Learning Objectives Week 1 Flashcards

Question

Human Genome Organization (Repetitive DNAs - type, location, frequency) -Tandem Repeats

Answer 1

Tandem Repeats (satellite DNAs) - Not clustered locally, some are in different parts of genome (used as basis for cytogenetic binding) - Can be found in heterochromatic regions on long arms of Chr 1, 9, 16 and Y ( these are hotspots for human-specific evolutionary changes) - "alpha-satellite" repeats (171 bp repeat unit) found near centromeres of all human chromosomes (suggested role in chromosome segregation)

Answer 2

-Alu family (ex. of Short Interspersed Repetitive Elements --> 300 bp related members and 500,000 copies in genome) -L1 family (ex. of Long Interspersed Repetitive Elements --> 6kb releated members and 100,000 copies in genome *Alu's and L1's can be medically relevant because retrotransposition of the copy in the middle of another gene may inactivate that gene, or activate them. -repeats may facilitate bad recombination events between different copies of dispersed repeats leading to disease --> NAHR, non-allelic homologus recombination NAHR is a form of homologous recombination that occurs between 2 chunks of DNA that have high sequence similarity, but are not alleles. When NAHR occurs between these DNA chunks, can get more deletions or duplication.

Answer 3

25,000-30,000 genes comprised of protein-encoding genes, RNA-encoding genes, and pseudogenes (non-functional, homologous copies of existing genes; can be "intron-containing or intronless".

Answer 4

Gene Families Genes with high sequence similarity (85-90%) that have similar but distinct functions (some clustered, some dispersed) ( they duplicate, so have copies that may be better, old ones there to still carry the load * look at(Gene Duplication Evolutionary Mechanism)card )

Answer 5

Gene families arise through gene duplication. This is a major mechanism underlying evolutionary change because when a gene duplicates, it frees up one copy to vary, while the other copy carries out the critical function. Allows for innovation.

Answer 6

You can have multiple copies of a gene which can give you extra capabilities, but at the same time put you at risk for disease because you have all these increases in gene copy number (DUF1220).

Answer 7

“Missing heritability” for complex diseases: Many large-scale studies implicate loci (e.g. SNPs) that account for only a small fraction of the expected genetic contribution Many regions of the genomes are unexamined by available “genome-wide” screening technologies: is this where the “missing heritability” lies? Missing Heritabilty problem, explains that simple mendelian genetics doesnt explain everything, genetic issues in heterochromatin with CNVS and we cant analyze them.

Answer 8

Better sequencing needed, because we need more insight into these CNV regions ( because they are so long and full of repeats that with normal sequencing, they are full of giberish) Next gen sequencing, uses short read sequences and the complex highly duplicated regions go unexamined ( which is bad because they can be disease-linked). (ex. 1q21)

Answer 9

• Broadest sense: all changes in the genome not due to single base-pair substitutions: • Copy number variations (CNVs) – Primary type of structural variation – CNV loci may cover 12% of genome – Implicated in increasingly larger number of diseases – Some CNV regions involved in rapid & recent evolutionary change - Such regions are often - enriched for human specific gene duplications - enriched for genome sequence gaps - enriched for recurrent human diseases - 1q21.1; 9p13.3-9q21.12, 5q13.3 - Link between evolutionarily adaptive copy number increases and increase in human disease (e.g. 1q21) - Role of genome architecture

Answer 10

In meiosis, you get recombination during which homologous cross over occurs ( again remember this is not between sister chromatids, which is why you end up with 4 diff haploid products). In particular meiotic prophase 1 is critical during meiosis. Maternal and paternal homologous of each chromosome become paried or synapsed along their entire lengths, forming structures known as "bivalents". This process requires the formation of a proteinaceous structure called the "synaptonemal complex", which promotes inter-homolog interactions. Reciprocal recombination events occuring at this stage generate physical links between homologous. These crossovers are known as "chiasmata". On average 2-3 crossovers occur on each chromosome resulting in genetic re-assortment. In short, random shuffling of genetic material due to crossover events, resulting in a vast increase in genetic variability.

Answer 11

Mitosis A. one round of chromosome segregation, resulting in two 2n daughter cells identical in chromosomal content to the parental cell B. DNA replication precedes each round of chromosome segregation C. NO pairing of homologous chromosomes D. infrequent recombination E. centromeres on paired sister chromatids segregate at each anaphase F. occurs in somatic cells and in germ line precursor cells prior to entry into meiosis

Answer 12

A. two rounds of chromosome segregation without an intervening round of DNA replication B. parental cells must be diploid and the chromosome number is halved in the resultant cells C. requires the pairing of homologous chromosomes and recombination for its successful completion D. centromeres on paired sister chromatids divide only at anaphase II in a normal meiosis E. occurs only in the germ line

Answer 13

In normal meiotic recombination, you get four, genetically variable haploid cells. If you have nondisjunction in meiosis I, your homologous pairs don’t split properly in the first division, so you end up with one 4N cell and one 0N cell (as opposed to two 2N cells) --> your resulting gametes will be 100% abnormal (two 2N [or N+1] cells, and two 0N cells [or N-1]). -->two diploid cells, two non-genetic cells.

Answer 14

In normal meiotic recombination, you get four, genetically variable haploid cells. If you have nondisjunction in meiosis II, the homologs separate fine, but the sister chromatids do not. So you get two, normal haploid cells, one 2N cell, and one 0N cell 50% abnormal gametes.

Answer 15

Chromosomes have been classified historically on the basis of several characteristics. p= short arm; q= long arm. A major determinant in this classification system is the relative position of the centromere (primary constriction) on the chromosome. On this basis, human chromosomes are divided into three categories: 1. Metacentric: the centromere is located in the middle of the chromosome, such that the two chromosome arms are approximately equal in length. 2. Submetacentric: the centromere is slightly removed from the center. 3. Acrocentric: the centromere is near one end of the chromosome.

Answer 16

Chromosomes are also classified cytogenetically based on banding patterns observed microscopically after treatment with stains such as Giemsa, quinocrine, DAPI (4’,6-diamino-2-phenylindole), Hoechts, etc. These patterns result from the differential staining of various chromosomal regions (e.g. regions with high G+C, or A+T base compositions, or the presence of heterochromatin) with the dyes listed above. The banding pattern is unique to each human chromosome and allows the unequivocal identification of each chromosome. Primarily we visualize karyotype via G-stain in which we isolate pt’s lymphocytes during metaphase and stain the chromosomal proteins (high GC-content stains lighter)  use banding patterns to identify chromosomes. There are other ways to visualize

Answer 17

The classification of human chromosomes is decided and updated by the Standing Committee of Human Cytogenetic Nomenclature and reported as the International System for Human Cytogenetic Nomenclature (ISCN). Short arm locations are labeled p (petite) and long arms are labeled q. Each chromosome is considered to be divided into different regions labeled p1, p2, p3; q1, q2, q3 etc., counting outwards from the centromere. Chromosomal regions are defined by specific landmarks (distinct morphological features) that include telomeres, centromeres, and banding patterns. Depending on the level of microscopic resolution, regions are subdivided into bands labeled p11 (pronounced “one-one”, not eleven!), p12, p13, and then p11.1 (p one-one point one), again counting outwards from the centromere. The centromere is designated “cen” and the telomere “tel”. It is conventional to refer to relative chromosomal locations in terms of proximity to the centromere. Thus, proximal 2q means the segment of the long arm of chromosome 2 that is closest to the centromere, and distal Xp means the portion of X most distant from the centromere, and therefore closest to the telomere.

Answer 18

Polyploidy = extra copies of all chromosomes (3n, 4n)  generally caused by 1 egg fertilized by 2 sperm. Aneuploidy = loss or gain of certain chromosomes (trisomy 21, monosomy X)  generally due to nondisjunction events involving frequency/location of recombination in Meiosis I. Maternal age also a contributing factor. -Maternal age effect = perhaps when women age, their cellular machinery gets worse at dealing with bad recombination events (1st hit = bad recombination event, 2nd hit = bad machinery). Terminalization = loss of cohesion between sister chromatids = movement of chiasmata towards ends of homolog pairs -->precocious separation of homologous chromosomes and nondisjunction.

Answer 19

``` Trisomy 21 – Down syndrome Characteristic facies, short stature, hypotonia, moderate intellectual disabilities Congenital malformations – endocardial cushion defects, duodenal atresia (closing off or narrrowing) and other gastrointestinal anomalies, Hirschprung disease(large intestine disease, makes it hard to poop, loss motility or peristalstic movements). Down syndrome (trisomy 21) is the most common human chromosomal disorder ascertained in liveborn infants (~1/900). In more than 95% of trisomy 21 cases, the additional chromosome 21 is maternal in origin, and dosage studies indicate that nondisjunction during maternal meiosis I is by far the most common cause. ```

Answer 20

Trisomy 18 – Edwards syndrome Intrauterine growth retardation, characteristic facies, severe intellectual disabilities, characteristic hand positioning. Congenital malformations – valvular heart disease, posterior fossa CNS maldevelopment, diaphragmatic hernias, renal anomalies

Answer 21

Trisomy 13 – Patau syndrome Characteristic facies, severe intellectual disabilities Congenital malformations – holoprosencephaly, facial clefts, polydactyly, renal anomalies

Answer 22

47, XXY – Klinefelter syndrome | Tall stature, hypogonadism, elevated frequency of gynecomastia, high frequency of sterility, language impairment

Answer 23

45, X -Turner syndrome Short stature, webbed neck, edema of hands and feet, broad shield-like chest, narrow hips, renal and cardiovascular anomalies, gonadal dysgenesis (failure of ovarian maintenance).

Answer 24

Balanced and unbalanced rearragements. Chromosomal rearrangements require two DNA double strand breaks (DSBs) (fixed by NHEJ) and can be induced by a variety of DNA damaging agents. Ionizing radiation directly induces breaks, but numerous other agents that damage DNA produce DSBs during repair. Because DSBs are necessary for meiotic recombination, rearrangements during meiosis are common. Duplications, deletions, inversions, insertions and translocations all appear to have breakpoints in chromosomal regions in which repeated sequences are prevalent. Nuclear protein complexes having both DNA repair and recombination activities share enzymes and associate with chromatin containing repetitive sequences. Structural rearrangements can be inherited and can also lead to further rearrangement during meiosis.

Answer 25

Inversion: -INTRAchromosomal rearrangements -Inverted Segments -Normal phenotype for carrier in most cases -familial more common -de novo is less common -incidence is 1% occurs when one chromosome undergoes two double strand breaks of the DNA backbone and the intervening sequence is inverted prior to the rejoining of the broken ends. Pericentric inversions: include the centromere. Break in both the p and q arms. Orient inversions by rotating the inverted segment, holding fast the flanking segments of the chromosome. Think Rec 8 in San Luis Valley. Paracentric inversions: exclude the centromere. two breaks within the same chromosome arm. Chromosomes with inversions can have normal genetic complements, and therefore may produce no phenotypes in carriers of the rearrangement. However, inversions may generate abnormal gametes during meiosis. During the pairing of homologs in meiosis, a loop is introduced in the homolog containing the inversion, which maximizes the association of homologous sequences. If a crossover occurs within the inverted region of a paracentric inversion, both dicentric (two centromeres) chromosomes and acentric chromosomes can be generated, leading to chromosome breakage or loss. -Pericentric carrier recombination (with another WT individual) = During meiosis, there’s a drive to align homologous sequences --> can sometimes induce a loop formation to maximize this alignment. Get 1 normal gene, 1 inverted gene, and 2 genes susceptible to deletion/duplication. Pericentric indicated by p and q in the karyotypic classification. -Paracentric carrier recombination (with another WT individual). Get 1 normal gamete, 1 deletion dicentric, 1 deletion acentric, and 1 inversion.

Answer 26

``` BALANCED: Individuals with balanced rearrangements have normal complements of chromosomal material, meaning there is no loss or gain of genetic material. There is no phenotypic effect for heterozygote carrier. Exception is when it is at a break point of a gene, disrupts function (rare) However, these rearrangements have varying stabilities during meiosis and mitosis. -inversion -reciprocal translocation -Robertsonian translocation UNBALANCED: the chromosome set has additional or missing material. Phenotypes of these individuals are likely to be abnormal. Duplication of genetic material in gametes can lead to partial trisomy after fertilization with a normal gamete, while deletions lead to partial monosomy. -Deletions -Isochromosomes -Duplications -Ring chromosomes ```

Answer 27

Reciprocal translocation: results from the breakage and rejoining of non-homologous chromosomes, with a reciprocal exchange of the broken segments. As with inversions, carriers of reciprocal translocations have an increased risk of producing unbalanced gametes; balanced translocations are often found in couples that have had two or more spontaneous abortions, and also in infertile males. When the chromosomes of a carrier of a balanced reciprocal translocation pair at meiosis, a quadrivalent figure is formed. Alternate segregation, the most frequent meiotic segregation pattern, produces gametes that have either the normal chromosome complement or two reciprocal translocation chromosomes, both of which are balanced with respect to chromosome complement. However, adjacent segregation leads to unbalanced gametes. -If they separate in an ‘alternate’ way --> produce gametes that have either the normal chromosome complement, or 2 reciprocal translocation chromosomes, both of which are balanced. If they segregate via adjacent-1 or adjacent-2 --> unbalanced gametes who have both partial monosomy and partial trisomy of certain genes. (Ex: CML happens because of translocation between Chr. 9 and 22--> activated a tumorigenic tyrosine kinase.) Adjacent 1 segregation = homologous centromeres go to different daughter cells. Adjacent 2 = both homologs go to the same daughter cell.

Answer 28

Robertsonian translocation: the fusion of two acrocentric chromosomes within their centromeric regions, resulting in the loss of both short arms (containing rDNA repeats such as alpha/beta satellites, satellities I- IV, and rRNA encoding regions). The human acrocentric chromosomes are: 13, 14, 15, 21, 22. Can be homologous or nonhomolgus but both are BALANCED. Robertsonian translocations result in the reduction of chromosome number, but are considered balanced rearrangements because the loss of some rDNA repeats is not deleterious. Carriers of Robertsonian translocations are phenotypically normal, but these rearrangements may lead to unbalanced karyotypes for their offspring, resulting in monosomies and trisomies. Increased risk of balanced RT in infertile men. Most common between 13:14 (75% of cases) but can also happen in 14:21 and 21:21; all can be denovo or familial. Very common between chromosomes 14 and 21. Results in Trisomy 21, but still have 45 chromosomes. During meiosis, chromosomes form a trivalent figure to arrange homologous sequences. Carrier has a normal C21, normal C14, and a Robertsonian translocated 14/21. The alternate segregation pathway can once again produce a normal and a balanced gamete. Alternatively, can get 4 unbalanced gametes (one trisomic 21, and 3 lethal [just 14, just 21, or trisomic 14]). 6 potential gametes, 3 viable ones. In Robertsonian translocation, chromosome count still goes down by 1.

Answer 29

Deletions = can be terminal (at end of chromosome) or interstitial (in middle). Results from a ds break, with one chunk getting excised out, or unequal crossing over, or from an abnormal segregation. Unless the excised fragment has a centromere and can form a ring, it is not stably transmissible to offspring and you get missing chromosomal information. Results in haploinsufficiency in which normal allele isn’t enough to prevent disease (ex: del(5)(p15) = cri-du-chat).

Answer 30

Isochromosomes = refers to chromosome in which one arm is missing, so the other arm is duplicated in a mirror-like fashion. Happens either through mis-division through the centromere in meiosis II, OR by exchange between one arm of a chromosome and its homolog at the proximal edge of the arm, adjacent to the centromere. Most commonly involves long arm of X chromosomes, but small % of Down Syndrome pt’s have the 21q21q rearrangement. All gametes will contain the 21q21q chromosome (inherited this from parental carrier who had the isochromosome event) plus Chr. 21 from the WT parent = trisomic. (Still, most trisomy 21 happens due to maternal non-disjunction event).

Answer 31

Duplications = | gain of genetic info; less harmful but can lead to abnormalities (partial trisomy 21)

Answer 32

Ring chromosomes = | chromosome fragment that circularizes and acquires kinetochore activity  stable transmission

Answer 33

Semi-related = non-allelic homologous recombination when 2 homologous chromosomes with unique genes undergo a bad recombination event due to misalignment  produces 1 duplication and 1 deletion homolog that causes an unbalanced chromosomal rearrangement. Example: hereditary sensory motor neuropathy. CMT = duplication at 17p11.2 (gene for peripheral myelin protein-22). Hereditary neuropathy = deletion at 17p11.2. Weakness of foot/lower leg muscles, foot deformities (hammertoes), and weakness of hands (late in disease). Always, normal function of peripheral nerves affected

Answer 34

Most of these abnormalities found in fetuses are due to a random event and are unlikely to re-occur. However, if the abnormality can be inherited from a carrier parent then recurrence risk is increased (ex: isochrome 21  recurrence risk is 100%).

Answer 35

defined as abnormal phenotypes caused by gain (over expression) or loss of a set neighboring genes. **(Potentially add table later)

Answer 36

del(22q11.2) -DiGeorge syndrome: absent or hypoplastic thymus and parathyroids, congenital heart disease neural crest, branchial pouches, great vessels, outflow tract defects in heart -Velo-Cardio-Facial syndrome: cleft palate, lateral nasal buildup cardiac septal defects

Answer 37

Epigenetics = mitotically and meiotically heritable variations in gene expression that are not caused by changes in DNA sequence. Example = post-translational modifications of histone proteins and/or DNA methylation -->alter chromatin structure --> affects gene expression.

Answer 38

Genetic imprinting = sex-dependent epigenetic modulation. Whereas most genes are expressed by both inherited alleles, some genes are inherited in a silent form from one parent and an active form from another parent. (Imprinted = methylated = silenced.) Methylation of CpG repeats (in promoter region, generally) by MBD family (methyl CpG binding domains). Ex: MeCP2 recognizes methylated CpGs (methylation via methyltransferases) and binds them; its associated proteins (like HDACs and histone methylators) can then alter chromatin structure to cause transcriptional repression/silencing. (In rare cases, the expressed allele can be methylated = exception.) Methylation happens at imprinting centers in gametes. DNA demethylation happens by inhibiting DNMT1 or the chromatin-remodeling proteins. Then, non-coding DNA sequences bind imprinter RNA transcripts (BD transcripts)  recruit DNMT to methylate CpG islands on same chromosome (cis mechanism). AKA = we’re hemizygous, kind of, for these genes because we have one working copy only with no backup. Only about 1% of genes are imprinted, and they are either maternally or paternally expressed.

Answer 39

Methylation marks are established in the gamete (can’t happen after fertilization because need to know what’s silenced beforehand). These modifications must be reversible for gametes. In other words methylation patterns must be erased and then reset for healthy devlopment. Or else it will cause problems when male and female gametes come together during fertilization. In somatic cells, methyltransferases propagate the epigenetic markers. They recognize hemimethylated DNA after synthesis of a new strand and methylates it accordingly. This continues the epigenetic mark in somatic cells. In germ-line cells, it starts with erasure of methylation marks so you get biallelic expression of everything temporarily. Then methyltransferases re-establish methylation patterns in a gender-specific way. All oocytes get methylated one way, and all spermatocytes methylated another way. I will re-methylate all my gametes so even the DNA that I’m passing on from my dad now has my maternal methylation marker on it. Ensures that all genes coming from father have only one specific set of imprinted genes, and all genes coming from mother have a different set of imprinted genes (so you don’t get two active copies or two silenced copies).

Answer 40

Some Background: imprinted region on long arm of chromosome 15 is the prader-willi angelman syndrome region. Prader-Willi = excessive eating, short stature, hypogonadism, and some intellectual disability. Caused by del(15q11-q13). Normal gene comes from father, and is silenced on mother; this deletion happens on paternal chromosome. (Paternal insufficiency). Caused by defects in SNORD116 snoRNA (misregulated mRNA.)

Answer 41

Angelman = short stature, severe intellectual disability, spasticity, and seizures. Caused by del(15q11-q13). Normal gene comes from mother and silenced on father; this deletion happens on maternal chromosome. (Maternal insufficiency.) Caused by defects in UBE3A (codes for ubiquitin ligase needed in brain development). So dad is responsible for carrying active PW genes and mom is responsible for carrying active Angelman genes to create normal phenotype. Any deletions and you won’t have any working copies of the gene as backup due to imprinting.

Answer 42

Disomy = if both autosomes are inherited from one parent (particularly bad with imprinted genes). If that gamete fuses with a WT gamete  zygote has trisomy for that autosome. Here, this relies on a nondisjunction in mitosis that gets rid of the third copy, but leaves you with 2 copies from one parent. (So whatever active genes you were supposed to inherit from one parent, you don’t have anymore.) So, maternal disomy for C15 = no copies of C15 from dad = Prader-Willi. Paternal disomy for C15 = no copies of C15 from mom = Angelman. For PW: 70% of time due to a deletion in paternal gene; 25% from maternal disomy. Angelman = 70% of time from deletion in maternal gene; less than 5% of time from paternal disomy (because non-disjunction meiotic events so rare in men).

Answer 43

3 main features: Macrosomia, Macroglossia, & Midline abdominal defects and will have hemihypertrophy and an increased risk of cancer (abdominal); normal intellectually but can have hypoglycemia on shrt arm of 11 paternal UPD; (growth factor here)ear lobes also messed

Answer 44

main features are tiny size,short stature, mildly abnormal facial features, and 5th finger clinodactyly, can also have hemihypertrophy and increased risk of cancers associated with maternal UPD on chromosome 7 ; linked to use of assisted reproductive techs like in vitro fert

Answer 45

Acute myeloid Leukemia (AML) = translocation between C15 and C17 (and sometimes between C8 and C21). If between 15 and 17 = promyeloid leukemia--> treat with retinoic acid. Due to an issue with PML-RAR-alpha and disruption of a TF. Treatment with Retinoic Acid --> differentiation therapy. Kids with Down Syndrome are at elevated risk for developing ALL and AML.

Answer 46

Chronic Myeloid Leukemia (CML) = | translocation between C9 and C22. Treat with tyrosine kinase inhibitors (GLEEVEC). Due to an issue with BCR-ABL.

Answer 47

A common finding in childhood B-cell acute lymphoblastic leukemia (ALL) is high hyper-diploidy revealed by chromosome and FISH analyses. Hypodiploidy = worse prognosis than hyperdiploidy (hyperdiploidy of 4, 10, 17 most favorable). Likely because hypodiploidy leads to loss of important TSGs.

Answer 48

(cen) - used for enumeration-leukemias - examples: cen 4, 8, 10, 17 - parental diagnosis of trisomy - ALL panel; prenatal dx

Answer 49

(LIS) - used for deletion/ duplication - leukemias, cancer - ex: p53

Answer 50

(F) (DF) - used for translocations-leukemias - ex: BCR-ABL; PML-RARA

Answer 51

WCP: used to find indentifying markers and translocations -ex:WCP 1-22, X, Y (all studies) BAP: used to detect translocation re-arrangement in cancer -ex: MLL (cancer)

Answer 52

SNP chromosomal microarrays consist of synthetic DNA oligomers ‘spotted’ onto a ‘platform’ (usually a specially treated, microscope slide called a bead chip) using robotic technologies. Extensive quality control goes into the testing of the ‘probes’ (SNPs) both at the production laboratory and the cytogenetics laboratory. Our current clinical platform interrogates 850,000 regions of the genome.

Answer 53

Sample—usually peripheral blood--DNA is amplified and labeled. After post hybridization washes, the arrays are viewed via an optical scanner, and a statistical test is performed for all the spots/color intensities for each probe, comparing to a population of 50 normal individuals’ DNA. The SNP platform provides information on intensity and on runs of homozygosity, possibly revealing autosomal recessive conditions. Thus, the whole genome can be investigated simultaneously—like performing thousands of FISH tests! CMA testing frequently reveals duplications or deletions of genetic material that cannot be seen by standard cytogenetics and light microscopy.

Answer 54

An important consideration is that all human populations contain multiple genomic variants—that is duplications or deletions within the DNA for which there is no phenotypic consequence. These cannot be detected at the chromosome level. An important resource exists that has banked known genomic variants in the normal human population, the Database of Genomic Variants (DGV): http://dgv.tcag.ca/dgv/app/home. This resource contains published literature as well as the precise mapping of the variants and known disease regions. There are over 35,000 definitive CNVs in our human population, and these are known to be heritable. Each normal individual carries ~10-20 CNVs. The size of the copy number variant may be 100’s of kilobases to megabase-pairs of genomic DNA.

Answer 55

1.If deletion or duplication is detected by CMA consult DGV 2.Parental FISH studies will be offered to determine if this finding is a rare, normal, familial variant. 3.If a deletion or duplication is found in one or both parents, other family members may be tested by FISH. Often extensive consultation between the clinical geneticist, genetic counselors and cytogeneticist are required. 4.If the deletion or duplication is not found in either parent, and it is not found in the genomic variants Database, further data-base mining, literature searches are performed. Often a gene or genes mapped in the region of deletion or duplication reveals a syndromic association.

Answer 56

FISH = fluorescent in situ hybridization  using fluorescently labeled DNA to examine subtle deletions/changes in chromosomes that wouldn’t be picked up by normal G-staining (Like small deletions, testing for how vs. donor marrow cells after transplant, looking at lots of cells at once). Red versus green signals to discern condition. Used for initial diagnosis and to monitor disease progression.

Answer 57

Causes of DS = 1) Trisomy 21. 95% of pts have full extra 21. Caused by a nondisjunction event. 2) Unbalanced translocations between C21 and another acrocentric chromosome (happens a lot with C13, 14, 15)  be sure to check karyotype of parents to see if they have a balanced translocation. 3) Mosaic Tri 21 = mixture of normal cells and cells containing extra C21. Milder phenotype. 1st trimester screening = ultrasound measurement of nuchal folds or beta-hCG/PAPP-A screening. 2nd trimester screening = quad screening = beta-hCG, AFP, unconjugated estriol, and inhibin levels. Confirm via amniocentesis or chorionic villus sampling.

Answer 58

Infants: - midfacial hypoplasia = structures in middle of face too small (flattened bridge of nose). - Upslanting palpebral fissures - epicanthal folds. - Small ears. - Large-appearing tongue.(really smaller mouth compartment) - Low muscle tone - increased joint mobility, - short fingers, - transverse palmar crease, -5th finger incurving, - increased space between toes 1 and 2. - at birth growth parameters are usually normal

Answer 59

-Cardiac issues = can see all sorts of issues (congenital heart defects), but atrioventricular canal is common. -GI issues = esophageal atresia, duodenal atresia, Hirschsprung’s. Feeding problems, constipation, GERD, celiac dz. -Ophthalmologic problems = blocked tear ducts, lazy eye, myopia, nystagmus( jiggly eye), cataracts. -ENT = ear infections (narrowed ear canals), deafness (sensorineural and conductive), nasal congestion, enlarged tonsils and adenoids (obstructive apnea is an issue). -Endocrine issues = thyroid dz, insulin-dependent diabetes, alopecia areata, reduced fertility (normal puberty). -Orthopedic problems = hips, joint subluxation, atlantoaxial subluxation (c1 compresses spinal cord). -Hematalogic issues = myeloproliferative disorder, increased risk for leukemia (12-20x), iron-deficiency anemia. -Developmental issues = hypotonia effects gross motor development, spectrum of intellectual disability (generally mild-moderate), speech problems. -Neurologic problems = hypotonia, seizures. Psychiatric = increased depression, early AD, autism.

Answer 60

Important to note that in DS cognitive age is 8-10; if mild 10-12 (functional members; jobs with supervision)

Answer 61

PWS results most often when genetic info is missing from paternal allele of 15q11-q13 due to a deletion (and isn’t compensated for because maternal genes are silenced). Can also be caused be imprinting error that causes a virtual maternal uniparental disomy (caused by mutations at the imprinting center) Paternal chromosome gets mismarked and body reads it as not having paternal genes). Or can have actual maternal uniparental disomy. Paternal genes always lacking. Because maternal and paternal alleles marked by different methylation patterns --> use methylation testing of C15. FISH can detect deletions if that’s the case.

Answer 62

If PWS (or Angelman) not being caused by actual deletions on C15 or uniparental disomy, it could be because the upstream genes (at the imprinting center) involved in marking chromosomes have mutated, causing them to mark the genes incorrectly and causing a ‘virtual’ disomy that the body perceives as a deletion/silence. also think of these as well: IDIC 15 – associated with autism/hypotonia/Seizures/ID Maternally inherited Interstitial duplication – associated with autism/ hypotonia/seizures/ID

Answer 63

Infancy: -floppy (hypotonic), -almond-shaped eyes, -undescended testicles (cryptorchidism; repaired by surgery), -feeding problems that require feeding tube, - lighter pigmentation. Toddler/Preschooler: (2-4 years) -feeding problems reverse to hyperphagy, lack of satiation (treat with GH). -Eyes = strabismus( crosses eye), nystagmus (jiggly eye) -Orthopedics = scoliosis -Respiratory = obstructive sleep apnea; can be compounded by GH treatment -Developmentally mild-moderate cognitive disability, behavioral issues ( like pulling out hair)

Answer 64

look at it

Answer 65

Population genetics = study of allele frequencies and changes in allele frequencies in whole populations. (In which mutation = any change in DNA sequence. If in germ-line/gonadal tissue, can be passed on. Not true for somatic). Polymorphism = any genetic variant found in >/= 1% of population. Whereas nuclear DNA sequence is 99% similar between any 2 people so in a clinical basis (in which doctor serves one community), may not get this full appreciation for the population at large?

Answer 66

``` Fitness = probability of transmitting one’s genes to the next generation; f=1 if one’s chances are the same as the normal population; f=0 if genes not passed on (infertility, etc.) Coefficient of selection = s = measure of forces that reduce fitness = 1-f. Mutation rate (mu) = frequency of new mutations at a given locus. For an autosomal dominant disease that is fully penetrant, the number of new conditions with no previous family history = number of new gene mutations (‘direct method’). ‘Indirect method’ = if f=0, then incidence I = 2(mu). Also, mu = 0.5F(1-f) where mu = mutation rate/gene/generation, F = frequency of disease, and f=reproductive fitness.  In the example, mu = # of condition of interest/(total population x 2 alleles). (Have to divide by generation if question covers multiple) Consanguinity is definitely going to increase the mutation rate since you’re keeping the allele in question present as opposed to ‘diluting’ it out. Allele frequencies also affected by mutations, natural selection, genetic drift (random changes), and gene flow (adding/subtracting genes in a population). Fitness also affected by things like diet, medicine, etc. ```

Answer 67

Population is large and mating is random. Allele frequencies remain constant over time. This means no appreciable rate of mutation, all genotypes are equally fit/equal chance to be passed on, and that there’s no significant immigration/emigration of individuals with different allele frequencies into/out of the population. ( no genetic drift)

Answer 68

Based on alleles p (A) and q (a; the rare/mutant one), where p+q=1. p2 + 2pq + q2 = 1, in which p2 = AA, 2pq = Aa, and q2 = aa. The autosomal recessive carrier population is thus 2pq and the number of affected individuals is the q2 population. If a disease is very rare (1/10,000), 2q can be estimated as 2pq since q is so small and p pretty much equals 1. The rarer the disease, the less likely you’ll run into a carrier since the frequency of q is so small. SEE EXAMPLE PROBLEMS!

Answer 69

Pharmacogenetics: is the study of differences in drug response due to allelic variation in genes affecting drug metabolism, efficacy, and toxicity. (The key conceptual elements here are that pharmacogenetics typically involves the study of just a few genes and these genes are selected based on a priori knowledge of their role(s) in drug metabolism.) *Variable response due to individual gene!!

Answer 70

Pharmacogenomics: the genomic approach to pharmacogenetics, is concerned with the assessment of common genetic variants in the aggregate for their impact on the outcome of drug therapy. (Instead of analyzing individual genes and their variants according to what is known about how they influence pharmacokinetic and pharmacodynamic pathways, sets of alleles at a large number of polymorphic loci are being identified that distinguish patients who have responded adversely to what was considered a beneficial drug from those who had no adverse response) *Variable response due to multiple (all) loci across the genome!!

Answer 71

Pharmacokinetics: the rate at which the body absorbs, transports, metabolizes, or excretes drugs or their metabolites. (Genetic Examples: Cytochrome P450, glucuronyltransferase, thiopurine methyltransferase) -pharmacokinetics is concerned with whether or how much drug reaches the target(s) ADME *Absorption, distribution, metabolism, excretion

Answer 72

Pharmacokinetics is broken down further into two basic ways that drugs are metabolized through biotransformations: • Phase I (simplified): attach a polar group onto the compound to make it more soluble; usually a hydroxylation step • Phase II (simplified): attach a sugar/acetyl group to detoxify the drug and make it easier to excrete

Answer 73

Pharmacodynamics: the response of the drug binding to its targets and downstream targets, such as receptors, enzymes, or metabolic pathways (Genetic Examples: Glucose-6-phosphate dehydrogenase, vitamin K epoxide complex) -pharmacodynamics is concerned with what happens when the drug successfully reaches its target (note both phenomenon occur simultaneously in the race between drug effect (dynamics) and removal (kinetics).

Answer 74

The cytochrome P450 (CYP450) genes encode important enzymes that are very active in the liver and to a lesser extent in the epithelium of the small intestine. CYP450 enzymes metabolize a wide number of drugs. See Figure (18-3) of the CYP genes involved in Phase I metabolism. -CYP 1a1, 1a2, 2c9, 2c19, 2d6, 3a4,(40%) and all do 90% (Look at handout for more specifics)

Answer 75

``` Drugs: Cyclosporine Mechanism: -Genetically is less important than other drug metabolism genes because the population distribution of activity is continuous and unimodal Comments: -CYP3A Inhibitors ( Ketoconazole, Grapefruit juice) -CYP3A Inducers (Rifampin) ```

Answer 76

. In medicine, as in life, variation is much more interesting than uniformity. In the area of medication response, medical school will teach you that one drug should lead to one effect and an occasional side effect(s). Life experiences (clinical years, residency, etc) will show you that the actual responses of patients are broad and include (expected response, hyper/hypo response, no response, adverse-medication event). Again, recognize that genetic variation in Pharmacokinetics/dynamics and/or Phase I/II metabolism that causes phenotypic variation in drug responses between humans becomes important clinically every time you write a prescription.

Answer 77

Drugs: Tricyclic antidepressants, Codeine Important Point: While most CYP genes are important in the rate of inactivation of a drug, in some cases the CYP gene(s) is required to activate a drug. The classic example of this is CYP2D6 activity being necessary to convert codeine (inactive, almost no analgesic effect) to morphine (active with a potent analgesic effect). Comments: -CYP2D6 Inhibitors:( Quinidine, Fluoxetine)

Answer 78

Drugs: | warfarin

Answer 79

Drugs: | Isoniazid for tuberculosis

Answer 80

Drugs: 6-mercaptopurine 6-thioguanine

Answer 81

``` Drugs: sulfonamide, dapsone Mechanism: -X linked enzyme Comments: G6PD deficient individuals are susceptible to hemolytic anemia after drug exposures ```

Answer 82

Drugs: Warfarin Comments: -Warfarin, a ‘blood thinner’ is one of the most commonly prescribed medicines given to >20,000,000 patients in the US annually

Answer 83

Turner Syndrome: - 45,XO - Signs at Birth: Prenatal cystic hygroma, Webbed neck, Puffy hands & feet ,Heart defects like coarctation of the aorta - Short stature - Normal intelligence - Infertility due to non-functioning ovaries - Hormone dysfunction - Distinctive traits such as low set ears, broad chest - Occurs in 1/2,500 newborn girls

Answer 84

``` Kleinfelter Syndrome: -47, XXY Seen in childhood: Learning disabilities, delayed speech and language, tendency towards being quiet -Tall stature -Small testes -Reduced facial and body hair -Infertility -Hypospadias -Gynecomastia -Occurs in 1/500, – 1/1000, newborn boys ```

Answer 85

Jacobs Syndrome: - 47,XYY - Learning disabilities - Speech delays - Developmental delays - Behavioral and emotional difficulties - Autism spectrum disorders - Tall stature - Occurs in 1/1000 newborn boys

Answer 86

Triple X Syndrome: - 47 XXX - May have tall stature - Increased risk of: - Learning disabilities - Delayed speech - Delayed motor milestones - Seizures - Kidney Abnormalities - Occurs in 1/1000 newborn girls

Answer 87

Primary Sex Determination--> Determination of the Gonads - Gonad determination is Chromosomal, presence of normal Y is male, absence is female; * our default state is not female, both ovaries and tetes result from a common bipotential gonad, both are active in a gene directed process

Answer 88

Secondary Sex Determination; Gonadal development then determines secondary sex characteristics. *Includes sex-specific organs: -Penis, seminal vesicles & prostate gland -Vagina, cervix, uterus, fallopian tubes & mammary glands *Includes other phenotypic features -Body habitus & musculature -Hair growth -Vocal Cartilage

Answer 89

4th week of conception: -Primordial germ cells form in wall of yolk sac 5th week of conception: -Coelomic epithelium becomes genital ridge

Answer 90

6th week of conception: - Primordial germ cells migrate to the dorsal mesentary of the hindgut and enter the undifferentiated gonad - Epithelial cells of gonadal ridge proliferate and form primitive sex cords

Answer 91

``` 7th week of conception: -Differentiation of genital ridge into: Sertoli cells - eventually produce sperm Leydig cells – interstitial cells ```

Answer 92

8th week of conception: -Leydig cells begin producing testosterone -Sertoli cells begin producing Anti-Mullerian Hormone (AMH) -Primitive sex cords differentiate into: Testis cords & rete testis, eventually to become seminipherous tubules during puberty

Answer 93

7th – 8th week of conception: -Primitive sex cords dissociate into irregular clusters -Medullary (primitive) cords regress and cortical (secondary) cords are formed: Destined to become follicular cells of the ovary Follicular cells will eventually surround an oogonium which together are the primary ovarian follicle

Answer 94

Genital Ducts (at 6 weeks): Initially, 2 pairs of genital ducts in both males & females Mesonephric (Wolffian) duct Paramesonephric (Mullerian) duct

Answer 95

Mesonephric (Wolffian) duct: -Results in male structures -SRY gene (on the Y chromosome) & SOX9 gene: Both transcription factors Responsible for production of Anti-Mullerian Horomone (aka Mullerian Inhibitory Substance - MIS) Causes regression of the paramesonephric duct -FGF9 : Chemotactic factor causes tubules from mesonephric duct to penetrate the gonadal ridge Essential for differentiation of the testis -SF1/NR5A1: Stimulates differentiation of the Sertoli & Leydic cells *Under the influence of testosterone, mesonephric ducts elongate to form the: Epidymis Seminal vesicles Vas deferens

Answer 96

``` Paramesonephric (Mullerian) Ducts: -Results in female structures -WNT4 protein: Extracellular signaling factor responsible for differentiation of the ovary Inhibited by SOX9 -DHH gene: A nuclear hormone receptor Up-regulated by WNT4 Downregulates SOX9 -RSPO1 gene: Coactivator of the WNT pathway *Under the influence of estrogens (from maternal and placental sources), the following structures are formed: Uterus Cervix Broad ligament Fallopian Tubes Upper 1/3 of the vagina ```

Answer 97

At 3 weeks, originating from mesenchymal cells in the primitive streak, cells migrate to form a genital tubercle and genital swellings)

Answer 98

*Both originate from the urogenital sinus -Male structures: Androgen exposure (in this case Dihydrotestosterone) from the testis results in the formation of the following: Penis Scrotum Location of the urethral opening at the tip of the penis

Answer 99

*Both originate from the urogenital sinus- Female structures: Estrogen exposure resulting from maternal and placental sources results in the formation of the following: Clitoris Labia majora and minora Lower 2/3 of the vagina

Answer 100

``` 1st Day: -If ambiguous, -Obtain FISH studies for Sex Chromosomes and a Karyotype (or Chromosomal Microarray) -Consider ultrasound study -Evaluate for gonads & uterus Surgical consult with Urology ```

Answer 101

-Order hormone studies: | LH, FSH, Testosterone, Dihydrotestosterone, +/- AMH

Answer 102

Androgen Insensitivity Syndrome (AIS): -46, XY -X-linked gene, AR -Mutation causes abnormality of the androgen receptor: Even though the body makes androgens (testosterone), it doesn’t necessarily recognize or respond to it Phenotypes range from mild under-virilization (Partial AIS) to full sex reversal (Complete AIS) -Previously called “Testicular feminization”

Answer 103

5-Alpha ReductaseDeficiencyy: - 46, XY - Gene: SRD5A2 - Autosomal Recessive - Mutation causes decreased ability of the body to convert testosterone to dihydrotestosterone - Phenotype shows undervirilized male with increased virilization at the time of puberty

Answer 104

Disorders associated with the SRY gene: - 46, XY or 46, XX - Y-linked gene - Deletion or absence of the gene results in full 46, XY sex reversal in most cases, a phenotypically normal female - Ectopic presence of the SRY gene in a 46, XX individual can result in a phenotypically normal male - Mutations in the SRY gene in a 46, XY individual results in decreased or absent production of Anti Mullerian hormone & under virilization of a male

Answer 105

``` Denys-Drash & Frasier Syndrome: -Sex reversal with 46, XY -Due to mutations in the WT1 gene -Both cause different types of chronic kidney disease Diffuse mesangial sclerosis Focal segmental glomerulosclerosis -Increased risk for Wilms Tumor -WT1 – transcription factor for SRY gene ```

Answer 106

``` Congenital Adrenal Hyperplasia: -Ambiguous genitalia in 46, XX -21-hydroxylase deficiency -Complicated by salt wasting in the first few weeks of life and with times of metabolic stress: Decreased sodium and chloride Increased potassium ```

Answer 107

- Thrombocytopenia = low blood platelet count. Causes = leukemia, immune system problem, medication side effect. - Jaundice = yellow pigmentation of skin (and whites of eyes) caused by increased levels of bilirubin in blood. Generally happens with liver disease. - Scleral icterus = eye is yellow due to jaundice. - Hematemesis = vomiting of blood, generally from upper GI tract. - Arthralgia = joint pain. - Hemoglobinopathy = genetic defect that causes abnormal structure of one of the chains of the Hb molecule. Single-gene disorders, generally autosomal co-dominant. - Epistaxis = nosebleeds; can be anterior or posterior.

Answer 108

-chronic hemolytic anemia -myeloproliferative disorders -reticulocytiosis malignancies

Answer 109

In 1882, - the French medical student Phillipe Charles Ernest Gaucher described a 32-year old woman whose spleen was very enlarged. A postmortem exam revealed that cells in the spleen were themselves enlarged. Gaucher described these clinical and pathological findings in his doctoral thesis. The enlarged cells (now called "Gaucher cells") and spleen became signs of the disease, and enabled physicians to diagnose people with Gaucher disease.

Answer 110

Cell Pathology: -cells in the spleen were themselves enlarged. -chemical cause of the enlarged spleens and liver: a buildup of a lipid (fatty substance) called glucocerebroside -showed that people with Gaucher disease made the lipid normally but did not make enough of the enzyme "glucocerebrosidase" to break it down and clear it out of the body. Clinical Manifestations: Most patients describe their first symptom as a swollen stomach. This is because the spleen has swollen. Gaucher disease symptoms may include: -Skeletal abnormalities, including thinning of your bones (osteopenia), bone pain and bone fractures, due in part to bone marrow infiltration of lipid-laden macrophages -Enlarged liver (hepatomegaly) or spleen (splenomegaly), or both -Anemia, due to fewer healthy red blood cells and decreased production from bone marrow -Excessive fatigue -A greater susceptibility to bruising, which is often a consequence of low platelets (thrombocytopenia) -Cognitive deterioration, including mental retardation or dementia in the rare Type II (and sometimes mild problems in Type III)

Answer 111

Enzyme assay and genetic testing. Testing glucocerebrosidase activity. Genetic testing 50-70% accurate in general population. More accurate in Jewish population.

Answer 112

Enzyme replacement therapy; sometimes substrate reduction therapy so they don’t even make these kinds of lipids. No real treatment for bone pain besides supportive treatment. Way too expensive, it’s an orphan drug. Can cost >$450k a year. Imiglucerase, 1 unit = $10, annual cost = $75k - $400k. Drug shortages due to viral contamination.

Answer 113

``` Whom it Strikes: young adults/adults (6-80 years old) Distinguishing Symptom: no nervous system problems Effects on disease: varies from mild to severe Glucocerebrosidase activity: less than 30% ```

Answer 114

``` Whom it Strikes: infants (birth-2 years) Distinguishing Symptom: early nervous system problems Effects on disease: dies in infancy Glucocerebrosidase activity: very little activity ```

Answer 115

``` Whom it Strikes: children/young adults (2-60 years old) Distinguishing Symptom: later onset of nervous system problems Effects on disease: becomes severe Glucocerebrosidase activity: little activity ```

Answer 116

- Only males are affected - only males can be carriers. - If a dad has it, so will all of his sons. ----Daughters cannot carry or pass on traits. You get mitochondrial DNA from your mom's eggs. Never dad.