic methods are conventional cell culture (primarily for detection of enteroviruses, although PCR is preferred) and serologic tests for viruses that cause encephalitis (western equine, eastern equine, Venezuelan equine, St Louis, Japanese, and La Crosse and West Nile).

Answer 62

A rare benign cartilaginous bone tumor arising in young adults aged 15-25 years that often occurs in the metaphysis of long tubular bones or in the small bones of the feet. Grossly: well circumscribed, solid and glistening. It is often lobulated with zonation. Older tumors are more hyalinized. Microscopic: well circumscribed, hypocellular lobules of poorly formed hyaline cartilage composed of chondroblasts with abundant pink cytoplasm, and myxoid tissue with fibrous septae containing spindle cells and osteoclasts. Atypia is common, including large, hyperchromatic nuclei. Scattered calcification and osteoclast-like giant cells are present. At the periphery, the tumor is more cellular and vascular. No/rare mitotic activity. Tumors often have 6q13 rearrangements, with recurrent 6p25 and 6q25 anomalies.

Answer 63

HIV testing is accomplished by ELISA, and repeat-reactive tests are confirmed by western blot testing for the presence of antibodies directed against the HIV proteins of the gag, pol, and env genes.

Answer 64

Platelets only have HLA-A, HLA-B, and HLA-C antigens, which are all part of the HLA class I structure. In routine clinical practice, only HLA-A and HLA-B are generally considered when the transfusion service is matching platelets in immune refractory patients.

Answer 65

HLA-A, HLA-B, and HLA-C antigens are part of the HLA class I structure. HLA-DP, HLA-DQ, HLA-DR antigens are part of the HLA class II structure.

Answer 66

A number of methods are utilized in HLA typing for compatible platelets (primarily patient lymphocytes are used in testing because of the increased density of the class I HLA antigens), including: Anti-Human Globulin augmented Complement Dependent lymphoCytotoxicity Assay (AHG-CDC) – Antibodies against the HLA antigen will fix complement and cause lysis, visualized with a supravital stain. ELISA – Purified HLA gene products are adsorbed to the plate wells. Flow cytometry – Fluorescent markers identify cell surface antigens.

Answer 67

Mechanisms of loss of E-cadherin protein include mutations in the gene, which is located on chromosome 16q22.1, loss of heterozygosity of chromosome 16, and silencing of gene expression by promoter methylation.

Answer 68

Familial neutrophilia, an autosomal dominant disorder of prominent leukocytosis (>20,000/mL), splenomegaly, and widened diploe of the skull, is caused by a mutation in the G-CSF receptor gene (CSF3R). Neutrophils in this disorder are functionally normal and the leukocytosis has no clinical consequences.

Answer 69

Pelger-Huet anomaly (PHA) is characterized by mature neutrophils with bilobed nuclei, rather than the characteristic multilobed nuclear morphology. PHA is caused by a mutation in the lamin B receptor gene. Neutrophil function in PHA is normal, but automated cell counters may indicate a left-shifted WBC because they mistakenly classify the cells as immature granulocytes.

Answer 70

Transient myeloproliferative disorder (TMD) is seen in up to 10% of patients with Down syndrome (trisomy 21). TMD may also be seen in patients with trisomy 21 mosaicism who are phenotypically normal. TMD is characterized by peripheral blood leukocytosis in early infancy, and may include circulating myeloblasts in association with an accumulation of megakaryoblasts in the blood, liver, and marrow. TMD typically persists for several weeks and resolves spontaneously in most patients, but up to 30% of affected patients later develop acute megakaryoblastic leukemia.

Answer 71

Blotting, genomic sequencing, bisulfite sequencing, methylation-specific PCR, methylated DNA immunoprecipitation, microarray analysis, matrix-assisted laser desorption time-of-flight mass spectroscopy (MALDI-TOF MS), a nanowire transistor detection procedure, a quantum-dot (QD) nanoassay, single-molecule real-time (SMRT) detection, a fluorimetric assay, electrochemical detection, and atomic force spectroscopy.

Answer 72

DNA methylation, an epigenetic alteration, plays a key role in transcriptional control; it occurs when a methyl group is added to the fifth carbon of cytosine or at the sixth carbon of adenine and is catalyzed by specific DNA methyl transferases. Aberrant cytosine methylation is associated with silencing of tumor suppressor genes and plays a decisive role in the development of many cancers, such as colorectal, lung, liver, and breast cancers. Apart from carcinogenesis, DNA methylation is crucial for a variety of processes, such as genomic imprinting, X-chromosome inactivation, and suppression of repetitive elements.

Answer 73

Genome-wide hypomethylation results in chromosomal instability and increased mutation rates, whereas promoter hypermethylation suppresses gene transcription by either preventing transcription factors from binding to the gene or altering chromatin structure. DNA hypermethylation contributes to oncogenesis by point mutation and inactivation of tumor suppressor gene, whereas hypomethylation may lead to chromosomal instability and activation of proto-oncogene. Tumor growth is characterized by genome-wide hypomethylation, accompanied by hypermethylation of tumor suppressor gene promoters caused by increased expression of DNA methyltransferases. Changes in DNA methylation in cancer include both global hypomethylation and gene-specific hypermethylation. Whether global hypomethylation and gene-specific hypermethylation are mutually exclusive or not remains ambiguous.

Answer 74

CellSearch (Veridex LLC, Raritan, NJ). The CellSearch system, which is the current industry standard, uses EpCAM-coated immunomagnetic particles to capture and align CTCs for subsequent microscopic analysis.

Answer 75

Size filtration, size streamline sort, size and particle polarizability, binding cell surface markers, binding cell surface markers and electrokinetic manipulation, size and binding cell surface markers.

Answer 76

Pathogenic variants for HCM have been described in eight genes encoding sarcomere proteins, with most (∼80%) present in the MYH7 and MYBPC3 genes. As is typical for structural proteins, most sarcomere variants are believed to act in a dominant negative manner (ie, by adversely affecting the normal gene product). Loss-of-function variants leading to haploinsufficiency occur less frequently but are prevalent in the MYBPC3 gene. Collectively, sarcomere variants are identified in up to 60% of patients with HCM who also have a family history and in ∼40% of patients with sporadic HCM.

Answer 77

Pathogenic variants for HCM have been described in eight genes encoding sarcomere proteins, with most (∼80%) present in the MYH7 and MYBPC3 genes. Storage cardiomyopathies masquerading as HCM are caused by mutations in LAMP2 (Danon disease), PRKAG2 (Wolff-Parkinson-White syndrome), and GLA (Fabry disase).

Answer 78

2011 clinical guidelines for hypertrophic cardiomyopathy recommend comprehensive testing for five HCM genes (MYBPC3, MYH7, TNNI3, TNNT2, and TPM1).

Answer 79

Compared with HCM, which is mainly a disease of the sarcomere, DCM shows a considerably higher degree of locus heterogeneity with a steadily growing number of genes implicated (currently ∼40, with HCM

Answer 80

Most pathogenic ARVC variants are present in five genes encoding desmosomal proteins [plakoglobin (JUP), desmoplakin (DSP), desmocollin-2 (DSC2), desmoglein-2 (DSG2), and plakophilin-2 (PKP2)].

Answer 81

Isolated LVNC is characterized by a heavily trabeculated or spongy appearance of the LV myocardium. An arrest of myocardial compaction during the first trimester of embryonic development is widely believed to be a cause. The left ventricle is typically affected, but 50% of patients with LVNC also have right ventricular involvement. There is a suggestion that LVNC is frequently associated with mitochondrial disorders, followed by Barth syndrome. Because LVNC is rare, its genetic etiology is not well understood. Variants have been described in known DCM and HCM genes encoding components of the sarcomere (ACTC1, MYH7, MYBPC3, and TNNT2), the Z-disk (LDB3), the nuclear lamina (LMNA), the dystrophin-associated glycoprotein complex (DTNA), as well as the Barth syndrome gene tafazzin (TAZ), a nuclear-encoded mitochondrial protein.

Answer 82

Activating somatic point mutations of the KIT gene are associated with mastocytosis and are encountered in most (>80%) of sporadic cases.

Answer 83

Classic EATL: Represents 80-90% of all EATL. Is a complication of celiac disease, with >90% having celiac disease-associated HLA-DQ2/-DQB. Patients with refractory celiac disease are at highest risk. Most common in Northern Europe (population has a high prevalence of celiac disease). Type II EATL: Represents 10-20% of all EATL. May be associated with celiac disease, but in most cases occurs sporadically in individuals with celiac-associated HLA types similar to those in the general population. Most common in Asia (celiac disease is uncommon in the population).

Answer 84

Classic EATL: CD3+, CD5-, CD7+, 80% CD8-, >90% CD56-. Type II EATL: CD3+, CD5-, CD7+, 80% CD8+, >90% CD56+.

Answer 85

Classic EATL: 86% +9q31.3 or -16q12.1. 73% +1q32.2-q41. 80% +5q34-q35.2 27% +8q24 (MYC). Type II EATL: 83% +9q31.3 or -16q12.1. 27% +1q32.2-q41. 20% +5q34-q35.2 73% +8q24 (MYC).

Answer 86

Variants in the gene for UPD-glucuronosyltransferase (UGT1A1) were included by the CAP Working Committee for PT because patients with colon cancer who have the 7 TA repeats (*28) are at increased risk for hematopoietic toxicity while taking irinotecan. Patients with variant alleles for cytochrome P450 (CYP) 2C9 (*2, *3) and vitamin K epoxide reductase complex subunit 1 (VKORC1) (A alleles at −1639 promoter region) have increased sensitivity toward warfarin. As the CYP2C19 enzyme is important for the metabolism of clopidogrel to an active metabolite, the presence of loss-of-function variant alleles (*2, *3) results in a higher rate of adverse cardiac events in patients undergoing percutaneous coronary intervention. The FDA has included pharmacogenetic information regarding CYP2D6 testing for dozens of drugs including codeine, tamoxifen, atomoxetine, and the tricyclic antidepressants.

Answer 87

Sanger (AKA terminator sequencing) and pyrosequencing (AKA sequence-by-synthesis). Pyrosequencing is less complex, involves fewer steps, and has a superior limit of detection compared with Sanger sequencing.

Answer 88

The Sanger method is also known as terminator sequencing because DNA fragments of varying lengths are synthesized by incorporating both nucleotides and dideoxy terminators (deoxyribonucleotide triphosphates [dNTPs] and dideoxynucleotide triphosphates [ddNTPs], respectively). Random incorporation of the ddNTPs causes chain termination that produces DNA fragments of every possible length. In a more recent adaptation, each ddNTP (A, C, T, or G) carries a unique, fluorescent molecule, such that the extension products are both terminated and labeled with the appropriate fluorophore. Terminated products must be purified from unincorporated ddNTPs, and the fragments are subsequently separated by size using capillary electrophoresis, in which the terminal nucleotide of each fragment is detected by fluorescence at wavelengths unique to each of the terminators. PCR amplification and DNA sequencing reactions are most commonly run separately, although they can be combined into a single reaction. Read lengths have increased for Sanger sequencing, and 800 base reads can now be achieved routinely.

Answer 89

Pyrosequencing is designated as a sequence-by-synthesis technique because DNA synthesis is monitored in real time. After an oligonucleotide is annealed to the template strand of DNA to be sequenced, a DNA polymerase synthesizes DNA by extending the 3′ end of the nascent strand using the information encoded in the template strand. During pyrosequencing, dNTPs are sequentially dispensed into the chamber containing the template with the primer and DNA polymerase bound. When the correct complementary dNTP is injected and added by the polymerase, inorganic pyrophosphate (PPi) is released during a condensation reaction. Through a sequence of another 2 reactions, the released pyrophosphate is converted into ATP, a cofactor for the enzyme luciferase, oxidizing luciferin to oxyluciferin and light. Thus, light emission is proportional to the amount of pyrophosphate produced, which is directly proportional to the number of nucleotides added. Apyrase catalyzes the degradation of excess dNTPs via the following reaction and before the next dNTP is dispensed.

Answer 90

Sanger sequencing: Strengths are longer read lengths (800 bases). Weaknesses are worse limit of detection (~20%). Common applications are somatic and germline mutation detection. Pyrosequencing: Strengths are better limit of detection (~5%). Weaknesses are shorter read lengths (100-400 bases); homopolymers. Common applications are oncogene detection, methylation analyses, and resolving complex Sanger results. Next-generation sequencing: Strengths are massively parallel sequencing or extremely high depth of coverage; cost reduction for gene panels. Weaknesses are costs. Common applications are whole-genome sequencing, whole-exome sequencing, RNASeq, amplicon sequencing, rapid microbial identification, gene panels, early detection of cancer.

Answer 91

Because, like ribose adenosine 5'-triphosphate (rATP), it is a substrate for luciferase. Accordingly, the dATP analog, deoxyadenosine alpha-thio triphosphate (dATP-alpha-S), is used in lieu of dATP, but that produces a higher peak than the other dNTPs, which needs to be considered when comparing homopolymers of A that are equal in length to the other nucleotides.

Answer 92

Also called BSAP, a B cell-lineage specific activator protein at 9q13. Member of paired box (PAX) family of transcription factors, which have a novel, highly conserved DNA-binding motif, known as the paired box; encodes BSAP expressed at early stages of B-cell differentiation, also in developing CNS and testis. Detected in B cells from pro-B cell stage to plasma cell stage where it is downregulated. Required for progression of B cell development beyond the early pro-B cell stage. Uses: Detection of pre-B cells (PAX5+, more sensitive and specific than CD20). Diagnosis of Reed-Sternberg cells in classic Hodgkin lymphoma (PAX5+) versus T / null cell anaplastic large cell lymphoma (PAX5-), although rarely positive in T cell lymphomas. Diagnosis of lymphoplasmacytic lymphoma / plasmacytoid differentiation in marginal zone lymphoma (PAX5+) versus plasmacytoma (PAX5-).

Answer 93

Phosphatase and tensin homolog (PTEN) gene is on chromosome band 10q23.31. In addition to its role as a tumor suppressor, it has important roles in embryogenesis and maintenance of physiologic functions in many organ systems and is constitutively expressed in normal tissues. It is one of the most frequently inactivated genes in sporadic cancer. Sporadic mutations of PTEN occur frequently in many tumors such as glioblastoma, breast carcinoma, endometrial carcinoma, thyroid neoplasms, skin neoplasms, and advanced prostate cancer.

Answer 94

The role of PTEN as a tumor suppressor is due to its lipid phosphatase activity, including dephosphorylating phosphatidylinositol-3,4,5 triphosphate (PIP3), the product of phosphatidylinositol 3-kinase (PI3K) function, to form phosphatidylinositol-3,4 bisphosphate. The dephosphorylation of PIP3 antagonizes the PI3K function, thereby abolishing the PIP3-mediated activation of survival kinases, such as phosphoinositide-dependant kinase 1, and the AKT/mammalian target of rapamycin (mTOR) pathway. PTEN is the only known lipid phosphatase abrogating the PI3K pathway, and therefore, loss of PTEN has a significant impact on multiple aspects of tumorigenesis.

Answer 95

CCS share many features with malignant melanoma, including expression of melanoma markers, but, in contrast to most melanomas, they lack BRAF (v-raf murine sarcoma viral oncogene homolog B1) mutations. In addition, most CCS show rearrangement of the EWSR1 (Ewing sarcoma breakpoint region 1) locus, which in most cases leads to fusion of the EWSR1 gene with the activating transcription factor-1 gene (ATF1) in a recurrent translocation, t(12;22)(q13;q12). This translocation is not present in melanoma. On rare occasions, CCS of soft tissues can also show EWSR1-CREB1 (cAMP responsive element–binding protein 1) gene fusion.

Answer 96

The E-cadherin complex, essential for the formation of intercellular tight junctions, is composed of the transmembrane E-cadherin protein and α, β, γ, and p120 catenins, which anchor the E-cadherin protein to the cytoplasmic actin filaments. The α and β catenins are complexed with the carboxy-terminal cytoplasmic tail of E-cadherin, whereas the p120 catenin is anchored to the E-cadherin in a juxtamembranous site. p120 is actively involved in cell motility, E-cadherin trafficking and turnover, promotion of cell junction formation, and regulation of the actin cytoskeleton. β-Catenin is a cofactor implicated in the Wnt-signaling pathway, a powerful regulator of cell proliferation.

Answer 97

Molecular studies have demonstrated that PLC and ILC share several molecular features such as alterations in the gene CDH1 on chromosome band 16q22 that results in changes in E-cadherin protein function, as well as recurrent genomic changes affecting 1q+, 11q−, 16p+, and 16q− and genomic amplifications in the region of 8q24, 11q13, 12q13, 17q12, and 20q13. The aggressive biology of pleomorphic lobular carcinoma relates to the acquisition of genetic alterations typical of high-grade ductal carcinoma, such as overexpression of HER2/neu and c-myc, p53 positivity, and amplification of 8q24, 12q13, and 20q13.

Answer 98

Somatic mutations in the IDH1 gene (on 2q33.3, exon 4 (codon R132), mutations R132H, C, L, S, or G) encoding cytosolic NADP+ - dependent isocitrate dehydrogenase have been shown in the majority of astrocytomas, oligodendrogliomas, and oligoastrocytomas of WHO grades II and III. IDH2 (on 15q26.1, exon 4 (codon R172), mutations R172G, M, or K) encoding mitochondrial NADP+ - dependent isocitrate dehydrogenase can also be mutated in gliomas, although in much lower frequencies. Isocitrate dehydrogenases catalyze the oxidative decarboxylation of isocitrate to alpha-ketoglutarate, and mutations inactivate enzyme activities.

Answer 99

The DNA-repair enzyme MGMT (O^6-methylguanine-DNA methyltransferase) rescues the cell from damage induced by TMZ (temozolomide) and leads to resistance to therapy. Gliomas with inactivation of the MGMT gene are less capable of repairing DNA, which leads to increased sensitivity to alkylating chemotherapy.

Answer 100

It produces a BCR-ABL1 fusion with an abnormal tyrosine kinase activity that promotes the characteristic proliferation of progenitor cells in CML and ALL. BCR-ABL1 kinase signaling constitutively activates downstream proteins that promote growth factor-independent proliferation, altered adhesion, resistance to DNA repair, and inhibition of apoptosis that culminates in the malignant transformation of hematopoietic stem cells. The BCR-ABL1 fusion transcript and its resulting kinase have become a key target and biomarker in the treatment and monitoring of CML.

Answer 101

Clinically, patients with exon 12 mutations typically present with isolated erythrocytosis and suppressed erythropoietin, in contrast to the trilineage hyperplasia characteristic of patients with V617F mutation. Bone marrow from patients with exon 12 mutation often exhibits nonspecific morphology, with isolated erythroid proliferation and absence of prominent megakaryocyte atypia and clustering. Demonstration of exon 12 mutation in these patients is particularly helpful for ruling out reactive erythrocytosis.

Answer 102

JAK2 V617F (~96%) or JAK2 exon 12 mutations (~3%).

Answer 103

False. Other hematological neoplasms (eg, myelodysplastic syndrome, chronic myelomonocytic leukemia, acute myeloid leukemia, and acute lymphoblastic leukemia) may harbor JAK2 and MPL mutations in low frequencies. Because JAK2 and MPL mutations are not completely specific for MPN, finding of these mutations in isolation does not warrant a diagnosis of MPN.

Answer 104

The JAK2 gene maps to chromosome band 9p24 and encodes a tyrosine kinase protein composed of 1132 amino acids. It contains three critical domains: JH1, JH2, and four-point-one, ezrin, radixin, moesin (FERM) homolog domains. JAK2 protein kinase activity is activated by phosphorylation of its kinase domain. Activation of JAK2 induces signal transduction from both type 1 and type 2 cytokine receptors. Constitutive activation of JAK2 by either point mutation or fusion protein causes activation of the JAK/STAT pathway. The activated JAK2 causes phosphorylation of STATs, which then dimerize and translocate to the nucleus, where they regulate gene transcription. The constitutive tyrosine phosphorylation activity promotes cytokine hypersensitivity.

Answer 105

The MPL gene maps to chromosome band 1p34 and encodes the thrombopoietin receptor, which binds to thrombopoietin, the primary cytokine that regulates megakaryocyte development and platelet production, as well as hematopoietic stem cell homeostasis. Binding to thrombopoietin to MPL leads to activation of JAK2, which phosphorylates MPL and initiates a cascade of downstream signaling events that regulate cell survival, proliferation, and differentiation. The mutation W515L results in impaired function of the autoinhibitory region and subsequent ligand-independent thrombopoietin receptor activation. This then leads to subsequent activation of downstream tyrosine kinases and activation of transcription factors STAT3 and STAT5, which in turn leads to transformation of hematopoietic cells into cytokine-independent clones, resulting in megakaryocytic hyperplasia and marrow fibrosis. The mutation Y252H, which is located in the extracellular domain of MPL, confers hypersensitivity to thrombopoietin and increases the generation of megakaryocyte colonies in vitro and leads to increased thrombopoietin signaling and cell growth and survival.

Answer 106

The Ewing sarcoma breakpoint region 1 (EWSR1; also known as EWS) represents one of the most commonly involved genes in sarcoma translocations. In fact, it is involved in a broad variety of mesenchymal lesions which includes Ewing's sarcoma/peripheral neuroectodermal tumor, desmoplastic small round cell tumor, clear cell sarcoma, angiomatoid fibrous histiocytoma, extraskeletal myxoid chondrosarcoma, and a subset of myxoid liposarcoma. The fusion products between EWSR1 and partners usually results in fusion of the N-terminal transcription-activating domain of EWSR1 and the C-terminal DNA-binding domain of the fusion partner, eventually generating novel transcription factors.

Answer 107

Ewing's sarcoma/peripheral neuroectodermal tumor, desmoplastic small round cell tumor, clear cell sarcoma, angiomatoid fibrous histiocytoma, extraskeletal myxoid chondrosarcoma, and a subset of myxoid liposarcoma.

Answer 108

The Ewing sarcoma/PNET family of tumors is characterized by chromosomal translocations involving the EWSR1 gene on chromosome 22 with one of several members of the ETS family of transcription factors on various different chromosomes including 2, 7, 11, 17 and 21. The most common translocation (over 70% of cases in bone/soft tissue) is t(11;22)(q24;q12) which leads to the formation of the EWS-FLI1 fusion protein.

Answer 109

Typically in bone and soft tissues, PNET tumors with variant gene fusions (non-FLI1) are associated with a worse outcome.

Answer 110

MSI testing is performed by extracting DNA from paraffin-embedded neoplastic and nonneoplastic tissue. PCR is used to amplify 5 specific microsatellite regions: BAT25, BAT26 (both of which are regions of mononucleotide repeats), D2S123, D5S346, and D17S250 (regions of dinucleotide repeats). These regions from the tumor are compared to those from nonneoplastic tissue to assess for differences in length, indicative of MSI.

Answer 111

They are somewhat more indolent than sporadic tumors (metastasize only when quite large).

Answer 112

Hemangioblastomas (CNS and retinal), pheochromocytoma, clear cell RCC, pancreatic cysts, islet cell tumors, epididymal and ovarian cystadenomas, endolymphatic sac tumors.

Answer 113

~20% of cases of vHL disease are caused by de novo mutations, with the remaining caused by inherited vHL gene mutations.

Answer 114

Type 1 often has deletion or nonsense mutations. This group manifests mostly as hemangioblastomas whereas clear cell RCC and pheos are rare. Type 2 is subdivided into types 2A, 2B, and 2C, and are characterized mostly by missense mutations. Type 2A is at risk of hemangioblastomas and pheos, but not clear cell RCC. Type 2B is at risk of all 3 tumors, with a higher risk of clear cell RCC. Type 2C is at risk for only pheos. Type 3 has a risk of Chuvash polycythemia.

Answer 115

VHL disease is an AD disorder caused by a germline mutation in the VHL gene, a tumor suppressor gene on 3p25-26. The VHL protein (pVHL) is involved in the regulation of the protein hypoxia inducible factor 1-alpha.

Answer 116

Facial angiofibromas (adenoma sebaceum) or forehead plaque. Nontraumatic ungual or periungual fibroma. >3 hypomelanotic macules. Shagreen patch (connective tissue nevus). Multiple retinal nodular hamartomas. Cortical tuber. Subependymal nodule. SEGA. Cardiac rhabdomyoma, single or multiple. LAM. Renal AML. Definite TSC is either 2 major features or one major plus 2 minor features.

Answer 117

5% of all women with breast cancer and 25% of Ashkenazi Jewish women with breast cancer have a BRCA mutation. The lifetime risk of breast cancer in women is 10% and the lifetime risk in BRCA1 or BRCA2 is 70%.

Answer 118

A two base pair deletion in codon 23 (185delAG) in BRCA1, a 5832insC mutation in BRCA1, and a 6174delT mutation in BRCA2.

Answer 119

Facial angiofibromas, collagenomas, lipomas, and meningiomas.

Answer 120

C-cell hyperplasia and numerous small foci of medullary carcinoma.

Answer 121

Cutaneous lentigenes (simple lentigos). Blue nevi, particularly the cellular blue nevus. Cardiac myxomas (as well as myxomas of breast, female genital tract, and skin (especially on eyelid and external ear)). Endocrine tumors including thyroid follicular adenomas, pituitary adenomas (GH-secreting), and the so-called primary pigmented nodular adrenocortical disease (a form of multinodular hyperplasia of the adrenal cortex that causes Cushing syndrome). Large-cell calcifying Sertoli cell tumor. Psammomatous melanotic schwannoma.

Answer 122

Peutz-Jeghers syndrome and Carney complex.

Answer 123

Large cell calcifying Sertoli cell tumor of the testis is a unique variant of Sertoli cell tumor that can be sporadic (60%) but can also be part of Peutz-Jeghers and Carney syndromes (40%). This variant tends to occur in young individuals with an average age of 16 and can be bilateral in 40% of cases.

Answer 124

Alkaptonuria, an autosomal recessive disorder of amino acid metabolism. Increased homogentisic acid is secreted in urine and polymerized homogentisic acid deposits accumulate in connective tissue. The pigment is Fontana-Masson positive and Prussian blue negative.

Answer 125

Cases with trisomy 12 have predominantly unmutated Ig variable gene regions and therefore have a more aggressive course and worse prognosis. Cases with 13q14 abnormalities usually have mutated immunoglobulin and better prognosis.

Answer 126

t(8;14), Ig heavy chain gene, ~80%. t(2;8), kappa light chain gene, ~15%. t(8;22), lambda light chain gene, ~5%.

Answer 127

The genetic defect implicated in the pathogenesis of Wilson disease is localized to chromosome 13, and involves the gene encoding the protein ATP7B. ATP7B is an ATP-dependent copper transport protein that plays a pivotal role in the biliary excretion of copper and in the incorporation of copper into apoceruloplasmin to form ceruloplasmin, the major circulating copper carrying protein.

Answer 128

Analbuminemia is a rare AR disorder manifested by the absence or severe reduction of circulating serum albumin. Analbuminemic individuals usually have surprisingly minimal findings, since the absence of albumin is partially compensated for by an increase of other serum proteins, such as globulins, transferrin, and coagulation factors. The main clinical symptoms include mild edema and occasionally chronic fatigue or lipodystrophy, especially in women, while the most common biochemical signs are gross hyperlipidemia with hypercholesterolemia and elevated LDL-cholesterol levels. The finding of a low albumin concentration during routine SPEP, with normal liver function and no GI or renal protein loss, suggests the clinical diagnosis. This needs to be confirmed by the molecular diagnosis, based on the identification of the causative mutation within the albumin (ALB) gene by DNA sequence analysis.

Answer 129

Congenital adrenal hyperplasia (11-beta hydroxylase or 17-alpha hydroxylase deficiency). Glucocorticoid-remediable hypertension. Bartter syndrome. Gitelman syndrome. Liddle syndrome. Gullner syndrome. Glucocorticoid receptor deficiency. Hypokalemic periodic paralysis. Thyrotoxic periodic paralysis (TTPP). Seizures, sensorineural deafness, ataxia, mental retardation, and electrolyte imbalance (SeSAME syndrome).

Answer 130

t(2;13) with PAX3-FOXO1 (formerly known as FKHR) fusion and t(1;13) with fusion of PAX7 and FOXO1. As many as 20% of cases of alveolar rhabdomyosarcoma are negative for either translocation, and usually the solid variants.

Answer 131

Mammary analogue secretory carcinoma of the salivary gland, secretory carcinoma of the breast, infantile fibrosarcoma, cellular congenital mesoblastic nephroma, and some types of acute myelogenous leukemia.

Answer 132

Chondroblastoma is not associated with recurrent translocations or specific genetic abnormality.

Answer 133

The EWSR1-NR4A3 translocation t(9;22) is seen in about half of cases.

Answer 134

Aneuploidy in some, as well as balanced translocation involving a common breakpoint on the long arm of chromosome 19 (band 19q13.4) with alternative partners on chromosomes 11 and 15.

Answer 135

Most common form of skeletal dysplasia: achondroplasia (1 per 10-30,000 live births). Most common lethal form of skeletal dysplasia: thanatophoric dysplasia (1 per 35-50,000 births).

Answer 136

Fibroblast growth factor receptor 3, encoded by the FGFR3 gene on chromosome 4p16.3. 75% of cases are caused by sporadic new mutations.

Answer 137

Lipoblastomas are characterized by rearrangements of 8q11-13 involving the PLAG1 gene.

Answer 138

The most common genotype of complete moles is 46,XX; a small number are 46,XY. Triploid and tetraploid complete moles are much less common. Triploid conceptions which have duplication of paternal chromosomes are partial moles, typically with a 69,XXX or 69,XXY genotype. Triploid conception resulting from a duplication of maternal chromosomal material (also 69,XXX or 69,XXY genotype) represent non-molar triploidy and lack the trophoblastic proliferation which is the hallmark of a molar pregnancy.

Answer 139

Triploid conceptions which have duplication of paternal chromosomes are partial moles, typically with a 69,XXX or 69,XXY genotype. Triploid conception resulting from a duplication of maternal chromosomal material (also 69,XXX or 69,XXY genotype) represent non-molar triploidy and lack the trophoblastic proliferation which is the hallmark of a molar pregnancy.

Answer 140

IHC cannot distinguish HA (biparental diploidy) from PHM (diandric triploidy). Short tandem repeat genotyping, which determines the parental source of polymorphic alleles, is useful.

Answer 141

Alexander disease has 3 clinical phenotypes: infantile (63%), juvenile (24%), and adult (13%). The majority of infantile and juvenile types are caused by a heterozygous (dominant) gain of function mutation in the gene encoding GFAP, located on chromosome 17q21. These mutations are typically sporadic and de novo. In Alexander disease, a heterozygous missense mutation in the GFAP gene appears to interfere with polymerization of the protein, and results in abnormal protein folding with overexpression and accumulation of the abnormal GFAP protein within Rosenthal fibers.

Answer 142

Alexander disease AKA fibrinoid leukodystrophy.

Answer 143

AGS is a multisystem disorder with AD inheritance and variable penetrance and expressivity. The traditional diagnostic criteria have consisted of paucity of the interlobular bile ducts in association with 3 of 5 major findings, including chronic cholestasis, cardiac disease (most frequently peripheral pulmonary artery stenosis), skeletal manifestations (short stature, butterfly vertebrae), ocular abnormalities (most commonly posterior embryotoxon, a circular opacity of the posterior peripheral cornea), and characteristic facial features (triangular face with a prominent forehead, deep-set eyes, a pointed chin, and a straight nose with a bulbous tip). Mutations are in the JAGGED1 (JAG1) gene.

Answer 144

Mutations are in the JAGGED1 (JAG1) gene, which encodes a cell surface protein that functions as a ligand in the Notch signaling pathway regulating cell proliferation and differentiation. The precise mechanisms by which JAG1 mutations cause AGS is still incompletely understood. JAG1 mutations have been identified in >90% of clinically diagnosed probands; additionally, NOTCH2 mutations have been detected in the small minority of AGS patients lacking JAG1 mutations.

Answer 145

Hepatic complications do contribute significantly to the morbidity of AGS but it is the cardiovascular sequelae that are most directly responsible for the early mortality. Specifically, intracardiac anomalies, which affect ~25% of AGS patients (most commonly tetralogy of Fallot).

Answer 146

These include six EBV nuclear antigens (EBNA-1, 2, 3A, 3B, 3C, and LP), three latent membrane proteins (LMP1, 2A, 2B) localized in the plasma membrane of the infected B cells, and two small non-polyadenylated nuclear RNAs, EBER1 and EBER2 (which far often used as sensitive markers for the presence of EBV within a cell). Three patterns of latency (I, II, and III) are identified depending on the expression of these genes.

Answer 147

EBV belongs to the gamma-herpesvirus subfamily of herpes virus along with HHV-8. The virus gains entry into the body by infection of B-lymphocytes by the interaction between the major viral glycoprotein gp350 and the complement receptor CR2 which is expressed on B-cells. Following primary infection there is the expression of lytic cycle proteins resulting in the release of infectious virus and generalized seeding of B-cells throughout the body.

Answer 148

Turcot syndrome (recently renamed Crail syndrome)/APC gene mutations: medulloblastoma, rarely ependymoma. Tuberous sclerosis: subependymal giant cell astrocytoma. Von Hippel Lindau disease: hemangioblastoma. Li-Fraumeni syndrome (with germline TP53 mutations): medulloblastoma, astrocytic tumors, meningioma, schwannoma, choroid plexus tumors, and central PNET. NF type 1: optic glioma, astrocytoma, glioblastoma multiforme. NF type 2: multiple meningiomas, bilateral vestibular schwannomas, spinal ependymomas. Gorlin syndrome: desmoplastic/nodular variant of medulloblastoma.

Answer 149

While no specific translocation or chromosomal anomalies are found in GCT, normal karyotypes are rarely encountered. The most frequent genetic abnormality seen in giant cell tumor of bone is reduction in telomere length (11p, 13p, 14p, 15p, 19q, 20q, 21p). Telomeric fusion is detected in ~70% of GCT. A higher incidence of chromosomal anomalies have been reported for recurrent benign GCT or metastatic GCT than for GCT cured after initial surgery. There are no known genetic syndromes predisposing to giant cell tumor.

Answer 150

Ollier disease (enchondromas, chondrosarcoma). Mafucci syndrome (enchondromas, chondrosarcoma). Bloom syndrome (osteosarcoma). Li-Fraumeni (osteosarcoma). Rothmund-Thompson syndrome (osteosarcoma). Werner syndrome (osteosarcoma). McCune-Albright syndrome (polyostotic fibrous dysplasia, osteosarcoma). Mazabraud syndrome (polyostotic fibrous dysplasia, osteosarcoma).

Answer 151

Ollier disease (enchondromas, chondrosarcoma). Mafucci syndrome (enchondromas, chondrosarcoma). Bloom syndrome (osteosarcoma). Li-Fraumeni (osteosarcoma). Rothmund-Thompson syndrome (osteosarcoma). Werner syndrome (osteosarcoma). McCune-Albright syndrome (polyostotic fibrous dysplasia, osteosarcoma). Mazabraud syndrome (polyostotic fibrous dysplasia, osteosarcoma).

Answer 152

Peutz-Jeghers syndrome is an autosomal dominant condition caused by inactivating mutations in the serine-threonine protein kinase 11 (STK11) gene, also called LKB1, on chromosome 19p13.3. Mutations in STK11 are found in ~70% of familial cases and ~30-70% of sporadic cases.

Answer 153

Although most juvenile polyps in children are sporadic, a subset of these patients develop numerous polyps (juvenile polyposis) due gene to mutations in SMAD4 or BMPR1A. In this syndrome, juvenile polyps may develop dysplasia and eventually carcinoma.

Answer 154

The PTEN hamartoma syndromes include Cowden syndrome and Bannayan-Riley-Ruvalcaba syndrome, both resulting from mutations in the tumor suppressor gene phosphatase and tensin homolog (PTEN) on chromosome 10q23.3. These syndromes are associated with increased risk of breast and thyroid carcinomas.

Answer 155

Cellular atypia/beta-catenin mutated adenoma. Steatotic/hepatocyte nuclear factor 1-alpha mutated adenoma. Telangiectatic/inflammatory adenoma. Those HA not fitting these three main subtypes are labeled as "unclassified" HA.

Answer 156

In Ewing sarcoma, a t(11;22) producing EWSR1/FLI-1 is present, while in desmoplastic small round cell tumor a different t(11;22) producing EWSR1/WT1 is present.

Answer 157

~75% of alveolar rhabdomyosarcomas have a balanced translocation involving chromosomes 2 and 13 or chromosomes 1 and 13. The most common, t(2;13)(q35;q14) generates a fusion gene and corresponding fusion protein involving the genes PAX3 and FKHR (AKA FOXO1). The second most common, t(1;13)(p36;q14), generates a fusion gene and protein involving PAX7 and FKHR. Several other translocations have been described involving the PAX3 and PAX7 genes. The remaining 25% of cases do not have translocations identifiable by karyotyping.

Answer 158

ATRTs are highly malignant (WHO grade IV) CNS neoplasms seen in very young children. INI1 is a ubiquitously expressed protein encoded by the hSNF5/INI1 gene on chromosome 22q11.2. Mutations in this gene are seen in ATRT. Cytogenetic studies often show monosomy or deletion of chromosome 22; however, this is not as specific or sensitive as IHC, since other tumors with complex karyotypes may show loss of 22 in addition to other events, and the INI1 gene may be mutated by a mechanism other than deletion (i.e. point mutations) not detectable by FISH or LOH studies. The presence of an hSNF5/INI1 gene mutation or loss of the INI1 protein expression by IHC is sufficient to confer a diagnosis of ATRT.

Answer 159

Mucinous tumors have a high prevalence of KRAS mutations. Serous tumors commonly have TP53 gene mutations. CTNNB1 (beta-catenin) gene mutations and PTEN mutations are common in endometrioid adenocarcinomas.

Answer 160

Attenuted FAP is a phenotype with fewer adenomas (<100), more proximal colonic location of polyps, delayed age of onset of carcinoma, and lower overall lifetime risk of carcinoma (69%) as compared to classic FAP. Patients with attenuated FAP also often lack family history of polyposis or extraintestinal manifestations. Attenuated FAP is typically caused by mutations in the most proximal or most distal portions of the APC gene.

Answer 161

The RBCs of HPP patients manifest a superimposed quantitative deficiency in spectrin, which has been termed a "thalassemia-like" defect of a-spectrin. Thus, the most common scenario leading to the HPP phenotype is the combination of an elliptocytogenic a-spectrin missense mutation within one parent and a silent "thalassemia-like" defect within the other parent; when this biochemically occult allele occurs in trans to the missense mutation, the expression of the mutant spectrin is promoted and the production of normal spectrin is significantly inhibited.

Answer 162

An AR lysosomal storage disorder caused by deficiency of the beta-galactosidase enzyme due to mutations in the GLB1 gene on chromosome 3p. The function of the enzyme is to hydrolyze the terminal beta-galactosyl residues from GM1 ganglioside, glycoproteins, and glycosaminoglycans. Without the enzyme function, GM1 gangliosides accumulate in lysosomes of various tissues, particularly the CNS. The 3 clinical phenotypes are: type 1 (infantile), type 2 (late infantile or juvenile), and type 3 (adult or chronic).

Answer 163

Alpha beta-Crystallin is one of many heat shock proteins that function as inhibitors of apoptosis by preventing accumulation of denatured proteins, thus prohibiting a signal for cell death and enabling survival. It impedes the proteolytic activation of caspase-3, a protease involved in the apoptotic cascade. Alpha beta-Crystallin is preferentially expressed in BLBCs and rarely in other molecular subtypes.

Answer 164

Based on a 70-gene set profile using an oligonucleotide array. A cDNA microarray-based test. Initially could be performed only on fresh frozen tissue but now FFPE tissue with RT-PCR can be used as well. The test helps in deciding whether the pt should receive adjuvant chemo by separating breast cancers by gene signatures into those with good vs poor prognosis. Pts with gene signature showing good prognosis will get hormone therapy (if the tumor is ER+). The poor prognosis signature consists of genes regulating cell cycle, invasion, angiogenesis, and metastasis. Pts with a gene signature showing poor prognosis will get chemo and hormone therapy (if the tumor is ER+). The test is offered for patients with tumors <5 cm, with LN-neg disease and low clinical stage (stage I or II). The advantage of MammaPrint is that the test can be performed on both ER+ and ER- tumors. However, the clinical utility of MammaPrint with ER- breast cancers is limited because only 0-4% of pts with ER- tumors are considered to have a good prognosis by the gene signature.

Answer 165

An RT-PCR-based assay performed on FFPE tissue of invasive breast cancer specimen (but also recently approved for testing DCIS) which provides predictive and prognostic information in ER+, LN- tumors. It gives a recurrence score based on a 21-gene panel, with RS given from 0 to 100 and divided into 3 risk groups: low risk, <18; intermediate risk, 18-31; high risk, 31 or greater. The low RS pts get no chemo, the intermediate RS pts may or may not get chemo, and the high RS pts do get chemo.

Answer 166

An assay that determines the risk of recurrence in women with LN neg, ER pos breast cancers who have received Tx with tamoxifen. The assay analyzes the ratio of homeobox B13 and interleukin 17 receptor gene expression using RT-PCR on FFPE tissue. To improve the assay, a numerical score called the molecular grade index was created by selecting 5 cell-cycle-related genes (BUB1B, CENPA, NEK2, RACGAP1, and RRM2) to be used concurrently with the H/I index to improve risk stratification. The combined MGI and H/I index stratifies pts into 3 risk groups: low risk, low for MGI and low or high H/I index; intermediate risk, high MGI and low H/I index; high risk, high for both MGI and H/I index.

Answer 167

Both typically have complex karyotypic abnormalities that are both numerical and structural, but no consistent karyotypic pattern has been identified. On a molecular level, homozygous deletions of the CDKN2A gene, which encodes the p16 cell cycle inhibitory molecule, occurs in the progression of neurofibromas to MPNST, being identified in ~50% of MPNST but not in neurofibromas.

Answer 168

~30% of FHLH cases are due to mutations in the gene encoding perforin (PRF1, 10q21-22), and 20-25% of cases are due to mutations in Munc 13-14 (UNC13D, 17q25). Acquired forms of HLH are typically triggered by infections, especially viral infection such as EBV, CMV, other herpes viruses, and parvovirus B19. Other forms of infection which trigger HLH include bacterial, fungal, and protozoan infections, especially Leishmaniasis. It is important to note that genetic forms of HLH may also be triggered by infection, and isolation of a causative agent does not distinguish primary and secondary forms. Malignancies associated with HLH include primary lymphomas, an association that is more common in adults than in children. Specifically, ALCL is a frequent associated malignancy. HLH in the setting of autoimmune disease has been distinguished from other forms and is called "macrophage activation syndrome" or " reactive hemophagocytic syndrome." This is most often reported in association with systemic-onset juvenile idiopathic arthritis, but may also be seen with LE and other collagen vascular diseases.

Answer 169

The locus on chromosome 11 that, in germline form, leads to MEN1 has been found to contain somatic mutation in ~25% of sporadic parathyroid adenomas.

Answer 170

The IDH1 gene is mutated in 80% of secondary GBMs.

Answer 171

The recombination frequency for 2 loci on the same chromosome is given by the Greek letter theta and varies from 0 (no recombination) to 0.5 (completely independent assortment, as if they were on different chromosomes).

Answer 172

A theta of 0.01 means that there is roughtly a 1% recombination rate between the 2 alleles. In honor of the geneticist Thomas Hunt Morgan, this is referred to as 1 centimorgan. Genetic distances are roughly additive, so if genes A, B, and C are on the same chromosome and A and B are 1 centimorgan apart, and B and C are 1 centimorgan apart, then A and C will be roughly 2 centimorgans apart and will recombine in about 2% of meiosis. However, there is only rough correspondence between genetic distance-the probability of recombination-and physical distance.

Answer 173

Because there are situations in which a recombination is followed by a second recombination that returns the chromatids to their original state.

Answer 174

Because crossing over is partially related to whether a region of DNA is recombination-rich or recombination-poor, some regions are not typically exchanged and other areas are exchanged with great frequency. Genes that are within the same region, between 2 breakage-prone points, tend to be inherited as a unit called a haplotype.

Answer 175

Pedigrees typically depict phenotypes, not genotypes, with a few exceptions.

Answer 176

A genetic family history is called a pedigree and is depicted by vertical lines representing different generations and horizontal lines representing one generation. Squares represent males, circles represent females, and diamonds indicate individuals of unknown or disguised gender. A diagonal line from the lower left to the upper right across a symbol indicates a deceased person. Offspring and their mates are denoted by a horizontal line (a sibship line) beneath a vertical line. In a sibship line, older children are depicted to the left of younger siblings Twins are indicated by diagonal lines connecting children to parents instead of a vertical line and a horizontal sibship line. A short horizontal connection between the diagonal twin line indicates that they are identical. Successive generations are numbered by Roman numerals, while individuals within a generation are numbered by Arabic numerals, starting on the left. A filled symbol indicates an affected person, while an open symbol indicates phenotypic normality, though complete openness of the symbol must not be construed as homozygosity for the wild-type genes because often, a heterozygous state will also be phenotypically normal. An open symbol comtaining a dot indicates known heterozygosity. A circle with a dot in the center often indicates a female carrier of an X--linked trait. For a dominant trait, a partially shaded individual is affected but is known to be heterozygous. An arrow pointing to a symbol indicates the proband (the person of principal study).

Answer 177

Congenital FXIII deficiency can be attributed to defects in both the FXIII-A and FXIII-B genes. It is an AR trait; patients with severe disease are homozygotes or compound heterozygotes. Congenital FXIII-A deficiency may be a quantitative defect (type I deficiency) or a qualitative defect (type II deficiency). Severe FXIII-B deficiency has been rarely reported.

Answer 178

The biochemical profiles of tumors associated with mutations of genes encoding succinate dehydrogenase subunits, (collectively referred to as SDHx; x refers to all subunits, SDHA refers to subunit A, etc) are characterized by dopamine and/or norepinephrine production. VHL-related tumors are associated with norepinephrine production. RET- and NF1-related tumors are associated with epinephrine production.

Answer 179

Patients with multiple paragangliomas (including multiple pheochromocytomas in the same adrenal gland) should be evaluated for the possibility of underlying genetic susceptibility and thus genetic testing for RET (rearranged during transfection), NF1 (neurofibromin 1), VHL (von Hippel-Lindau), SDHx (succinate dehydrogenase subunits, (collectively referred to as SDHx; x refers to all subunits, SDHA refers to subunit A, etc)), TMEM127 (transmembrane protein 127), MAX (MYC-associated factor-X), and KIF1Bbeta (kinesin family member 1B) mutations should be considered.

Answer 180

VHL-related tumors often exhibit a thick vascular capsule, hyalinized and myxoid stroma, round tumor cells intermingled with small vessels, cells with predominantly amphophilic and clear cell cytoplasm, absence of intracytoplasmic hyaline globules, lipid degeneration, and lack of nuclear atypic or mitoses.

Answer 181

Adrenal medullary hyperplasia is a precursor lesion of pheochromocytomas arising in MEN 2 syndrome and is characterized by a nodular and/or diffuse enlargement of the adrenal medulla. Other predisposing genetic syndromes are not usually associated with adrenal medullary hyperplasia.

Answer 182

Expansion of CGG triplet repeats in the FMR1 gene is the basis, with normal having 6 to 54 CGG repeats, 55-200 is permutation, and >200 is full mutation. Occasionally, point mutations can also cause a similar phenotype. The FMR1 gene produces the protein FMRP, which is a regulator of synaptic translation, selectively binding brain mRNAs and blocking their translation. Absence of FMRP allows unregulated translation of mRNAs, producing excessive internalization of the AMPA receptor, a signal of a weakened synapse.

Answer 183

Parental karyotyping (karyotyping of an abortus is often indicated as well). Endometrial bxs may be obtained to exclude luteal phase defect (endometrial histology that is 2 or more days discrepant with dates). Endometrial culture may be obtained to exclude subclinical infection with U. urealyticum or C. trachomatis. Thyroid function tests. Tests for lupus anticoagulants.

Answer 184

AKA BCL1 (B-cell leukemia/lymphoma 1) AKA PRAD1 (parathyroid adenomatosis 1). On 11q13.3. Encodes the cyclin D1. Mainly nuclear localization. No normal expression in lymphocytes.

Answer 185

It is also found in B-prolymphocytic leukemia, plasma cell leukemia, and splenic lymphoma with villous lymphocytes. It is found rarely in chronic lymphocytic leukemia and multiple myeloma.

Answer 186

BCL2 (B-cell leukemia/lymphoma 2) is located on 18q21.33. In normal and reactive lymph nodes, it is expressed by mantle cells and the small number of mantle cells that normally permeate the follicle center. It is an inhibitor of apoptosis (although there are other members of the bcl-2 family that are pro-apoptotic), so its expression is inhibited in germinal centers, where apoptosis forms part of the B-cell production pathway.

Answer 187

BCL6 (B-cell Lymphoma 6) AKA BCL5, LAZ3, ZBTB27, ZNF51, and BCL6A is located on 3q27.3. The gene product is a critical transcription factor responsible for normal secondary follicle formation during the germinal center reaction in lymphoid tissues and for proper T-cell-dependent Ab responses upon exposure to Ag. Accordingly, BCL6 is strongly expressed by germinal center B cells (GCBs) but is not present in naive or post-GCBs. BCL6 is thought to protect normal GCBs during the affinity maturation process (i.e., somatic hypermutation) in part by downregulating proapoptotic stimuli elicited by physiologic DNA double-strand breakage.

Answer 188

It results from the loss of genetic material on one chromosome and subsequent duplication of the missing material from the other chromosome.

Answer 189

Isochromosome 7q.

Answer 190

The 5q- syndrome is a myelodysplastic syndrome characterized by a defect in erythroid differentiation. Patients have severe macrocytic anemia, normal or elevated platelet counts, normal or reduced neutrophil counts, erythroid hypoplasia in the bone marrow, and hypolobated micromegakaryocytes. It is seen mostly in middle-aged to older women. Survival is usually long and cytogenetic evolution is uncommon.

Answer 191

Favorable Cytogenetics: inv(16)(p13;q22), t(8;21)(q22;q22), t(15;17)(q22;q12). Intermediate Cytogenetics: +8, t(6;9)(p23;q34), t(9;11)(p22;q23) in children, normal cytogenetics. Unfavorable Cytogenetics: -7, -5, del 7q, t(11q23), inv(3q), t(9;22), complex abnormalities, post-chemotherapy or post-radiation therapy.

Answer 192

Favorable Cytogenetics: inv(16)(p13;q22), t(8;21)(q22;q22), t(15;17)(q22;q12). Intermediate Cytogenetics: +8, t(6;9)(p23;q34), t(9;11)(p22;q23) in children, normal cytogenetics. Unfavorable Cytogenetics: -7, -5, del 7q, t(11q23), inv(3q), t(9;22), complex abnormalities, post-chemotherapy or post-radiation therapy.

Answer 193

Low risk: Hyperdiploidy >50 and t(12;21)(p12;q22). Standard risk: t(1;19)(q23;p13). High risk: t(4;11)(q21;q23) and t(9;22)(q34;q11).

Answer 194

BCL6 (B-cell Lymphoma 6) AKA BCL5, LAZ3, ZBTB27, ZNF51, and BCL6A is located on 3q27.3. The gene product is a critical transcription factor responsible for normal secondary follicle formation during the germinal center reaction in lymphoid tissues and for proper T-cell-dependent Ab responses upon exposure to Ag. Accordingly, BCL6 is strongly expressed by germinal center B cells (GCBs) but is not present in naive or post-GCBs. BCL6 is thought to protect normal GCBs during the affinity maturation process (i.e., somatic hypermutation) in part by downregulating proapoptotic stimuli elicited by physiologic DNA double-strand breakage.

Answer 195

BCL2 (B-cell leukemia/lymphoma 2) is located on 18q21.33. In normal and reactive lymph nodes, it is expressed by mantle cells and the small number of mantle cells that normally permeate the follicle center. It is an inhibitor of apoptosis (although there are other members of the bcl-2 family that are pro-apoptotic), so its expression is inhibited in germinal centers, where apoptosis forms part of the B-cell production pathway.

Answer 196

It is also found in B-prolymphocytic leukemia, plasma cell leukemia, and splenic lymphoma with villous lymphocytes. It is found rarely in chronic lymphocytic leukemia and multiple myeloma.

Answer 197

AKA BCL1 (B-cell leukemia/lymphoma 1) AKA PRAD1 (parathyroid adenomatosis 1). On 11q13.3. Encodes the cyclin D1. Mainly nuclear localization. No normal expression in lymphocytes.

Answer 198

The CD45 family consists of multiple members that are all products of a single complex gene (PRPRC). Different subsets of hematopoietic cells express different CD45 isoforms due to variable exon splicing, which can change in response to cytokines. The gene contains 34 exons and three exons of the primary transcripts (these three exons generate the RA, RB and RC isoforms) are alternatively spliced to generate up to eight different mature mRNAs and after translation eight different protein products. The isoforms are: CD45RA, CD45RB, CD45RC, CD45RAB, CD45RAC, CD45RBC, CD45RO, CD45R (ABC).

Answer 199

AKA protectin, complement regulatory molecule, MAC-inhibitory protein (MAC-IP), or membrane inhibitor of reactive lysis (MIRL). Regulates complement mediated cell lysis by inhibiting formation of membrane attack complex (MAC); binds to C8 or C9 components, preventing incorporation of multiple copies of C9 required for complete formation of osmolytic core. It is present on nearly all human cells. Decreased cell surface expression, along with decreased CD55 - DAF, is a feature of the affected clone in paroxysmal nocturnal hemoglobinuria.

Answer 200

Genetic defects that reduce both CD55 and CD59 on erythrocytes produce PNH.

Answer 201

Genetic defects that reduce both CD55 and CD59 on erythrocytes produce paroxysmal nocturnal hemoglobinuria.

Answer 202

Rearrangements involving TCL1 (at 14q32.1) are common and relatively specific for T-PLL. These may take the form of either inv 14(q11;q32) or t(14;14)(q11;q32). Another abnormality, t(X;14)(q28;q11), involves a homolog of TCL1, MTCP1 (mature T cell proliferation 1 gene) that is on Xq28. Overall, approximately 90 percent of cases demonstrate chromosome abnormalities involving chromosome 14. Also, abnormalities in chromosome 8 are seen in ~75% of cases, including idic(8p11), t(8;8), and trisomy 8q.

Answer 203

Alkylating agent-related acute myeloid leukemia is characterized by initial presentation as a myelodysplastic syndrome and cytogenetic abnormalities similar to those seen in myelodysplastic syndrome. The risk is related to total cumulative dose and survival is short.

Answer 204

(1) Alkylating agents: Occurs median 5 years after initiation (range, 2-11 years). Presents as MDS, AML or MDS/MPN (CMML). Abnormalities of chromosomes 5 or 7 or complex cytogenetic abnormalities. (2) Topoisomerase II inhibitor therapy: Abrupt onset

Answer 205

The BCL1 gene is rearranged in virtually all cases of mantle cell lymphoma and in some plasma cell neoplasms. The BCL2 gene is rearranged in up to 95% of follicular lymphoma. The BCL6 gene is rearranged in up to 30% of diffuse large B cell lymphoma. BCL10 gene rearrangements have been reported in extranodal MALT lymphoma, but are not characteristic of any lymphoma.

Answer 206

t(11;18)(q21;q21). t(14;18)(q32;q21). Trisomy 3. Trisomy 18. t(1;14)(p22;q32). t(1;2)(p22;p12).

Answer 207

The segments of DNA that will encode the IgH chain are V (variable), D (diversity), J (joining), and C (constant). The segments that will encode the kappa and lambda light chains are V, J, and C.

Answer 208

SBH: sensitivity is 1-5% of all cells in the sample, and specificity is 60-80%. PCR: sensitivity is 0.001% of all cells in the sample, and specificity is >95%.

Answer 209

The variation comes from the fact that HS can be caused by any one of several defects in cytoskeletal proteins, including band 3, protein 4.2, spectrin (alpha and beta), and ankyrin. A deficiency in any of these components can lead to the cytoskeletal instability that underlies HS.

Answer 210

HS can be caused by any one of several defects in cytoskeletal proteins, including band 3, protein 4.2, spectrin (alpha and beta), and ankyrin. A deficiency in any of these components can lead to the cytoskeletal instability that underlies HS.

Answer 211

The most common genetic defect (present in ~60^ of all cases of HE) is in spectrin (alpha or beta). Other mutations that cause HE are in band 4.1, band 3, and glycophorin C.

Answer 212

Somatic activating mutations in BRAF, NRAS, or KIT are common and generally mutually exclusive in melanoma. Mutations in at least one of these genes can be found in ~90% of melanomas and each may render a patient eligible for systemic targeted therapy.

Answer 213

~50% of melanomas harbor activating mutations in BRAF. Mutations at codon 600, including V600E, V600K, V600D, and V600R, are likely to respond to BRAF-targeted agents such as vemurafenib and dabrafenib. Mutations outside of codon 600 should not be treated with a BRAF inhibitor.

Answer 214

BRAF mutation occurs as high frequency in nevi and does not, therefore, distinguish benign melanocytic lesions from malignant.

Answer 215

Primary GBMs: <5%.

Answer 216

TCR: 7. IgH: 14. Kappa: 2. Lambda: 22.

Answer 217

Beta-globin chains (beta, delta, gamma): 11 (2 copies of each per cells). Alpha-globin chains (alpha, zeta): 16 (4 copies of each per cell).

Answer 218

G6PD A- and G6PD Mediterranean. The G6PD Med mutation is much more severe due to the fact that even very young RBCs are depleted of G6PD.

Answer 219

With G6PD A- type, the steady state enzyme activity is 20-60% of normal, and reticulocytes maintain adequate G6PD levels for longer. With G6PD Med type, the steady state enzyme activity is 10% of normal, and even very young RBCs are depleted of G6PD.

Answer 220

The G6PD A- variant has steady state enzyme activity in the range of 20-60% of normal, and their reticulocytes maintain adequate G6PD levels for longer, while the G6PD Med variant has steady state enzyme activity that is 10% of normal, and their reticulocytes are already depleted of G6PD. Hence, G6PD A- will have a rise in enzyme concentration caused by reticulocytosis after a hemolytic episode, causing them to appear to have normal enzyme levels.

Answer 221

PNH is a disorder characterized by a defect in the glycosylphosphatidylinositol (GPI) anchor, due to an acquired abnormality in the PIG-A (phosphatidylinositol glycan class A) gene on the X chromosome. This leads to partial or complete absence of all GPI-linked proteins, particularly CD59 (membrane inhibitor of reactive lysis) and CD55 (decay accelerating factor), resulting in an increased sensitivity of the affected cells to the action of complement.

Answer 222

Congenital sideroblastic anemia: X-linked sideroblastic anemia. Mitochondrial transporter SLC25A38 defects. Glutaredoxin 5 (GLRX5) deficiency. Erythropoietic protoporphyria. Congenital sideroblastic anemia without identified molecular defects. Sideroblastic anemia as a component of genetic syndromes (X-linked sideroblastic anemia with ataxia. Myopathy, lactic acidosis, and sideroblastic anemia. Sideroblastic anemia, B cell immunodeficiency, periodic fevers, and developmental delay. Pearson marrow-pancreas syndrome. Thiamine-responsive megaloblastic anemia syndrome). Acquired reversible/metabolic sideroblastic anemia: Alcohol. Drugs (Isoniazid. Chloramphenicol. Linezolid.). Copper deficiency/Zinc toxicity (excess zinc ingestion leads to copper deficiency). Hypothermia.

Answer 223

X-linked sideroblastic anemia (XLSA). One-third of patients are women, who express the disorder because of highly skewed inactivation of their X chromosomes in hematopoietic tissue, favoring expression of the mutant allele. Numerous distinct mutations in the ALAS2 (the erythroid-specific form of 5-aminolevulinate synthase) gene have been identified. This type of sideroblastic anemia may be responsive to high doses of pyridoxine (B6).

Answer 224

One-third of patients are women, who express the disorder because of highly skewed inactivation of their X chromosomes in hematopoietic tissue, favoring expression of the mutant allele.

Answer 225

Diamond-Blackfan anemia. Aase syndrome has been described as another congenital pure red cell aplasia, but is not thought to probably be a variant of DBA rather than a distinct clinical entity.

Answer 226

Progressive normochromic, usually macrocytic anemia in infancy or early childhood. Reticulocytopenia. Normal cellularity of the bone marrow with markedly decreased or absent erythroid precursors. WBC count is generally normal; platelet counts are generally normal but can be increased or decreased. Congenital malformations (50 percent of patients). Increased risk of malignancies.

Answer 227

Fanconi anemia. Dyskeratosis congenita. Shwachman-Diamond syndrome. Amegakaryocytic thrombocytopenia. Other inherited causes include reticular dysgenesis and Down syndrome.

Answer 228

SCN due to ELANE (neutrophil elastase gene) mutations have autosomal dominant inheritance and occurs in 60 percent of patients. SCN due to HAX1 (HCLS1-associated X1) mutations have autosomal recessive inheritance. SCN due to WASP (Wiskott-Aldrich Syndrome Protein) gene mutations have X-linked inheritance.

Answer 229

It is an autosomal recessive or X-linked chromosomal breakage syndrome that occurs in all races and ethnic groups.

Answer 230

Characteristic congenital malformations are present in up to 60-70% of children affected with Fanconi anemia, including short stature, hypopigmentation and cafe-au-lait spots, hypoplastic thumbs, microcephaly or hydrocephaly, renal abnormalities such as horseshoe kidney, and developmental delay.

Answer 231

The diagnosis is made by the presence of increased chromosomal breakage in lymphocytes cultured in the presence of DNA cross-linking agents such as mitomycin C (MMC) or diepoxybutane (DEB).

Answer 232

Fanconi anemia. Bloom syndrome. Ataxia telangiectasia. Xeroderma pigmentosum. Nijmegen breakage syndrome. Werner syndrome. Cockayne syndrome. Trichothiodystrophy. Rothmund-Thomson syndrome. Progeria (Hutchinson-Gilford Progeria syndrome). HNPCC. Li-Fraumeni syndrome. SCID.

Answer 233

The 2 genomic types of EBV are EBV1 and EBV2. They do not differ in disease association, but EBV1 is the predominant type in the West, whereas EBV1 and EBV2 are evenly distributed elsewhere.

Answer 234

The mechanism of death is usually hepatic necrosis, associated with a pronounced T/NK cell infiltrate. In other cases, affected individuals have manifested hemophagocytosis, agammaglobulinemia, and B cell lymphoma. The underlying genetic defect is found in the SH2D1A (also called SAP) gene that is normally expressed in T and NK cells. The SAP protein is a transmembrane signaling protein that becomes involved in the usual course of immune reaction to viral infection. In those harboring this mutation, for as yet unknown reasons, EBV in particular results in uncontrolled activation of T/NK cells.

Answer 235

All six EBNA proteins are transcribed from a large precursor transcriptional unit, initiated from one of two promoters, one in the BamHI C fragment (Cp) and the other in the BamHI W fragment (Wp) of the EBV genome. During the initial stages of EBV infection, transcription originates from Wp, and then switches to Cp.

Answer 236

Pocainamide (hepatic clearance) is metabolized to N-acetylprocainamide (NAPA) (renal clearance), which is also biologically active. The rate of conversion to NAPA is determined by the concentration of hepatic acetyltransferase, which is genetically determined. So-called fast acetylators, who have genetically high levels of acetyltransferase, have higher levels of NAPA.

Answer 237

Hereditary methemoglobinemia can result from either deficiency in the reductase system or abnormal hemoglobins (HbM) upon which this enzyme cannot act. HbM is a group of hemoglobins that, due to various amino acid substitutions, prefer the ferric (methemoglobin) state, which binds oxygen poorly. Acquired methemoglobinemia results from exposure to drugs or chemicals that increase the formation of Hi, common examples being nitrites, quinones, phenacetin, and sulfonamides.

Answer 238

There are 2 copies of the alpha genes on each chromosome 16, for a total of 4 alpha chain-producing gene loci in each normal cell. There is one copy of the beta gene on each chromosome 11, for a total of 2 productive genes in each normal cell.

Answer 239

Alpha thalassemia syndromes usually result from a large structural deletion within the translated portion of the gene, but occasionally result from a point mutation in the untranslated region. The vast majority of mutations that cause beta thalassemia consist of point mutations.

Answer 240

Beta0 alleles result in complete absence of beta-chain production, usually the result of nonsense or frameshift mutations. Beta+ alleles result in diminished beta-chain production, resulting from mutations in the promoter sequence, locus control region, or 5' untranslated region. There are also silent alleles (almost no impact on chain production - due to mutation of the promoter's CACCC box or the 5' untranslated region) and complex alleles (fusion delta-beta- and gamma-delta-beta-chains resulting from deletion of noncoding intervening segments of the HBB gene cluster).

Answer 241

alpha thal 2 (alpha+ thal) refers to a genotype in which chromosome 16 has one normal and one delted alpha gene (- alpha/). This is most common in African Americans. alpha thal 1 (alpha0 thal) refers to a genotype in which chromosome 16 has two deleted alpha genes (- -/). This is prevalent in Asians.

Answer 242

Beta-globin chain. Delta globin chain. Gamma globin chains. There is also a pseudo-HBB gene.

Answer 243

Oncotype DX is a real-time RT-PCR assay measuring RNA expression in 16 cancer-related genes and five reference genes, using paraffin-embedded tissue. Results are given as a recurrence score between 0 and 100, which are translated as low risk (a score of 18 or lower), medium risk (19 to 30), or high risk (31 or above). MammaPrint microarray measures expression of 70 genes in fresh or FFPE tissue; it categorizes patients as either high risk, (a so-called poor signature), or low risk (a so-called good signature) for recurrence. Mammostrat is an IHC test measuring five markers: p53, HTF9C, CEACAM5, NDRG1, and SLC7A5. The results are combined into a quantitative risk index: low, moderate, and high. Oncotype DX and MammaPrint are send-out tests, with TATs of 10-14 days, while results from the IHC-based Mammostrat, also a send-out test, are available to local pathologists within 48-72 hours. As of 3/2014, only MammaPrint has FDA clearance.

Answer 244

CLL is thought to be 2 diseases based on molecular profile: One that arises from post germinal center cells which is CD38 and Zap70 negative and has a better prognosis, and another that arises from naive B cells which is CD38 and Zap70 positive and has a worse prognosis.

Answer 245

Del(13q) is a good prognosis. Del(11q), del(17p), and tri 12 are poor prognosis.

Answer 246

There are multiple possible breakpoints in 11q13 (MTC, mTC1, mTC2). Detecting the translocation via FISH with a fusion probe is easier.

Answer 247

E6 and E7 genes.

Answer 248

C, X, P, and S.

Answer 249

The core protein (HBcAg) is encoded by C, with HBeAg produced by proteolytic processing of the pre-core protein. S encodes the surface antigen (HBsAg). The HBsAg gene is one long open reading frame but contains three in frame "start" (ATG) codons that divide the gene into three sections, pre-S1, pre-S2, and S. P encodes the DNA polymerase. The function of the protein coded for by X is not fully understood.

Answer 250

The HBV genome can undergo mutation, altering clinical features, with one such mutation taking the form of so-called HBeAg-negative chronic hep B. This is characterized by circulating HBV DNA, fluctuating aminotransferases, and a tendency towards fulminant hepatitis with liver failure. This form of hep B results from mutations in the C region of the genome (encodes HBcAg and HBeAg), the most common mutation leading to a premature stop codon that impairs synthesis of HBeAg.

Answer 251

Mutations in the HBV P gene (encodes the DNA polymerase) often arise during treatment with lamivudine, resulting in decreased binding of lamivudine. These mutations may lead to abrupt progression of chronic hepatitis B in patients previously stable on treatment.

Answer 252

Genotype 1 has a low (40%) rate of response. Genotypes 2 and 3 have a high (70%) rate of response. Genotypes 4 through 9 have not been sufficiently studied due to low prevalence.

Answer 253

In the US, the most common HCV genotype is 1 (80%). Genotype 1 is further subdivided into 1a (60%) and 1b (20%), but significance has not been assigned to these subgenotypes. Genotype 2 represents 20%, and genotype 3 represents 5%.

Answer 254

Molecular or serologic assays are available. The molecular assays involve direct sequencing of portions of the HCV genome (such as the 5V noncoding region), hybridization with genotype-specific sequences, or RFLP analysis. Serologic assays detect serum antibodies against genotype-specific antigens.

Answer 255

Qualitative assays are based upon conventional PCR or TMA platforms. Quantitative assays for HCV RNA can be performed by RT-PCR, TMA, or bDNA. These techniques must be capable of detecting as little as 50 IU/mL, since this is the definition of a sustained virologic response. Furthermore, they must be equally sensitive to RNA from the different genotypes. The same testing platform should be used throughout treatment, since quantitative results are not directly comparable between methods.

Answer 256

RT-PCR. It demonstrates excellent sensitivity and same-day turnaround time. Cell culture should be performed as well, in case the PCR test is negative.

Answer 257

More than 225 mutations in PTCH1 have been found to cause Gorlin syndrome/nevoid basal cell carcinoma syndrome. Somatic mutations are associated with sporadic basal cell carcinoma, medulloblastoma, breast cancer, colon cancer, and keratocystic odontogenic tumors. At least seven mutations in PTCH1 have been found to cause nonsyndromic holoprosencephaly.

Answer 258

Familial hypercholesterolemia, an autosomal dominant deficiency in LDL receptors.

Answer 259

Familial combined hyperlipidemia, familial LPL deficiency, familial apo C-II deficiency, and familial hypertriglyceridemia.

Answer 260

Familial combined hyperlipidemia.

Answer 261

Low cholesterol, normal to increased TG, absent HDL, and absence of APO-A1. Cholesterol esters deposit in the tonsils, lymph nodes, vasculature, and spleen, and corneal opacities develop.

Answer 262

Insulinoma. Nesidioblastosis. ILGF-like hormone secreting tumors (sarcomas, HCC). Advanced malignancy. Anti-insulin receptor antibodies. Autoimmune insulin syndrome. Post-gastric surgery. Drug induced (insulin, sulfonylureas, alcohol, quinine, salicylates, haloperidol, beta blockers, quinolones, pentamidine, ACE inhibitors, IGF-1). Critical illness such as hepatic/renal/cardiac failure, sepsis, inanition (def: an exhausted condition resulting from lack of food and water or a defect in assimilation; starvation). Hormone deficiency (cortisol, glucagon and epinephrine in insulin-deficient DM). Inborn errors of metabolism (glycogen storage disease, hereditary fructose intolerance, galactosemia, carnitine deficiency). Starvation. Accidental, surreptitious, or malicious hypoglycemia.

Answer 263

ITP. May-Hegglin anomaly. Gray platelet syndrome. Bernard-Soulier syndrome. Velocardiofacial syndrome. Montreal platelet syndrome. Hereditary macrothrombocytopenia with hearing loss. Mediterranean macrothrombocytopenia. Sebastian syndrome. Fechtner syndrome. Epstein syndrome. Alport syndrome. Harris platelet syndrome.

Answer 264

Lacks alpha granules: Gray platelet syndrome and Quebec platelet disorder. Lacks delta/dense granules: Wiskott-Aldrich syndrome, Chediak-Higashi syndrome, and Hermansky-Pudlak syndrome.

Answer 265

Genes for light chains are found on chromosome 2 (kappa) and 22 (lambda). Genes for heavy chains are found on chromosome 14 (gamma, alpha, mu, delta, eta).

Answer 266

Chromosome 7.

Answer 267

Human leukocyte antigen proteins are encoded by genes located within the major histocompatibility complex. The MHC complex is separated into MHC class I, class II, and class III genes which are located sequentially on chromosome 6p. Also embedded in the MHC region are the genes for hereditary hemochromatosis, 21-hydroxylase, and tumor necrosis factor. These and the MHC genes are such closely linked loci that they are inherited en bloc from each parent, with no crossing over.

Answer 268

Class I antigens are found on nearly all nucleated cells and platelets (minimal to absent expression on RBCs). Class II antigens are found on macrophages, B cells, and activated T cells.

Answer 269

HLAs corresponding to MHC class I (A, B, and C) present peptides from inside the cell (including viral peptides if present). HLAs corresponding to MHC class II (DP, DQ, DR, DM, DOA, and DOB) present antigens from outside of the cell to T-lymphocytes. HLAs corresponding to MHC class III encode components of the complement system.

Answer 270

The 3 major genes: HLA-A, HLA-B, HLA-C. The 3 minor genes: HLA-E, HLA-F, HLA-G. Beta2-microglobulin binds with major and minor gene subunits to produce a heterodimer.

Answer 271

Modern HLA alleles are typically noted with a variety of levels of detail. Most designations begin with HLA- and the locus name, then * and some (even) number of digits specifying the allele. The first two digits specify a group of alleles. Older typing methodologies often could not completely distinguish alleles and so stopped at this level. The third through fourth digits specify a synonymous allele. Digits five through six denote any synonymous mutations within the coding frame of the gene. The seventh and eighth digits distinguish mutations outside the coding region. Letters such as L, N, Q, or S may follow an allele's designation to specify an expression level or other non-genomic data known about it. Thus, a completely described allele may be up to 9 digits long, not including the HLA-prefix and locus notation.

Answer 272

Since each MHC complex is closely linked and inherited en bloc, each parental chromosome can be thought of as a haplotype. Thus, the chance that 2 siblings are HLA-identical is essentially 25%. The chance of having an HLA-identical sibling goes up with the number of siblings: with 1 sibling, the chance is 25%, with 2 it is around 45%, and with 3 it is nearly 60%.

Answer 273

HLA testing does not normally have a role in the evaluation of immunodeficiency. It may be undertaken in other scenarios: pre transplantation compatibility testing, platelet refractoriness, paternity/forensic identity testing, and the evaluation of several HLA-linked autoimmune disorders.

Answer 274

The test detects either HLA antigens or antibodies. For Ag typing, it is best at detecting class I Ags (another technique, especially a DNA-based method, is preferred for detecting class II). For detecting Ags, HLA antisera are incubated with pt lymphocytes enriched from peripheral blood in the presence of excess complement, followed by the addition of dye. Microscopic examination shows either intact lymphs (a negative reaction) or damaged lymphs that internalize the dye (a positive reaction). For detecting Abs, pt serum is incubated with lymphs of known HLA type, and a similar procedure is carried out. The pt's serum can be run against a panel of known lymph to determine the panel reactive antibody (PRA) level.

Answer 275

This test detects HLA class I (HLA-D) differences between a potential donor and recipient. After a B cell enrichment step (since class II molecules are numerous on B cells but not resting T cells), prospective donor and recipient B cells are cultured together. They proliferate if stimulated by one another's HLA dissimilarities. At the end of the incubation period, the assay is pulsed with radioactive thymidine to determine the extent of DNA synthesis, a reflection of the amount of proliferation and thus the amount of incompatibility. By first subjecting the donor lymphocytes to irradiation (rendering them incapable of proliferation), the reaction can be made more specific for recipient intolerance of the potential donor.

Answer 276

In organ transplantation, ABO compatibility is most important, followed by HLA class II compatibility.

Answer 277

PCR has the advantage of eliminating many of the biologic uncertainties of the serologic techniques such as microlymphocytotoxicity and mixed lymphocyte culture assays. Furthermore, it can resolve HLA types with much greater specificity than the serologic techniques. The DNA is usually obtained from peripheral blood.

Answer 278

Primers can be used that either amplify the locus of interest (regardless of its allele) for additional study; alternatively, primers may be used that will amplify the locus only if a specific allele is present - if a band results from this latter amplification, then that genotype is confirmed. In the former amplification, sequence-specific oligonucleotides can be applied to the amplified DNA to determine the identity of the alleles. For example, if looking for HLA-B27, the pt's HLA-B locus can first be nonspecifically amplified then treated with HLA-B27-specific oligonucleotide probe to see if hybridization occurs. Alternatively, HLA-B27-specific primer sequences can be used in the amplification step; the presence of an identifiable band after PCR confirms HLA-B27. Also, an unknown allele can be directly sequenced and compared to known sequences.

Answer 279

HLA-A, HLA-B, and HLA-DR.

Answer 280

HLA matching for transplantation usually involves at least 3 loci: HLA-A, HLA-B, and HLA-DR. Since each person has 2 alleles (one on each 6p) for each locus, there are 6 possible alleles. The potential recipient may have been sensitized to these and other not-normally-tested alleles through pregnancy or transfusion, so a crossmatch is still necessary. The lymphocyte crossmatch can detect pre-existing HLA allo-antibodies in the serum of the potential recipient that have specificity for HLA antigens in the potential donor. These HLA antibodies are the mediators of hyper acute rejection.

Answer 281

Transplantation crossmatch is usually performed by incubating donor lymphocytes with recipient serum in the presence of excess complement. An auto-crossmatch is performed to control for auto-antibodies (which do not appear to impact transplant survival).

Answer 282

For renal transplantation, one seeks ABO-compatible, HLA-matched (6 of 6 ideally), and crossmatch-compatible donor and recipient. Similar requirements are made for marrow and progenitor cell transplants. For other organs, such as heart and lung, such stringency is not required, and ABO-compatibility is the main concern.

Answer 283

A gene on the X chromosome encoding a tyrosine kinase called Atk (agammaglobulinemia tyrosine kinase) or Btk (Bruton's tyrosine kinase).

Answer 284

CVID is a group of approximately 150 primary immunodeficiencies characterized by hypogammaglobulinemia (low IgG, IgA, and IgM) but which have different underlying causes. In CVID, the B cells are normal in numbers but they lack the capacity to differentiate into plasma cells, so the pts do not make an effective amount of Ig. The clinical severity and age of onset are somewhat variable; the typical onset is around the 2nd or 3rd decade.

Answer 285

Salient clinical features are described by the CATCH: Cardiac abnormality (especially tetralogy of Fallot), Abnormal facies, Thymic aplasia, Cleft palate, Hypocalcemia/Hypoparathyroidism. The 22 refers to the deletion of 22q11.2 that causes DiGeorge syndrome.

Answer 286

A small number of patients with the phenotypic features of DiGeorge syndrome have deletions on 10p13-p14 (DiGeorge syndrome II locus) instead of at the 22q11.2 locus typical of DiGeorge syndrome. But this is now thought to be a separate entity from DiGeorge syndrome.

Answer 287

50% are X-linked and due to a defect in the IL-2 receptor. 40% are autosomal recessive and due to deficiency in the enzyme adenosine deaminase. The remainder are also autosomal recessive and due to numerous defects such as in JAK3, CD45, IL7R, TCR, PNP, RAG1, RAG2, STAT5a, ZAP-70, and many others.

Answer 288

WASP is found mainly within hematopoietic cells and appears to be responsible for the cytoskeletal malleability that is necessary for physiologic activities.

Answer 289

AKA Ataxia-telangiectasia.

Answer 290

The ATM (Ataxia-telangiectasia Mutated) gene on 11q22.3.

Answer 291

The gene encodes the ATM protein kinase, which is involved in DNA repair.

Answer 292

Immunoblotting assay for the ATM protein in nuclear lysate ~90% have no ATM, ~10% have trace amounts, and ~1% have a normal amount of protein that lacks ATM serine/threonine kinase activity). Assays for ATM kinase activity (uses immunoblotting of cell lysates and commercial antibodies to many phosphorylated ATM target substrates). Radiosensitivity assay (determines the survival of patient lymphoid cells following irradiation, and this is abnormal in more than 95% of affected individuals). A t(7;14) is found in 5-15% of cells in peripheral blood chromosome studies in affected individuals. Sequence analysis of the ATM coding region detects about 90% of ATM sequence variants.

Answer 293

Typically as a fulminant and often fatal immune response to EBV infection. EBV infection induces a fulminant hemophagocytic syndrome, the development of a neoplastic B cell proliferation, and/or fulminant hepatic failure, concomitant with an inverted CD4:CD8 ratio in the peripheral blood.

Answer 294

Affected individuals often have a common variable immunodeficiency-like immune system defect, especially manifesting hypogammaglobulinemia with or without decreased B, T, or NK subsets. The median survival is about 10 years of age.

Answer 295

SH2D1A, which encodes for SH2 domain protein-containing protein 1A/SLAM-associated protein (SAP). XIAP (also known as BIRC4), which encodes for baculoviral IAP repeat-containing protein 4 (X-linked inhibitor of apoptosis; XIAP), respectively. The former is sometimes referred to as XLP1, and the latter XLP2.

Answer 296

SH2D1A: 83-97%. XIAP: 12%.

Answer 297

Molecular testing (sequence analysis or deletion/duplication analysis) for one of the causative genes: SH3D1A or XIAP. Also, SAP and XIAP protein expression by flow cytometry may be used as a screening test prior to molecular genetic testing of the SH2D1A or XIAP genes.

Answer 298

CGD is caused by mutation of one of five genes that encode the subunits of phagocyte NADPH oxidase: biallelic mutations in CYBA, NCF1, NCF2, and NCF4 cause autosomal recessive CGD; mutation of CYBB causes X-linked CGD.

Answer 299

Permanently stained slides - 3 yrs. Fluorochrome stained slides - at the discretion of the lab director. Wet specimen/tissue - until adequate metaphase cells are obtained. Fixed cell pellet - 2 wks after final report. Final reports - 20 yrs. Diagnostic images (digitized, prints or negatives) - 20 yrs.

Answer 300

A false-positive test. An HIV-1 primer site mutation causing failure of PCR amplification (some methods address this concern by interrogating multiple gene targets). HIV-2 infection. Use of an insensitive viral load assay (some HIV-1 quantitative methods are unable to accurately distinguish the presence of absence of HIV-1 RNA below the limit of detection; with this type of assay, a result of less than 75 copies/mL could represent either no HIV-1 RNA or less than 75 copies/mL). An elite controller AKA elite suppressor (these patients develop Ab to HIV-1 but have extremely low level or undetectable viral loads (less than 50 copies/mL); they are asymptomatic and have HIV-1 control that is similar to that of those taking ART).

Answer 301

In cutaneous lesions, BPDCN typically infiltrates the dermis but spares the epidermis. As the disease progresses, it frequently extends into the subcutaneous fat. Extracutaneous disease is present in most pts at diagnosis, often involving the regional lymph nodes. As the disease continues to progress, the peripheral blood and bone marrow become involved. There is enhanced expression of CD4, CD56, and CD123. Karyotypic analysis frequently shows complex aberrations similar to those seen in MDS or AML arising from MDS. There is frequent deletion of tumor suppressor genes, including RB1 CDKN1B, CDKN2A, and TP53.

Answer 302

Characterized by the progressive proliferating and infiltrating smooth musclelike cells (lymphangioleiomyomatosis cells/LAM cells) which lead to the cystic destruction of the lung parenchyma; obstruction of airways, blood vessels, and lymphatics; and loss of pulmonary function. LAM cells were recently recognized as perivascular epithelioid cells, and LAM is categorized as one of the perivascular epithelioid cell tumor family, which includes angiomyolipomas, clear cell "sugar" tumors of the lung and extrapulmonary sites, clear cell myomelanocytic tumors of the falciform ligament or ligamentum teres, and rare clear cell tumors of other anatomic sites. LAM occurs in 2 main forms: tuberous sclerosis complex (TSC-)-associated LAM, and sporadic LAM (S-LAM), with most being the latter form. Primarily affects women of childbearing age and worsens during pregnancy and following the administration of estrogens. Dyspnea on exertion and recurrent pneumothorax are the MC clinical features.

Answer 303

Macroscopic features are enlarged lungs with a cystic, honeycomb appearance. The cysts are usually evenly distributed through the lung and may contain air or fluid (serosanguinous or chylous). Microscopically, the LAM cells are characteristically found in small clusters or nests at the edges of the cysts and along the alveolar walls, pulmonary blood vessels, lymphatics, and bronchioles. The proliferating LAM cells are morphologically heterogenous and can be classified into 2 types: spindle-shaped cells (usually centrally located) and epithelioid cells (usually in the peripheral regions of the LAM cell nodules). Lymphangioleiomyomatosis cells coexpress smooth muscle markers and melanocytic markers. Somatic or genetic mutations of tumor suppressor genes TSC1 or TSC2 (Tuberous Sclerosis Complex 1 or 2) are closely related to LAM.

Answer 304

HPV is a nonencapsulated double-stranded DNA virus. Integration of viral genetic material into the host genome is the critical event in malignant transformation of the cell, which results in disruption of the viral genome E1-E2 region. Disruption of the E2 gene causes overexpression of E6 and E7 genes. The integration sites in the host genome as random.

Answer 305

Loci associated with susceptibility to basal cell carcinoma have been identified on chromosome 1 (BCC1 and BCC2), 5 (BCC3), 12 (BCC4), 9 (BCC5), and 7 (BCC6). Mutations in the PTCH1 (chromosome 9), PTCH2 (chromosome 1), and SMO (chromosome 7) genes predispose patients to BCC. P53 (chromosome 17) gene may be involved in the development of sporadic BCC. Other possibly involved genes are the SUFU and MC1R genes.

Answer 306

Pancreatic: usually in the head of the pancreas; are not associated with NF-1; contain fewer psammoma bodies; have poorer prognosis; more commonly have the somatostatinoma syndromes. Duodenal: 6 times more common than pancreatic; functional ones are distinctly unusual in the duodenum; duodenum and periampullary location is more common in patients with NF-1; psammoma bodies are seen in over half of sporadic tumors and all of the NF-1 associated ones.

Answer 307

It is not actually CML. Consider aCML (atypical CML) or CMML instead.

Answer 308

These look like CML but don't have the Philadelphia chromosome. JMML, aCML, and CMML.

Answer 309

The negative/pale/clear staining areas on G or Q banded chromosomes are G-C rich. The positive/dark staining areas on G or Q banded chromosomes are A-T rich.

Answer 310

The clear bands are the gene-rich areas.

Answer 311

Fanconi anemia. There is an inability to repair chromosome breaks.

Answer 312

13, 14, 15, 21, and 22.

Answer 313

Acrocentric only.

Answer 314

Negligible.

Answer 315

The most common mechanism is 2 haploid sperm (dispermy) + haploid egg (70-80%).

Answer 316

About 25% of spontaneous abortions are trisomic.

Answer 317

Multiple chromosomal abnormalities have been found in MCC, the most common of which is the deletion of 1p36, a structural aberration found in up to 40% of MCCs. The pathogenesis is unclear may may involve MCPyV (Merkel Cell Polyoma Virus).

Answer 318

Recent studies have shown the characteristic molecular feature: a balanced translocation t(12;15), resulting in an ETS variant 6-neurotrophic tyrosine kinase receptor type 3 (ETV6-NTRK3) fusion gene encoding a chimeric tyrosine kinase.

Answer 319

The X chromosome that is present in | a 45,X conceptus (Turner syndrome) is the maternal X approximately 80% of the time.

Answer 320

A marker chromosome (mar) is a structurally abnormal chromosome in which no part can be identified. The significance of a marker is very variable as it depends on what material is contained within the marker. It is essentially a partial trisomy. However sometimes the marker is composed of inactive genetic material and has little or no effect. There are some markers that are passed down through a family with little effect. There are some markers that arise as new events. Often, markers are not passed down as they can be lost during cell division due to their small size. There are some individuals who have multiple markers.

Answer 321

A high proportion of markers derive from chromosome 15. There is a common marker called inverted duplication of chromosome 15. This is a specific syndrome that has developmental delays and physical variations and often seizures as its features.

Answer 322

Severe growth deficiency, severe to profound mental retardation with the onset of convulsions in early infancy, microcephaly, sacral dimples and characteristic facies.

Answer 323

An isochromosome is a chromosome that has lost one of its arms and replaced it with an exact copy of the other arm.

Answer 324

Reciprocal translocations are found in approximately 1 in 500 phenotypically normal individuals.

Answer 325

A derivative chromosome (der) is a structurally rearranged chromosome generated either by a rearrangement involving two or more chromosomes or by multiple aberrations within a single chromosome (e.g. an inversion and a deletion of the same chromosome, or deletions in both arms of a single chromosome). The term always refers to the chromosome that has an intact centromere.

Answer 326

46,XY,der(4)t(4;8)(p16;q22)t(4;9)(q31;q31) would refer to a derivative chromosome 4 which is the result of a translocation between the short arm of chromosome 4 at band 16 and the long arm of chromosome 8 at band 22, and a translocation between the long arm of chromosome 4 at band 31 and the long arm of chromosome 9 at band 31.

Answer 327

Deletion in the PWS region on chromosome 15 that is inherited from the father (present in about 70% of patients). Both chromosomes 15 are inherited from the mother and the PWS region from the father is missing (present in about 25% of patients). A defect in methylation (C5 position of cytosine 5-methyl-cytosine) inherited from the father (present in less than 5% of patients).

Answer 328

Expansion of the CGG repeat from the premutation to the full mutation occurs in maternal meiosis and not paternal meiosis.

Answer 329

t(17;22)(q22/q13), resulting in a COL1A1-PDGFB fusion gene.

Answer 330

Cytogenetic: Complex. Molecular: IDH1 and IDH2 mutations.

Answer 331

t(11;22)(q24;q12) / EWSR1-FLI1 fusion. t(21;22)(q12;q12) / EWSR1-ERG fusion. t(2;22)(q33;q12) / EWSR1-FEV fusion. t(7;22)(p22;q12) / EWSR1-ETV1 fusion. t(17;22)(q12;q12) / EWSR1-E1AF fusion. inv(22)(q12q12) / EWSR1-ZSG. t(16;21)(p11;q22) / FUS-ERG. t(2;16)(q35;p11) / FUS-FEV.

Answer 332

Low grade central osteosarcoma: Cytogenetic events - simple; Molecular events - MDM2 amplification. Parosteal osteosarcoma: Cytogenetic events - ring chromosomes; Molecular events - 12q13-15 amplification. High grade osteosarcoma: Cytogenetic events - complex; Molecular events - ?.

Answer 333

Cytogenetic events: t(X;17)(p11;q25). Molecular events: TFE3-ASPL fusion.

Answer 334

Cytogenetic events: t(16;17)(q22;p13). Molecular events: CDH11-USP6 fusion.

Answer 335

t(12;16)(q13;p11) / FUS-ATF1 fusion. t(12;22)(q13;q12) / EWSR1-ATF1 fusion. t(2;22)(q33;q12) / EWSR1-CREB1 fusion.

Answer 336

t(9;22)(q22;q12) / EWS-NR4A3 fusion. t(9;17)(q22;q11) / TAF2N-NR4A3 fusion. t(9;15)(q22;q21) / TCF12-NR4A3 fusion.

Answer 337

Cytogenetic events: ring form of chromosomes 17 and 22, t(17;22)(q21;q13). Molecular events: COL1A1-PDGFB fusion.

Answer 338

t(1;2)(q22;p23) / TPM3-ALK fusion. t(2;19)(p23;p13) / TPM4-ALK fusion. t(2;17)(p23;q23) / CLTC-ALK fusion. t(2;2)(p23;q13) / RANB2-ALK fusion.

Answer 339

Complex with frequent deletion of 1p.

Answer 340

Ring form of chromosome 12.

Answer 341

Inversion chromosome 12 / NAB2-STAT6.

Answer 342

NPM1 is on chromosome 5q35. The mutation is in exon 12. The exon 12 mutations are variable but all lead to small insertions that are usually 4 bp in size (rare cases may result in 5 bp or larger insertions). Normal allele size is 239/240 bp, which mutant is 244 bp. The mutation can be detected by direct sequencing, allele specific PCR reactions designed for individual mutations, or by PCR with subsequent capillary electrophoresis to identify abnormal insertions.

Answer 343

CEBPA is on chromosome 19q31.1. Over 100 non-silent mutations are identified. Most are in-frame insertions in the basic/leucine zipper region or truncations of the N-terminus region. Mutations may be identified by PCR amplification followed by sequencing.

Answer 344

Because there is an approximate doubling of PCR product with each PCR cycle during the linear phase of PCR amplification, a three-log (1000-fold) reduction or increase corresponds to a difference of approximately ten cycles.

Answer 345

17p13 deletion > 11q22.3 deletion > trisomy 12 > 13q14 deletion. Deletions of 17p13 and 11q22.3 predict a higher risk of disease progression and poorer outcomes following therapy. Deletion of 13q14 (as the sole FISH abnormality) is associated with a lower risk of disease progression and better responses to therapy.

Answer 346

NOTCH1 mutation results in a gain-of-function that is associated with more aggressive disease, poorer treatment responses to chemoimmunotherapy (CIT), and a marked increase (~20x) in the risk of transformation to diffuse large B-cell lymphoma. SF3B1 mutations selectively disrupt spliceosome function and are associated with more aggressive disease and poorer treatment responses to CIT.

Answer 347

CLL patients with more than 98% IGHV sequence identity to the germline allele are considered to be negative for somatic hypermutation (“unmutated”). These patients have a shorter time from diagnosis to disease progression requiring treatment and a poorer prognosis. In contrast, patients with evidence of somatic hypermutation of IGHV (≤ 98% sequence identity to the germline allele) are considered to be “mutated” and have a longer time to first treatment and a better prognosis. It has been observed, however, that CLL patients whose malignant cells utilize the IgVH family VH3-21 allele have a poor prognosis irrespective of the somatic mutation status of the IgVH gene.

Answer 348

DLBCL arising in the setting of CLL. This can be caused by clonal evolution of a CLL cell (~80% of cases) or de-novo development of clonally unrelated DLBCL (~20% of cases).

Answer 349

Clonally related DLBCL has a considerably poorer response to treatment and prognosis.

Answer 350

Interphase FISH testing of CLL cells can detect 17p13 deletion that results in loss of one allele of TP53. This deletion is detected in ~5% of patients requiring initial treatment for CLL and is usually monoallelic. In ~80% of patients with 17p13 deletion, the remaining TP53 allele has a mutation predicted to be dysfunctional - these patients have disrupted p53 function and have poor responses to chemoimmunotherapy regimens because DNA damaging agents are ineffective in patients without an intact DNA damage response pathway.

Answer 351

In ~5% of patients with progressive CLL, TP53 is disrupted in the absence of 17p13 deletion. This may occur due to biallelic mutation, a single mutation with uniparental disomy, or by generation of a dominant negative mutant.

Answer 352

No. This fusion has been detected, at lower frequency, in breast and colorectal adenocarcinomas, although its role in the pathogenesis of these tumors is unknown.

Answer 353

The other 1% is caused by a variety of other mutations, primarily including gross deletions and duplications, regulatory mutations, and missense and nonsense mutations.

Answer 354

45 to 54 CGG repeats. This range is not associated with fragile X syndrome, and gray zone alleles expanding to a full mutation in one generation have not been observed.

Answer 355

33-50% are thought to arise from preexisting neurofibromas, and 50% arise de novo. 50% of MPNSTs are associated with NF1.

Answer 356

MSH2 - 40%. MSH6 - 7-10%. MLH1 - 50%. PMS2 - less than 5%. EPCAM - 1-3%.

Answer 357

MSH2-, MSH6-, MLH1+, PMS2+.

Answer 358

85-90% of autosomal dominant polycystic kidney disease is due to mutations in the PKD1 gene on 16p13.3, while 10-15% are due to mutations in the PKD2 gene on 4q22.

Answer 359

Autosomal recessive polycystic kidney disease is due to mutations in the PKHD1 gene. The high phenotypic variability of this disease is due to alternative splicing of 86 exons assembling a variable number of transcripts with the longest being fibrocystin/polyductin.

Answer 360

PKD1 gene --> polycystin-1 (PC-1) protein. PKD2 gene --> polycystin-2 (PC-2) protein.

Answer 361

NPM1 mutations are the most common genetic lesion(s) in AML. They are present in 30% of all AMLs and in 50-60% of cytogenetically normal AMLs.

Answer 362

NPM1 mutations occur in exon 12 with greater than 95% occurring as a 4 bp insertion at position 960.

Answer 363

NPM1 mutations occur in exon 12 with greater than 95% occurring as a 4 bp insertion at position 960. Type A mutation is a TCTG insertion, type B is a CATG insertion, and type D is a CCTG insertion.

Answer 364

Type A - 80%, type B - 10%, type D - 5%.

Answer 365

FLT3-ITD is seen in ~15-30% of AML, while FLT3-TKD mutation is seen in ~7% of AML.

Answer 366

CEBPA is first expressed with commitment to the myeloid line and is upregulated during granulocyte differentiation. As a transcription factor, it down regulates c-MYC expression and upregulates myeloid-specific genes, allowing differentiation.

Answer 367

N-terminal mutations lead to increased translation of an alternative 30-kDa isoform with dominant negative activity on the full-length 42-kDa protein. C-terminal mutations result in deficient binding and/or homodimerization activity.

Answer 368

Most T-cell large granular lymphocytic leukemias have a surface CD3+/CD4-/CD8+/CD57+ immunophenotype and express the alpha-beta TCR.

Answer 369

Microsatellite stable CRC with BRAF V600E has a worse prognosis than MSI-high CRC with BRAF V600E.

Answer 370

Sporadic FGPs show a very high frequency of activating mutations in the beta-catenin gene, whereas syndrome FGPs occur through an inherited germline mutation in the APC gene coupled with additional somatic mutations, leading to complete inactivation of both copies of the APC tumor suppressor gene. But when low-grade dysplasia is present in either sporadic or syndromic FGPs, truncating mutations in the APC gene occur in both settings.

Answer 371

TET2 - 50-60%, SRSF2 - 46%, ASXL1 - 40%, RUNX1 - 15%, SETBP1 - 15%.

Answer 372

TET2 - 20-25%, SF3B1 - 14.5% (80% with ring sideroblasts), ASXL1 - 14%, SRSF2 - 12.4%, RUNX1 - 9-20%.

Answer 373

Innate immune resistance and adaptive immune resistance. In innate immune resistance, the up-regulation of PD-L1 expression is secondary to constitutive oncogenic signaling within tumor cells including EGFR mutations and ALK rearrangements. In adaptive immune resistance, PD-L1 expression is induced on tumor cells secondary to local inflammatory signals, which in turn induces PD-1 on T cells.

Answer 374

When engaged by PD-L1 or other ligands, PD-1 inhibits kinases that are involved in T cell activation through the phosphatase SHP250 leading to apoptosis of T cells, although additional signaling pathways are likely also induced. Thus, blockade of PD-1/PD-L1 interaction will reinstitute the active anti-tumor immune response. KRAS-mutated NSCLC, especially those with significant smoking history, may harbor large mutation burdens (large numbers of neoantigens) leading to adaptive immune resistance (due to immune microenvironment with significant local inflammatory signals).

Answer 375

KRAS-mutated NSCLC, especially those with significant smoking history, may harbor large mutation burdens (large numbers of neoantigens) leading to adaptive immune resistance (due to immune microenvironment with significant local inflammatory signals).

Answer 376

of DNA base pairs - ~3 billion. # of genes - ~25,000. Each gene makes an average of 3 proteins. Coding DNA (ie exons) makes up

Answer 377

M (major), O (outlier), and N (nonmajor and nonoutlier).

Answer 378

True. Regression models have shown that HIV-1 RNA viral load alone explains half of the variability in prediction of the onset of AIDS and death.

Answer 379

The 4th generation EIA tests simultaneously detect both p24 antigen and HIV-1 antibody, while the 3rd generation EIA tests detect antibody only.

Answer 380

>1,000 copies/mL.

Answer 381

Genotypic resistance testing and phenotypic resistance testing.

Answer 382

Portions of the RT and protease (PR) genes, which correspond to regions with mutations induced in response to therapy with NRTIs, NNRTIs, and PIs. Typically for ART-naïve individuals, sequencing of these regions is adequate to detect the important mutations.

Answer 383

Lymphomatoid papulosis, MGUS, multicentric Castleman disease.

Answer 384

Normal: 26 or fewer CAG repeats. Intermediate (also called "mutable normal alleles"): 27-35 CAG repeats. HD-causing alleles are subclassified into reduced penetrance (36-39 CAG repeats) and full penetrance (40 or more CAG repeats).

Answer 385

Acid sphingomyelinase (ASM) deficiency has been categorized in the past as either neuronopathic (Niemann-Pick disease type A [NPD-A]), with death in early childhood, or non-neuronopathic (Niemann-Pick disease type B [NPD-B]).

Answer 386

SMPD1 (sphingomyelin phosphodiesterase 1).

Answer 387

Normal gene product: Acid sphingomyelinase (sphingomyelin phosphodiesterase) is a lysosomal enzyme responsible for hydrolyzing sphingomyelin to ceramide and phosphorylcholine. Abnormal gene product: SMPD1 pathogenic variants result in an enzyme with altered activity that leads to decreased hydrolysis of the substrate and its subsequent accumulation in cells, particularly in the monocyte macrophage system.

Answer 388

All lysosomal storage diseases are inherited in an autosomal recessive manner, except for the X linked recessive Fabry, Hunter and Danon diseases.

Answer 389

t(11;17)(q23;q21) ZBTB16/RARA seen at 0.8% frequency. It is resistant to ATRA and has a worse prognosis.

Answer 390

Infants: t(4;11) AFF1-MLL. Children: t(12;21) ETV6-RUNX1. Adults: t(9;22) BCR-ABL1.

Answer 391

5% of Pfeiffer syndrome type 1 are due to mutations in FGFR1. 100% of Crouzon syndrome with acanthosis nigricans (AN) and Muenke syndrome are due to mutations in FGFR3.

Answer 392

Pfeiffer syndrome, Apert syndrome, Crouzon syndrome, Beare-Stevenson syndrome, FGFR2-related isolated coronal synostosis, Jackson-Weiss syndrome, Crouzon syndrome with acanthosis nigricans (AN), and Muenke syndrome.

Answer 393

In bacteria, "transfection" is generally understood to refer to transfer of a gene by a phage virus, and "transformation" implies nonviral means. In eukaryotes, because the term "transformation" was in previous use to indicate neoplastic growth, the term "transduction" refers to viral means of transferring DNA into cells while the term "transfection" refers to nonviral means of DNA transfer.

Answer 394

MEN1 and all MEN2 subtypes (MEN 2A, FMTC, and MEN 2B) are inherited in an autosomal dominant manner.

Answer 395

MEN1: 10%. MEN 2A:

Answer 396

Parathyroid tumors. Onset in 90% of individuals is between ages 20 and 25 years with hypercalcemia evident by age 50 years.

Answer 397

Familial isolated hyperparathyroidism (FIHP) is characterized by parathyroid adenoma or hyperplasia without other associated endocrinopathies. MEN1 germline pathogenic variants have been reported in between 20% and 57% of families with FIHP.

Answer 398

CT: cryptic plasmid, MOMP gene, unspecified "genomic" target in some FDA-approved assays, rRNA. NG: cytosine DNA methyltransferase, pilin inverting protein gene, Opa gene, repeat sequences, rRNA.

Answer 399

Hospital-acquired: type II. Community-acquired: type IV.

Answer 400

PBP2A AKA PBP2' (Penicillin binding protein 2A). This protein alters binding of beta-lactams.

Answer 401

The mecA gene codes for penicillin binding protein 2A (causes altered binding of beta-lactams and confers resistance to them), the mecI gene codes for a repressor protein (represses mecA transcription under conditions without beta-lactams in the environment), and the mecR1 gene for a β-lactam-sensing transmembrane signaling protein (mecR1 is a sensor-inducer of mecA - transcription of mecA is induced by beta-lactams when detected by the mecR1 protein product).

Answer 402

Mutations in UL97 viral protein kinase/phosphotransferase gene are associated with gancyclovir resistance. Mutations in UL54 viral DNA polymerase gene are associated with resistance to cidofovir and foscarnet.

Answer 403

RNases are more stable. DNases are easily denatured by heating or inhibited by sequestration of divalent cations necessary for nuclease activity. On the other hand, RNases are ubiquitous, highly stable, and active in virtually any aqueous environment, and they can regain their activity after denaturation.

Answer 404

Pure DNA has an A260 of 1.0 at 50 g/mL and an A260- to-A280 ratio of 1.8; pure RNA has an A260 of 1.0 at 40 g/mL and an A260-to-A280 ratio of 2.0. Lower ratios indicate protein contamination.

Answer 405

Influenza A infects humans, pigs, and birds. Influenza B only infects humans.

Answer 406

Influenza A cases the most severe illness, influenza B is not as severe as influenza A, and influenza C causes the least severe illness.

Answer 407

Influenza A changes by antigenic drift and antigenic shift. Influenza B changes by antigenic drift only.

Answer 408

The NA (neuraminidase) gene.

Answer 409

Approximately 95% of all individuals with the MEN 2B phenotype have a single nucleotide variant (SNV) in the tyrosine kinase domain of RET at codon 918 in exon 16, which substitutes a threonine for methionine.

Answer 410

Law enforcement agencies determining legal status of individuals. Laboratories licensed by an approved state (NY and WA). Forensics testing laboratories. In-vivo and externally attached patient‐dedicated monitoring. Testing for research purposes with no patient‐specific use. Self administration of tests at home. VA laboratories subject only to VA rules published and enforced. Department of Defense (DOD) laboratories subject only to rules published and enforced by the DOD.

Answer 411

For FDA approved or FDA cleared assays: Precision, accuracy, reference range, reportable range. For LDTs: Precision, accuracy, reference range, reportable range, analytic sensitivity, analytic specificity, other characteristics (such as interfering factors).

Answer 412

Laboratories can be CLIA certified and CAP accredited.

Answer 413

For laboratory proficiency testing, CLIA requires participation in a system that validates accuracy at least 2x/year.

Answer 414

The baseline phase (may be considered the lag phase, during which only a background signal is observed); the log-linear phase (the exponential growth phase); and then the reaction plateaus.

Answer 415

The Ct (cycle threshold) is defined as the number of cycles required for the fluorescent signal to cross the threshold (and enters the log-linear phase). It is the point at which specific fluorescence generated by amplification overcomes background “noise” level.

Answer 416

The slope of the log-linear phase reflects amplification efficiency, which can be determined by identifying the Ct of known standards and plotting a line of linear regression.

Answer 417

The slope of the log-linear phase reflects amplification efficiency, which can be determined by identifying the Ct of known standards and plotting a line of linear regression. Efficiency is determined with the equation E = 10^-1/slope (E = efficiency; slope is of the standard curve). Thus, the slope should be between 3 and 4, and 3.3 indicates efficiency close to or at 2.0.

Answer 418

In situ PCR can be performed directly on cellular material that is contained in solution or adhered to glass slides. Detection of the amplicons is usually accomplished indirectly with hybridization to specific probes or directly with the use of labeled nucleotides that have been incorporated into PCR. The practical effectiveness of in situ PCR is limited by amplicon diffusion and suboptimized target localization.

Answer 419

Activating mutations of the KRAS oncogene are seen in approximately 50% of invasive mucinous ovarian cancers, but they are relatively rare in high grade serous, clear cell, and endometrioid ovarian cancers. Missense mutations are commonly seen in codons 12, 13, and 61. In addition, most mucinous tumors of low malignant potential also harbor KRAS mutations, suggesting a possible common pathway of tumorigenesis.

Answer 420

They encode heme‐containing monooxygenase isoenzymes located on smooth endoplasmic reticulum membranes of hepatocytes and along mucosal surfaces of GI tract.

Answer 421

Statins bind to and enter liver cells via SLCO1B1 membrane transporters. Within the cell, statins inhibit HMG-CoA reductase, an enzyme that converts HMG-CoA to mevalonate (which goes on to form cholesterol and other metabolites). Because there is now decreased synthesis of cholesterol in the cells, there is up regulation of LDL receptors at the cell surface, which pulls LDL from the blood into the cell, decreasing blood concentration of LDL.

Answer 422

*5, which is c.521T>C V174A.

Answer 423

*1/*1 = 74%. *1/*5 = 24%. *5/*5 = 2%.

Answer 424

*1/*1 - if have been on 80 mg for >1 yr without side effects, ok to continue, otherwise start new patients at 40 mg. *1/*5 - 20 mg, and monitor CK levels. *5/*5 - use an alternative statin.

Answer 425

>80% of individual variability of response to clopidogrel (Plavix) is attributed to genetic effects (CYP2C19 genotype), while 35% of individual variability to warfarin (Coumadin) is attributed to genetic effects (CYP2C9 and VKORC1 genotypes).

Answer 426

Caused by biallelic mutations in the BLM gene (most commonly homozygous; less frequently compound heterozygous). Described mutations include missense, nonsense, insertions/deletions, and splicing defects due to intron mutations.

Answer 427

BLM is a tumor suppressor gene and belongs to the family of RecQ DNA helicases. RecQ helicases are important for repair of DNA damage. The protein product BLM permits unwinding of DNA in order to resolve disruptive structures that have developed during replication.

Answer 428

Hematolymphoid malignancies (AML, ALL, non-Hodgkin lymphoma) predominate in the first 2 decades of life while carcinomas (varied sites) predominate after the first 2 decades of life.

Answer 429

Carney complex and Peutz-Jeghers syndrome.

Answer 430

Large cell calcifying Sertoli cell tumor.

Answer 431

HRAS mutation is seen in 80-90% of cases. The most common mutation is p.G12S.

Answer 432

Almost all reported cases are secondary to new mutation (no prior history in family members).

Answer 433

Skin papillomas, rhabdomyosarcoma, urothelial carcinoma, neuroblastoma, fibrosarcoma.

Answer 434

TPMT inactivates these drugs through methylation. If TPMT activity is decreased, thioguanine nucleotide metabolites accumulate, incorporate into DNA, and cause hematopoietic toxicity.

Answer 435

Normal activity (wild type) - 90%, intermediate activity (heterozygous) - 10%, and low/deficient activity (homozygous mutant) - 0.2%.

Answer 436

For thiopurine methyltransferase (TPMT) genotypes/phenotypes, a *3A allele means the patient has both *3B and *3C alleles.

Answer 437

The UGT1A gene locus is complex—it encodes multiple genes and pseudogenes, and alternatively spliced isoforms also exist. The UGT1A locus contains multiple alternative first coding exons, each of which has its own promoter site, enabling the transcription of nine unique UGT1A enzymes. One of these transcripts is UGT1A1, which encodes the bilirubin-UGT enzyme (Whereas many UGT enzymes overlap in the substrates they glucuronidate, UGT1A1 is the only enzyme that glucuronidates bilirubin.).

Answer 438

The *28 allele is the most common variant allele. It contains an extra thymine-adenine (TA) repeat within the TATA box promoter region (7 TA repeats compared to 6 in the wild-type allele). This extra (TA) repeat decreases the rate of transcription initiation of the UGT1A1 gene, leading to decreased enzyme activity and decreased glucuronidation of bilirubin to about 30% of wild-type levels.

Answer 439

UGT1A1*37 has 8 TA repeats at this site, and results in reduced promoter activity to levels lower than that of promoters with the UGT1A1*28 allele. In contrast, the allele UGT1A1*36 has only 5 repeats, and is associated with increased promoter activity of the gene and a reduced risk of neonatal hyperbilirubinemia, a common and typically benign condition. Both UGT1A1*36 and UGT1A1*37 occur almost exclusively in populations of African origin.

Answer 440

Irinotecan is a prodrug that is converted to the active metabolite SN-38, which inhibits topoisomerase I activity ultimately inhibiting DNA replication and triggering apoptosis. SN-38 is inactivated by glucuronidation by UGT1A1 to SN-38G. Since SN-38 is 100x-1000x more cytotoxic than irinotecan, patients with hypoactive UGT1A1 alleles are at risk of ADRs.

Answer 441

Germline mutations in the UGT1A1, DPYD, GSTP1, XPD, and MGMT genes can affect therapy for colon cancer.

Answer 442

PNAs are nucleic acid analogues that contain a base, but have a peptide bond, as is found in proteins, in their backbones rather than the weaker sugar-phosphate bond of normal nucleic acids.

Answer 443

PNAs have 2 important properties. First, b/c PNAs lack a charged phosphate group, they do not experience mutual repulsion with the phosphate groups of the nucleic acid sequence to which they have bound and therefore bind to a complementary strand with greater affinity compared to normal oligonucleotides. This allows PNA-based primers to out-compete partially matched, allele-specific primers at binding sites on normal DNA and prevent inappropriate primer binding. Second, PNAs are not recognized by DNA polymerase, so there will be no amplification of any DNA to which PNA primers are bound. PNA oligonucleotides, therefore, bind to and "clamp" the DNA to which it has hybridized from any further amplification. If one constructs PNA primers that are specific for the normal sequence, while using normal nucleotide primers for the abnormal sequence of interest, only the latter sequence will be amplified.

Answer 444

LNAs are nucleotides that have been modified by using a methylene unit to link the 2'-oxygen and the 4'-carbon atoms of a ribose molecule in RNA. Oligonucleotides made from LNAs bind more strongly than natural nucleotides because they are fixed into the ideal conformation for hybridization. Because the affinity is higher, allele-specific primers made from LNAs not only support PCR but can also be shorter and can detect mutations even if only 1 base pair is abnormal (i.e., SNPs).

Answer 445

PNAs are nucleic acid analogues that contain a base, but have a peptide bond, as is found in proteins, in their backbones; LNAs are modified nucleotides that are modified in the sugar moiety, not in the backbone, and do contain phosphate groups.

Answer 446

COLD-PCR (CO-amplification at Lower Denaturation temperature-PCR) is a modified PCR protocol that enriches variant alleles from a mixture of wild type and mutation-containing DNA. Regular PCR will amplify both the major (wildtype) and minor (mutant) alleles with the same efficiency, occluding the ability to easily detect the presence of low-level mutations. The ability to preferentially amplify and identify minority alleles and low-level somatic DNA mutations in the presence of excess wildtype alleles is useful for the detection of mutations.

Answer 447

In COLD-PCR, a number of cycles of regular PCR at the usual denaturing temperature are performed, after which additional cycles are performed at a lower denaturing temperature. Because mutant sequences are rare, most of them will be paired with WT sequences in heteroduplexes instead of being in homoduplexes with other mutant sequences, as would be the case if they were present in greater numbers. These heteroduplexes are not hydrogen bonded as strongly as duplexes formed between 2 WT strands. At the lower temperature, heteroduplexes containing the mutant DNA sequence tend to separate and are amenable to further PCR, while duplexes formed from 2 WT strands will remain hybridized and are refractory to PCR, resulting in preferential amplification of mutant sequences.

Answer 448

Tamoxifen is converted to its active metabolites 4-hydroxytamoxifen and endoxifen primarily by CYP2D6.

Answer 449

CYP2D6. The gene also has a significant number of common CNV (copy number variant) alleles representing both gene deletions and duplications.

Answer 450

The *3 allele (splicing defect). However, the CYP3A5*3 allele is often linked to (in cis with) the CYP3A4*1A allele (normal/wild type). But CYP3A4 and CYP3A5 share overlapping substrates so even if 3A5 is defective, the 3A4 can compensate partially.

Answer 451

20% of African Americans and 3% of Caucasians.

Answer 452

HLA‐B*58:01 - allopurinol. HLA‐B*57:01 - abacavir. HLA‐B*15:02 - tegretol.

Answer 453

Caucasians

Answer 454

Allopurinol is contraindicated, so an alternative must be used. Febuxostat is an FDA-approved non-purine xanthine inhibitor.

Answer 455

Caucasians 8%, African American 2-3%, Hispanics 2%, and Asians 1%.

Answer 456

PPV ~50%, NPV >99%.

Answer 457

Germline mutations in TERT, TERC, DKC1, or TINF2 genes are seen in 50% of cases. All of these genes function in maintaining telomeres.

Answer 458

X-linked recessive when secondary to DKC1 mutations. Autosomal dominant when secondary to TERC or TINF2 mutations. Autosomal dominant or recessive when secondary to TERT mutations. Autosomal recessive when secondary to CTC1, WRAP53, NHP2, or NOP10 mutations.

Answer 459

G-positive bands.

Answer 460

A precore mutant is a variety of hepatitis B virus that does not produce hepatitis B virus e antigen (HBeAg). The G1764A and A1762T mutations are usually responsible for the decreased preCore (PC) mRNA synthesis. The G1896A mutation is the most prevalent and produces a translation stop codon at amino acid position 28 in the HBeAg sequence, with inhibition of HBeAg synthesis. Precore and core mutant HBV is associated with fulminant hepatitis and increased risk of HCC.

Answer 461

The RET proto-oncogene on chromosome 10q11.2 encodes a cell membrane receptor tyrosine kinase. In some papillary thyroid carcinomas, the tyrosine kinase domain of RET is fused with a heterologous gene that provides the promoter and the 5'-coding region. The product of this rearrangement is a chimeric oncogene named RET/PTC. Since the original report, at least 11 types of RET/PTC variants have been isolated.

Answer 462

Most of these rearrangements are between RET on chromosome 10 and genes located on different chromosomes. By contrast, RET/PTC1 and RET/PTC3 are intrachromosomal paracentric inversions because the genes involved H4 and RFG (also designated ELE1/ARA70/NCOA4) are also all located on chromosome 10. RET/PTC1 and RET/PTC3 account for the vast majority of the variants, while the others are very rare and have little clinical significance.

Answer 463

Target DNA in unknown = [Target DNA in standard] x 2^(CT of standard - CT of unknown). For example, if there were 1,000 copies in the standard, the CT of the standard was 30, and the CT of the patient sample was 25, the patient sample would contain 1,000 x 2^(30-25) = 32,000 copies.

Answer 464

1. The simplest method is the comparative CT method or the delta-delta CT method, which compares the CTs of the standard and the patient sample. The following equation can be used: Target DNA in unknown = [Target DNA in standard] x 2^(CT of standard - CT of unknown). The comparative CT method is an approximation that assumes there is 100% efficiency of replication with each cycle. 2. Using a series of dilutions of a known standard. For example, a patient sample may be compared to several controls with a known copy number of spiked in nucleic acid. The patient value can be plotted on a graph against the known CTs of the controls. 3. The Pfaffl method, which is similar to the delta-delta CT method but takes into account the fact that the efficiency of replication is

Answer 465

The Ras superfamily is a protein superfamily of small GTPases. There are more than a hundred proteins in the Ras superfamily. Based on structure, sequence and function, the Ras superfamily is divided into five main families (Ras, Rho, Ran, Rab and Arf GTPases). In general, the Ras family is responsible for cell proliferation, Rho for cell morphology, Ran for nuclear transport, and Rab and Arf for vesicle transport. The Ras family itself is further divided into 6 subfamilies: Ras, Ral, Rit, Rap, Rheb, Rad and Rit. Three Ras subfamily genes (HRas, KRas, and NRas) are the most common oncogenes in human cancer.

Answer 466

Three Ras subfamily genes (out of several subfamily members) (HRas, KRas, and NRas) are the most common oncogenes in human cancer. The three human ras genes encode extremely similar proteins made up of chains of 188 to 189 amino acids, their gene symbols are HRAS, NRAS and KRAS, which produces the K-Ras4A and K-Ras4B isoforms from alternative splicing). The three human RAS genes encode four highly related RAS proteins (82-90% sequence identity), with alternative gene splicing accounting for the expression of the highly related K-RAS4A and K-RAS4B proteins (90% identity).

Answer 467

UL23, which encodes a viral thymidine kinase. Nucleoside analogues, such as acyclovir, are selectively phosphorylated to a monophosphate derivative in infected cells by the virus-encoded thymidine kinase (TK). The affinity of ACV for HSV-TK is ~200 times greater than for human TK. Viral mutations conferring resistance to ACV have been found most in the UL23 gene, which encodes the activating/phosphorylating TK enzyme.

Answer 468

Responsible for resistance phenomena are mutations in the CMV phosphotransferase gene (UL97) and the polymerase gene (UL54). Most frequently, mutations in the UL97 gene are associated with resistance to gancyclovir. Resistance against gancyclovir, foscarnet, and cidofovir is associated to mutations in the UL54 gene. The manifestation of multidrug resistance is mostly associated with combined UL97/UL54 mutations. Normally, mutations in the UL97 gene occur initially followed by UL54 mutation after therapy switch. The appearance of UL54 mutation alone without any detection of UL97 mutation is rare.

Answer 469

Sequences in the 5' non-translated region. The 5' NTR is the most highly conserved region for all members of the genus and is involved in viral protein translation.

Answer 470

Mononucleotide repeats.

Answer 471

Germline deletions at the 3′-end of the EpCAM gene (formerly called TACSTD1), located immediately upstream of MSH2, are the cause of heritable somatic epimutation. The germline deletions of the 3′ region of EPCAM cause transcriptional read-through which results in silencing of MSH2 by hypermethylation.

Answer 472

KIT mutations are present in exon 11 (juxtamembrane domain) > exon 9 (extracellular domain) > exon 13 (TK1 domain/ATP-binding) = exon 17 (TK2 domain/activation loop). PDGFRA mutations are present in exon 18 (TK2 domain /activation loop) > exon 12 (juxtamembrane domain) > exon 14 (TK1/ATP-binding) domain.

Answer 473

KIT mutations are present in exon 11 (juxtamembrane domain) - 67%, exon 9 (extracellular domain) - 10%, exon 13 (TK1 domain/ATP-binding) - 1%, exon 17 (TK2 domain/activation loop) - 1%. PDGFRA mutations are present in exon 18 (TK2 domain/activation loop) - 5%, exon 12 (juxtamembrane domain) - 2%, exon 14 (TK1/ATP-binding) domain - 1%.

Answer 474

The KIT exon 9 mutated tumors respond better to higher doses of imatinib than needed for exon 11 mutated tumors.

Answer 475

Exons 13 and 14 (TK1 domain/ATP-binding) and exons 17 and 18 (TK2 domain/activation loop). They are usually single nucleotide substitutions and occur on the same allele as the original mutation.

Answer 476

SDH-deficient GISTs locate exclusively in the stomach, showing predilection for children and young adults with female preponderance. They have a distinct morphology - epithelioid and multinodular/plexiform. Nearly all are KIT and DOG-1 positive. Accepted GIST risk factors do not apply. The tumor generally pursues an indolent course despite lymph node and distant metastases and exhibits primary resistance to imatinib therapy in most cases. Loss of succinate dehydrogenase subunit B expression and overexpression of insulin-like growth factor 1 receptor (IGF1R) are common features of SDH-deficient GISTs.

Answer 477

KIT mutations in melanoma are more common in acral lentiginous (11-38%), mucosal (6-19%), and sun-damaged skin (17%). The mutations are mostly in exon 11, with 34% being the L576P mutation. This mutations confers sensitivity to tyrosine kinase inhibitors.

Answer 478

IDH1/2 is mutated in 80% of grade II‐III astrocytomas and oligodendrogliomas, and >90% of secondary GBMs. The wild type enzyme converts isocitrate to alpha-ketoglutarate while the mutant converts it to D‐2-hydroxyglutarate.

Answer 479

The condition of young-onset colonic polyposis and brain tumors originally termed Turcot's syndrome has been reclassified into 2 conditions depending on the underlying genetic condition. Brain tumors, typically medulloblastomas, in association with FAP-related colonic polyposis, is now termed Crail's syndrome. Lynch syndrome (HNPCC) in association with glioblastomas are properly classified as Turcot's syndrome.

Answer 480

A condition caused by biallelic pathogenic germline variants in MUTYH characterized by a greatly increased lifetime risk of colorectal cancer (43% to almost 100% in the absence of timely surveillance). Although typically associated with ten to a few hundred colonic adenomatous polyps that are evident at a mean age of about 50 years, colonic cancer develops in some individuals in the absence of polyposis. The colonic phenotype is similar to AFAP but the terminology "FAP/AFAP caused by MYH mutations" is not correct. Extracolonic manifestations include duodenal adenomas/carcinomas, ovarian CA, bladder CA, skin CA.

Answer 481

A molecular hallmark of carcinomas caused by MUTYH deficiency is the presence of a specific somatic KRAS pathogenic variant (c.34G>T in codon 12) which is found in 64% of MAP colorectal cancers. The majority of CRCs in persons with MAP are microsatellite stable. The normal gene product of the MUTYH gene, the MUTYH protein, is an A/G-specific adenine DNA glycosylase that plays a major role in DNA damage repair. Two common pathogenic allelic variants, c.536A>G (p.Tyr179Cys) in exon 7 and c.1187G>A (p.Gly396Asp) in exon 13, are missense variants carried by approximately 1%-2% of the general population; they account for at least 90% of all MUTYH pathogenic variants in northern European populations, and one or both of these founder pathogenic variants are identified in up to 70% of persons with MAP.

Answer 482

MMRCS is a rare childhood cancer predisposition syndrome caused by homozygous or compound heterozygous mutation in the mismatch repair MLH1, MSH2, MSH6, or PMS2. (Heterozygous mutations in the MMR genes result in Lynch syndrome.) Patients have childhood hematologic malignancies (mean age 5.5 yrs), CNS tumors (mean age 8 yrs), and Lynch syndrome-associated cancers (mean age 16 yrs). Almost all have NF1-like skin findings.

Answer 483

IHC would be uninterpretable, since both tumor and normal may lack protein expression. In MMRCS, PCR of brain tumors may not show MSI; MSI more likely to be seen in the Lynch syndrome‐associated tumors. Most report that PCR of normal tissue does not show MSI.

Answer 484

Menkes disease: ATP7A (Copper-transporting ATPase 1). Wilson disease: ATP7B (Copper-transporting ATPase 2).

Answer 485

The diagnosis is suspected in otherwise healthy males with abnormal sperm counts ranging from azoospermia to mild oligozoospermia and/or abnormal sperm morphology/motility for whom other causes of infertility have been eliminated. Chromosomal microarray or routine cytogenetic testing reveals chromosome abnormalities in 5%-10% of these men. Molecular testing reveals microdeletions of the long arm of the Y chromosome in another 5%-13% of these males. Pregnancies may be achieved by in vitro fertilization using ICSI (intracytoplasmic sperm injection), but retrieval of sperm has been successful mainly for most males with deletions of AZFc, and rarely for males with deletions of AZFb or AZFa.

Answer 486

Aneuploidy: Change in chromosome number that is not exact multiple of haploid set. Polyploidy: Chromosome number is a multiple of the haploid number (23).

Answer 487

Triploidy (usually 69,XXY or 69,XXX or 69,XYY) is seen in 15‐20% of chromosomally abnormal spontaneous abortions. 85% are diandric (2 paternal/1 maternal set of chromosomes), while 15% are digynic (2 maternal/1 paternal set of chromosomes).

Answer 488

PWS is caused by an absence of expression of imprinted genes in the paternally derived PWS/AS region (i.e., 15q11.2-q13) of chromosome 15 by one of several genetic mechanisms (paternal deletion, maternal uniparental disomy 15 and rarely an imprinting defect). The risk to the sibs of an affected child of having PWS depends on the genetic mechanism that resulted in the absence of expression of the paternally contributed 15q11.2-q13 region. The risk to sibs is typically less than 1% if the affected child has a deletion or uniparental disomy, up to 50% if the affected child has an imprinting defect, and up to 25% if a parental chromosome translocation is present. AS is caused by disruption of maternally imprinted UBE3A located within the 15q11.2-q13 AS/PWS region. The risk to sibs of a proband depends on the genetic mechanism leading to the loss of UBE3A function: typically less than 1% risk for probands with a deletion or UPD, and as high as 50% for probands with an ID or a pathogenic variant of UBE3A.

Answer 489

Approximately 70% of individuals with PWS have a deletion on one chromosome 15 involving bands 15q11.2-q13, which can be detected using high-resolution chromosome studies and FISH testing or chromosomal microarray. Approximately 1% of affected individuals have a detectable chromosome rearrangement (i.e., translocation or inversion) resulting in a deletion of bands 15q11.2-q13. Fewer than 1% of individuals have a “balanced” chromosome rearrangement breaking within 15q11.2-q13 and detectable by chromosome analysis and FISH.

Answer 490

The diagnosis of PWS is established in a proband with DNA methylation analysis demonstrating abnormal parent-specific imprinting within the Prader-Willi critical region (PWCR) on chromosome 15 in which the region demonstrates maternal-only imprinting (i.e., the absence of paternal-only expressed genes). Three main molecular mechanisms that result in PWS include paternal deletion, maternal uniparental disomy (UPD) 15 and imprinting defect (ID). DNA methylation analysis is the only technique that will diagnose PWS caused by all three genetic mechanisms as well as differentiate PWS from Angelman syndrome (AS) in deletion cases.

Answer 491

The molecular classes are assigned based on genetic mechanism: Molecular class Ia; genetic mechanism is interstitial 5- to 6-Mb 15q11.2-q13 deletion; proportion of PWS is 65-75%. Ib; unbalanced chromosome rearrangement;

Answer 492

Trisomy 13: 70% maternal error, MI more common. Trisomy 18: 90% maternal error, MII more common. Trisomy 21: 90% maternal error, MI more common.

Answer 493

Alternate (gametes are normal or balanced and zygotes are viable). Adjacent-1 (gametes are unbalanced and zygotes may be viable). Adjacent-2 (gametes are unbalanced and zygotes are presumably nonviable).

Answer 494

No. These are chromosomal microdeletion syndromes, caused by a chromosomal deletion smaller than 5 million base pairs (5 Mb), too small to be detected by conventional cytogenetic methods or high resolution karyotyping (2-5 Mb). Detection is done by FISH or other methods.

Answer 495

A clone is defined as a cell population derived from a single progenitor. A clone exists if two or more cells contain the same structural abnormality or supernumerary marker chromosome, OR there are at least three cells missing the same chromosome.

Answer 496

Homogeneously staining region (HSR) - Integrated region of amplification. Double minute chromosome (DM) - Small, paired, acentric extra-chromosomal body. Episomes - Submicroscopic extra-chromosomal body.

Answer 497

The two DNAs are mixed and hybridized to normal metaphase cells or normal DNA on a spotted array (aCGH). CGH may also be performed on spotted RNA.

Answer 498

A DNA segment (>1kb) with a variable copy number compared to normal reference genome. (CNVs occur on every chromosome and cover ~12% of genome.)

Answer 499

Karyotyping - ~5‐10 Mb of DNA. FISH - ~50‐200kb of DNA. Multicolor FISH - ~5‐10Mb of DNA. Metaphase CGH - ~5‐10Mb of DNA. BAC platform aCGH - ~200kb of DNA. Oligonucleotide aCGH - ~50kb of DNA.

Answer 500

The gradient of conserved sequences for HCV is: 5'UTR > core > NS5B (polymerase). The most conserved areas have the best chance of amplification and less chance of under-quantification so the 5'UTR is used for viral load. The less conserved areas give better genotype resolution so core or NS5B is used for genotyping. Using the 5'UTR for genotyping may not distinguish GT1a from GT1b, and GT1 vs some GT6.

Answer 501

The HCV protease (NS3/4 part of the genome) (protease inhibitors). The HCV polymerase (NS5B part of the genome) (nucleoside/nucleotide & nonnucleoside inhibitors).

Answer 502

Shorter therapy: genotypes 2 and 3 (24 weeks). Longer therapy: genotypes 1, 4, 5, and 6 (48 weeks).

Answer 503

The 2 subtypes have different codon usage. GT1b requires 2 nucleotide changes in the arginine codon for the mutation, while GT1a uses a different codon requiring only 1 change.

Answer 504

The IL28B SNP status. For the rs12979860 SNP, genotype CC is favorable while CT and TT are unfavorable. For the rs8099917 SNP, TT is favorable while TG and GG are unfavorable. The favorable genotypes have a higher chance of spontaneous clearance of the HCV infection, and higher sustained virology response to treatment. The unfavorable genotypes have a higher risk of HCV chronicity, and increased risk of treatment failure. These effects (positive and negative) are most pronounced in HCV genotype 1 .

Answer 505

E1 and E2. This is important to know because if you want an assay to detect integrated forms as well you can't target this region.

Answer 506

For detection, the 5'UTR. For typing, the VP1-3 regions (sequence based). However, EV is an RNA virus and the genome is still variable, so there are limited target sites and you still risk non-detection.

Answer 507

The insertion sequence IS481 has different copy numbers among species: B. pertussis 50‐100+copies/cell, B. holmesii 8‐10 copies/cell, and some strains of B. bronchiseptica 1 copy/cell, and some labs use this target for pertussis detection. The insertion sequence IS1001 is present in B. parapertussis and B. holmesii so can be used for parapertussis detection. The targets that are specific for B. pertussis include: Promoter region (PTp1 and PTp2); DNA region upstream of the porin gene; Repeated insertion sequences (IS); Pertussis toxin promoter (ptxA-Pr) (but the pertussis toxin operon is present in B. pertussis, B. parapertussis, and B. bronchiseptica); ACT gene; BP3385, BP283, and BP485.

Answer 508

tcdA - enterotoxin. tcdB - cytotoxin. tcdC - negative regulator. tcdD - positive regulator. tcdE - holin-like protein.

Answer 509

The haplotype is a collection of ~10 polymorphisms in exon 13 of FV, and is present in ~10% of the population. Some studies suggest that the HR2 haplotype alone is an independent thrombotic risk factor with mildly increased risk. The haplotype has never been observed on the same chromosome as FVL. Compound heterozygosity for the factor V HR2 haplotype and the factor V Leiden mutation is associated with an increased risk for venous thrombosis as compared with heterozygosity for factor V Leiden alone.

Answer 510

The most common mutation is 677C>T. This variant encodes a thermolabile enzyme that is less active at higher temperatures. 677C>T homozygous individuals tend to have mildly elevated homocysteine levels and low serum folate levels. Another MTHFR mutation, 1298A>C, does not cause increased homocysteine levels in heterozygous or homozygous individuals, but combined heterozygosity of 1298A>C and 677C>T results in an outcome similar to 677C>T homozygous individuals.

Answer 511

Renal failure, hypothyroidism, leukemia, psoriasis, drug therapy, and MTHFR mutations. Also, homocysteine may be spuriously elevated if the patient is non‐fasting, or can be seen with ex‐vivo release from RBCs.

Answer 512

Transcription mediated amplification (TMA) or self-sustained sequence replication (3SR), nucleic acid sequence-based amplification (NASBA), signal mediated amplification of RNA technology (SMART), strand displacement amplification (SDA), rolling circle amplification (RCA), loop-mediated isothermal amplification of DNA (LAMP), isothermal multiple displacement amplification (IMDA), helicase-dependent amplification (HDA), single primer isothermal amplification (SPIA), and circular helicase-dependent amplification (cHDA).

Answer 513

Severe - 50%. Moderate - 10%. Mild - 40%.

Answer 514

Point mutations are most common at 46%, but the single most common mutation is intron 22 inversion, seen in 45%. Large deletions (>50 bp) are seen in 5%. Intron 1 inversion is seen in 2%. Small deletions (

Answer 515

Only severe hemophilia A will have intron 22 or intron 1 inversions (47% of them will have one) so start with inversion testing first for severe disease. If negative, next do full gene sequencing (will pick up another 46%), and if negative go on and do del/dup testing (5%). If moderate or mild disease, start with full gene sequencing (95% will be positive), and if negative go on and do del/dup testing.

Answer 516

Fragile X Syndrome ‐ (CGG)n in 5’UTR. Myotonic Dystrophy ‐ (CTG)n in 3’UTR. Huntington Disease ‐ (CAG)n in coding region. Kennedy's Disease ‐ (CAG)n in coding region. Spinocerebellar Ataxias ‐ (CAG)n in coding region. Machado‐Joseph Disease - (CAG)n in coding region. Friedrich Ataxia ‐ (GAA)n in intron 1.

Answer 517

Biallelic pathogenic variants in FXN. The most common type of variant, which is observed on both alleles in more than 90% of individuals with FRDA, is an abnormally expanded GAA repeat in intron 1 of FXN. The remaining individuals with FRDA are compound heterozygotes for an abnormally expanded GAA repeat in the disease-causing range in one allele and another intragenic pathogenic variant in the other allele.

Answer 518

The normal gene product is the protein huntingtin, which is a housekeeping gene that is widely expressed in neuronal and non-neuronal tissues. HD mutation leads to a toxic gain of function: overactivity of normal or novel function; novel interaction with other proteins; multimerization of the protein; large insoluble aggregates leading to cell death.

Answer 519

DM1 is caused by a CTG trinucleotide expansion in the 3'-UTR of the gene DMPK. DM2 is caused by expansion of the CCTG repeat in intron 1 of the gene CNBP.

Answer 520

Each human cell contains 50-5000 mitochondria. 99.9% of mtDNA is maternal. One oocyte has ~100,000 mtDNA molecules. Sperm do have ~100 mitochondria, mostly in the tail, but most of the sperm the tail does not enter the egg and eventually sperm mitochondria are deleted or diluted out. Each mitochondrion contains 2‐10 mtDNA molecules. mtDNA makes up ~1% of total cellular DNA. Circular 16,569 bp genome, 37 genes. ~93% coding DNA. Introns absent. Continuous transcription of multiple genes. No recombination. High mutation rate (ten‐fold increase as compared to nuclear DNA). 13 protein subunits of the respiratory chain (of a total of ~67). 16S and 12S mt rRNAs. 22 mt tRNAs. The genetic code differs slightly for stop codons and one amino acid.

Answer 521

Kearns-Sayre syndrome (KSS), Pearson syndrome, and progressive external ophthalmoplegia (PEO). Also, rarely, Leigh syndrome can be a manifestation of a mtDNA deletion.

Answer 522

As a generalization, individuals with moderate levels (~70%-90%) of the m.8993T>G pathogenic variant present with the NARP phenotype, while those with mutant loads above 90% have maternally inherited Leigh syndrome.

Answer 523

Nonsyndromic mitochondrial hearing loss and deafness is characterized by moderate-to-profound hearing loss and a pathogenic variant in either MT-RNR1 or MT-TS1. Pathogenic variants in MT-RNR1 can be associated with predisposition to aminoglycoside ototoxicity and/or late-onset sensorineural hearing loss. Pathogenic variants in MT-TS1 are usually associated with childhood onset of sensorineural hearing loss.

Answer 524

The ppromoter region of the SNRPN gene contains CpG islands which are heavily methylated in the maternally‐derived allele and unmethylated in the paternally‐derived allele. In PW = only methylated (maternal) allele present. In AS = only unmethylated (paternal) allele present. Method: Genomic DNA is treated with sodium bisulfite, converting cytosine to uracil except where cytosine is methylated. Then PCR and melting analysis are performed.

Answer 525

Mutations in SMN1 are known to cause SMA; increases in SMN2 copy number often modify the phenotype. SMN1 (survival motor neuron 1) is the primary gene in which mutation causes SMA (Mutation in SMN2 alone does not cause SMA). 95%-98% of individuals with SMA are homozygous for a deletion or gene conversion of SMN1 to SMN2 and 2%-5% are compound heterozygotes for an SMN1 deletion or conversion mutation and an SMN1 intragenic mutation. SMN1 deletion or conversion mutation is typically detected by demonstrating the absence of exon 7, since it can be easily differentiated from exon 7 of SMN2 (SMN1 and SMN2 DNA have high homology with only 8 bp differences intronic and exonic combined; exon 7 has one bp difference. In SMN2 most of the pre-mRNA is spliced to SMN without exon 7, which is unstable and rapidly degraded). Note that SMN1 to SMN2 conversion mutations cannot be differentiated from SMN1 deletions by standard deletion testing, as both result in the absence of SMN1 exon 7. SMA carrier testing, a gene dosage assay, allows determination of the number of SMN1 copies by measuring the number of exon 7-containing SMN1 copies. This test can be difficult to interpret because instead of having the normal two copies of SMN1, one on each chromosome, some carriers have the two SMN1 copies on one chromosome (in cis configuration) and some carriers have an SMN1 intragenic mutation that is not detected by the dosage testing. Furthermore, 2% of individuals with SMA have one SMN1 allele resulting from a de novo mutation, meaning that only one parent is a carrier of an SMN1 mutation. SMA arises because SMN2 cannot fully compensate for the lack of expression of mutated SMN1. However, when the SMN2 copy number is increased, the small amount of full-length transcript generated by SMN2 is often able to produce a milder type II or type III phenotype.

Answer 526

The poly T tract, a string of thymidine bases located in intron 8 of the CFTR gene, can be associated with CFTR-related disorders depending on its size. The three common variants of the poly T tract are 5T, 7T, and 9T. Both 7T and 9T are considered polymorphic variants and 5T is considered a variably penetrant mutation. The 5T variant decreases the efficiency of intron 8 splicing - with 5T/5T ~90% of transcripts miss exon 9. Poly T testing is appropriate as a reflex test when an R117H mutation is detected or an adult male is being evaluated for CAVD (The severity of lung disease in individuals with one or two R117H mutations depends on the presence of a variation in the poly T tract of intron 8. Individuals with a CFTR disease-causing mutation plus the 5T variant in cis configuration with the R117H mutation usually develop the lung disease of CF, but those individuals with R117H and the 7T variant or the 9T variant have a highly variable phenotype that can range from no symptoms to mild lung disease.). The TG tract lies just 5' of the poly T tract. It consists of a short string of TG repeats that commonly number 11, 12, or 13. A longer TG tract (12 or 13) in conjunction with a shorter poly T tract (5T) has the strongest adverse effect on proper intron 8 splicing. Males with CAVD or suspected CAVD, individuals with non-classic CF, or adult carriers of 5T who wish to further refine their reproductive risks are all appropriate for 5T/TG tract typing.

Answer 527

The poly T tract, a string of thymidine bases located in intron 8 of the CFTR gene, can be associated with CFTR-related disorders depending on its size. The three common variants of the poly T tract are 5T, 7T, and 9T. Both 7T and 9T are considered polymorphic variants and 5T is considered a variably penetrant mutation. The 5T variant is thought to decrease the efficiency of intron 8 splicing. Poly T testing is appropriate as a reflex test when an R117H mutation is detected or an adult male is being evaluated for CAVD (The severity of lung disease in individuals with one or two R117H mutations depends on the presence of a variation in the poly T tract of intron 8. Individuals with a CFTR disease-causing mutation plus the 5T variant in cis configuration with the R117H mutation usually develop the lung disease of CF, but those individuals with R117H and the 7T variant or the 9T variant have a highly variable phenotype that can range from no symptoms to mild lung disease.). The TG tract lies just 5' of the poly T tract. It consists of a short string of TG repeats that commonly number 11, 12, or 13. A longer TG tract (12 or 13) in conjunction with a shorter poly T tract (5T) has the strongest adverse effect on proper intron 8 splicing. Males with CAVD or suspected CAVD, individuals with non-classic CF, or adult carriers of 5T who wish to further refine their reproductive risks are all appropriate for 5T/TG tract typing.

Answer 528

9T. Hence, if you have deltaF508/‐ with 5T/9T, you can assume the deltaF508 and 9T are on the same allele, and this patient has CBAVD.

Answer 529

5T/5T - CBAVD. R117H/5T in cis - CF mutation. R117H/5T in trans - CBAVD. DeltaF508/‐ with 5T/9T - CBAVD.

Answer 530

Apert syndrome, Muenke syndrome, and achondroplasia.

Answer 531

Apert syndrome, Muenke syndrome, and achondroplasia.

Answer 532

A specific mutation in FGFR3 - 749C>G (Pro250Arg) defines Muenke syndrome, and this mutation creates a restriction site, so relatively straight forward to test.

Answer 533

Other than Muenke syndrome, which has a mutation in FGFR3, and 5% of Pfeiffer syndrome type 1, which has a mutation in FGFR1, the craniosynostosis syndromes are caused by mutations in FGFR2. Do direct DNA sequencing of exons 7 and 9.

Answer 534

The Gly380Arg mutation in FGFR3 is present in 99% of cases.

Answer 535

Duchenne muscular dystrophy.

Answer 536

About one-third.

Answer 537

Whether the deletion preserves the translational reading frame or not. Most DMD has a disrupted reading frame, while BMD has a preserved reading frame. The reading frame hypothesis explains ~90% of DMD/BMD differences.

Answer 538

Hereditary hemochromatosis: HFE and HAMP. Familial exudative vitreoretinopathy: FZD‐4 and Factor V. Retinitis pigmentosa: ROM1 and peripherin/RDS. Bardet‐Biedl syndrome: BBS1, 2, 4, 6. Hirschsprung disease: RET and EDNRB, others. Insulin resistance: PPARG and PPP1R3A. Early onset glaucoma: MYOC and CYP1B1. Usher syndrome: USH1B and USH3. Epidermolysis bullosa: COL17A1 and LAMB3. DPKD: PKD1 and PKD2. Waardenburg syndrome and ocular albinism: MITF and TYR. HPE (holoprosencephaly): TGIF and SHH.

Answer 539

Hereditary hemochromatosis: HFE and HAMP. Familial exudative vitreoretinopathy: FZD‐4 and Factor V. Retinitis pigmentosa: ROM1 and peripherin/RDS. Bardet‐Biedl syndrome: BBS1, 2, 4, 6. Hirschsprung disease: RET and EDNRB, others. Insulin resistance: PPARG and PPP1R3A. Early onset glaucoma: MYOC and CYP1B1. Usher syndrome: USH1B and USH3. Epidermolysis bullosa: COL17A1 and LAMB3. DPKD: PKD1 and PKD2. Waardenburg syndrome and ocular albinism: MITF and TYR. HPE:TGIF and SHH.

Answer 540

Triallelic inheritance is a special case of digenic inheritance that requires homozygous mutations at one locus and heterozygous mutations at a second locus to express a phenotype.

Answer 541

Mutations in GJB2 (connexin 26 protein) account for 10% of all congenital hearing loss and ~70% of all non‐syndromic, recessive hearing loss. Carrier frequencies are 2-3% in Caucasians, 4-5% in Ashkenazi Jewish, and 1% in Japanese. The most common mutation is 35delG.

Molecular/Cytogenetics Flashcards

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