General Flashcards
(517 cards)
1
Q
If a parent has balanced translocation, which type of segregation leads to phenotypically normal offspring? Chromosomally?
A
Alternate -> phenotypically normal, 50% chromosomally normal
2
Q
G6PD heterozygote advantage
A
malaria resistance
3
Q
Common severe HFE variant, second variant
A
Cis282Tyr
His63Asp (homozygote unaffected)
4
Q
What does HFE do?
A
Regulate hepcidin signalling - iron response hormone that tells body to stop absorbing
5
Q
When do you treat hemochromatosis
A
Ferretin > 300 for men or 200 for women
- Goal <50
6
Q
Why does Factor IV leyden resolve with puberty?
A
mutation is on promoter which activates with hormone changes after puberty
7
Q
What gender is hirschsprung more common in?
A
Males
8
Q
Uplifted ear lobes, hirschsprung
A
Mowat Wilson
ZEB2
9
Q
HTT repeat expansion location and cutoffs
A
exon 1
Normal 10-25
At risk 26-35
Low penetrance 36-39
Classic 40-59
Juvenile 60
10
Q
What type of proteins do the most common HCM mutations affect?
A
Sarcomere or Z disk
11
Q
What does having DR3 and DR4 alleles place someone at increase risk for? Why?
A
Insulin dependent diabetes
They are linked with DQB1*0201 and DQB1*0302 alleles (antiben binding clefts in pancreatic island cells)
DR2, which is linked with DQB1*602 is protective
12
Q
Which 2 genes account for 80% of long QT
A
KCNQ1 and KCNH2
13
Q
What do you need to offer relatives of patients with Jervell and Lange-Nielsen syndrome?
A
EKG. Jevell and Lange Nielsen is AR, but allelic with Romano Ward syndrome (AD long QT)
KCNQ1 and KCNH2
14
Q
MSH2, MLH1, MSH6, PMS2
A
Mismatch repair genes -> Lynch Syndrome (HNPCC)
GI cancer (Colon, stomach, intestine, pancreas)
Endometrial/ovarian Ca
Renal Cancer
NO breast/lung ca
MSH6 and PMS2 low penetrance
15
Q
Lynch syndrome surveillance
A
Age 20: Colonoscopy (or 5 years before earlierst family hx)
Age 30: Endometrial biopsy every 1-2 yrs, Urine cytology
Age 40: Gastric - EGD every 3-5 yrs
Age 50: MRCP for Pancreatic CA annually
16
Q
What % of marfan mutations are de novo
A
~25-33%
17
Q
What is the skeletal features of marfan
A
Tall with long arms/long legs: Arm span to height > 1.05, Upper to lower segment
arachnodactyly
Pectus
Scoliosis
joint laxity
narrow palate
18
Q
Management of Marfan
A
Annual TTE (root, mitral valve), eye exam
Follow ortho
B-blocker
? Ace/Arb
19
Q
How is increased nuchal thickness defined?
A
3mm in 1st trimestery, 6mm in 2nd trimester
20
Q
What is the most common FAOD?
A
MCAD
ACADM gene
21
Q
17p.13 deletion
Brain dysgenesis
A
Miller-Dieker
Key gene: LIS1
Platelet activating factor acetylhydrolase 1 (PAFAH1)
- Lisencephaly (LIS1) + dysmorphic features (unknown genes)
22
Q
Recurrence risk for miller dieker
A
17p13.3 deletion
80% de novo (usual germline mosiacism risk)
20% translocation: 25% abnormal (either del or dup), 25% miscarriage
23
Q
Mt8344G>A tRNAlys
A
MERRF
Myoclonic epilepsy with RR fibers
Complex I and IV reduced - mostly synthesized within mitochondria
- Heteroplasmy
- Can also cause multisystemic diasese
- Mutant mitochondrial accumulate with age (mtDNA has 10x mutaton rate vs chromosomal DNA)
Tx: CoQ10 and Carnitine
24
Q
What % of NF patients have a de novo mutation?
A
50% - NF has a very high mutation rate
25
Pima Indian Tribe (Arizona)
Type 2 DM, MODY
26
Which type of diabetes have more twin concordance?
Type 2
27
What is the most common extra renal manifestation of ADPKD?
Colonic Diverticula
- PKD1 and PKD2 genes -\> encore parts of multimer compled that affect how cilia sense flow
+ Heptaic, biliary, pancreatic, ovarian, splenic cysts
Mitral/Aortic insufficiency
+ 10% have aneurysms in brain
PKD1 and TSC are next to each other on Ch16
28
Almond shaped eyes, triangular mouth, small hands and feet, narrow bifrontal diameter + OCD, hyperphagia
Prader Willi
15p11 paternally expressed genes
70% pat deletion, 25% maternal UPD, \<5% imprinting defect
+ obesity 2/2 hyperphagia,
Tx: growth hormone can normalize height
29
How often is RB1 germline mutation found in a patient with unilateral retinoblastoma?
40%, but only 10% of patients have a family history.
- All patients with bilateral retinoblastomas have germline RB1 mutations
30
What is the function of RB1
Cell cycle regulatory element
31
What secondary neoplasms can be seen in patients wtih RB1 mutations?
Retinoblastoma + osteosarcoma, soft tissue sarcoma, melanoma
32
Where do nearly half of RB1 mutations occur?
CpG dinucleotide (CG island, often methylated motif)
33
What genes cause RETT syndrome or similar phenotype?
MECP2 (classic for females or males with XXY)
CDKL5 (XL)
FOXG1 (AD)
34
Normal at birth -\> decelerating head circumference
Cortical and cerebellar atrophy **without neuronal loss** (densely packed neurons on path)
RETT syndrome - MeCP2
Clinical spectrum from neurodevelopmental to neurodegenerative disease
35
What is the most common cause of disorders of sexual differentiation
SRY
80% of 46XX males (transloction to X chromosome) - tx with androgens to complete virilization
30% of 46XY females (deletion/mutation - LOF) - tx with estrogen at 14, progesterone for periods, **remove gonads to avoid gonadoblastoma**
- also regulates sperm formation (Azoospermia factors AZFa, b, c)
36
Glu6Val - B Globin gene
SSD
- Can also be caused by compound heterozygousity in sickle cell mutation w/ B thal (non-expression) or Hg C (Glu6Lys)
37
What is HgbC?
Glu6Lys on B globulin gene -\> affects solubility and can cause mild splenomegaly/anemia but **not sickling**
- Can cause SSD phenotype when compound het w/ Glu6Val (SS mutation)
38
What do you do if SSD is seen on NBS?
Antibiotic prophylaxis due to 11% mortality from sepsis in first 6 month of life.
39
What is the prior probability for female mother of one son who is affected w/ XL-R disorder to be a carrier?
2/3rd
40
What phase of the cell cycles do cells spend the most time in?
Interphase
41
Phase of cell cycle where cellular contents are duplicated?
G1 (part of interphase)
42
Phase of cell cycles where chromosomes are duplicated?
S (part of interphase)
43
Phase of cell cycle when cell gets split into 2
Cytokinesis
44
The cell is 2n, 4c entering ___ phase of mitosis. After ___ cells are 2n, 2c again
Prophase, cytokinesis
45
After what phase of the cell cycle are meiotic cells 2n, 4c?
Interphase (after S)
46
After what phase of meiosis are cells 1n, 2c
meiosis 1
47
After which phase of mieosis are cells 1n, 1c
Meiosis 2
48
When do meiotic cells become haploid
After meiosis 1
Haploind = 1n
49
50
When are homologous chromosomes separated in meiosis?
Anaphase 1
51
When are sister chromatids separated in meiosis?
Anaphase 2
52
What are the stages of prophase 1?
Leptotein - chromosomes condense
Zygotene - synapsis form
Pachytene - bivalent + crossing over
Diplotene - Synaptonemal complex dissolve
Diakinesis - nuclear membrane fragment
53
Which stage of meiosis do bivalents form and crossing over occur?
Prophase 1 -\> pachytene
54
What are chiasma?
point between homologous chromosomes across which exchange of genetic maternal occur
55
When does meiosis start in males?
puberty
56
At what stage of meiosis does Oogenesis arrest in? Until what times?
Prophase 1 until puberty
Metaphase 2 until fertilization
57
What charactersitics must a cell have to be usable for karyotyping?
- have a nucleus
- spontaneously divide (marrow, prenatal tissue, skin) or can be induced to divide (blood)
58
What cell type(s) can be available for metaphase analysis immediatly? After 3 days? After 2 weeks?
Immediately: Bone marrow
3 days: Blood
10-14 days: amniotic fluids, CVS, skin
59
How many metaphases are counted in routine karyotype? When would you count more?
Routine = 20
Do more when looking for mosiacism (50)
60
Level 1 mosiacism
Only single cell is seen in multiple cultures
- Most likely artifact (pseudomosiacism)
NOT reported
61
When does level 2 mosiacism get reported?
2 or more abnormal cells in the sinple flask, or a single abnormal colony in culture among many - usually pseudomosaicism
Report if:
- additiona studies inadequate
- fetal anomalies identified
- well recognized anomaly in mosaic state
62
What is level 3 mosiacism
multiple cells/colonies in independent cultures/dishes share same anomaly -\> true mosaicism
63
What are the advantages of FISH analysis?
Rapid turnaround, high sensitivity
64
When would you choose a dual color break apart FISH probe instead of a dual-fusion probe?
When there are many possible translocation targets
65
What is an emumeration probe in FISH
Centromere control + target probe to look for amplification
66
Name 6 common tumor suppressor genes
RB1 - retinoblastoma
TP53 - Li frameni
APC - FAP
VHL
BRCA1/2 - familial breast/ovarian ca
MLH1 and MLH2 - Lynch
67
Which agent is used to prevent coagulation in cultures of liquid tumor cytogenetic analysis?
Sodium Heparin
68
What translocation is associated with CML?
How do you detect it?
t(9:22) - philadelphia chromosome
- BCR-ABL fusion expressed in der22
- detect w/ dual fushion FISH
69
What cytogenetic anomaly is seen in Polycythemia vera?
Trisomy 9 (JAK2 is on 9)
Polycythemia also seen in JAK2 GOF mutations
70
What ca is t(8:21) seen in?
AML
71
What is the only STAT cytogenic lab cancer case
Acute promyelocytic leukemia
t(15;17)
- Patients may go into DIC
72
What is the purpose of testing for Her-2 amplification?
Poor prognostic factor in invasive cancers, but also target for therapy (Trastuzumab)
73
t(8:14), t(8:22), or t(2:8)
Burkitt lymphoma - MYC is on 8
74
What type of tumor is associated with each translocation?
9: 22
8: 21
15: 17
11: 14
14: 18
8: 14
8: 22
2: 8
9: 22 - CML - BCR-ABL
8: 21 - AML
15: 17 - APML (Promyelocytic)
11: 14 - Mantle cell
14: 18 - Follicular
8: 14/8:22/2:8 - Burkitt (MYC)
75
Pleuroplumonary blastoma, pulmonary cysts, thyroid ca, ovarian ca, cystic nephroma
DICER 1
- also CNS sarcoma, pituitary, embryonal rhabdo
- Monitor w/ chest CT/CXR at birth and Thyroid/pelvic/abd US at age 8
76
Which populations have increased incidence of Tay Sachs?
Ashkenazi Jews, (1/30 carrier risk)
French Canadians,
Louisiana Cajuns,
Pennsylvania Amish
77
Which populations are at risk for HbH and Hydrops?
Southeast Asia and Mediterranean Basin - carreirs of a-globin deletions in cis
Hb H = 1 of 4 funcitonal a-globin genes
Hydrops = 0 of 4
78
High HbA2 and HbF
B thal trait
HbA2 = α2δ2
HbF=α2γ2
- Both use alternative proteins from B globin cluster
79
TPMT (thiopurine methyltransfarse)
Pharmacogenomic test for azathioprine toxicity -\> catalyzes methylation/inactivation of drug (prevents myelosuppression)
TPMT\*1 = wt
TPMT\*2, \*3A, \*3C homozygotes = hematopoetic toxicity -\> decrease dose to 10% of usual
80
What is the pathophys of FV Leiden and Protein C?
Factor V leiden - Arg506Gln = GOF - removal of preferred clevage site by protein C -\> reduced inactivation of activated FV -\> prothrombus formation
Proctein C = LOF - inability to cleave activated Factor V -\> prothrombus formation
81
What % of turner syndrome patients are mosaic?
25%
50% 45, X
25% structural abnormality involving X
25% Mosaic
82
What % of 45, X conceptions result in a livebirth?
\<1%
83
How is Turner Sydnrome managed?
GH until bone age 15
Estrogen after 15 to promote 2nd sexual characteristics
Progesterone to promote menses
TTE monitoring for root dilation (2/2 bicuspid AV)
Monitor for Diabetes and renal disease
84
Nucleotide excision repair
Xeroderma Pigmentosum
Photosensitivity, freckling, photophobia -\> premature skin again
- Actinic keraotsis + skin ca (melanoma, BCC, SCC)
+ ocular abnormlaities, neurodegeneration
(Also Trichothiodystrophy but no skin ca)
85
What are the 3 disorders of UV damage DNA repair
XP, Cockyne, and Trichothiodystrophy
XP, TTD = nucleotide excision, CS = transcription coupled repair
All three: thin skin w/ photosenstivity + neurodegeneration
XP = skin Ca
Cockayne = RP, deafness
TTD = brittle hair/nails, ichthyosis
86
What is the incidence of single gene disorders? prevalence?
Incidence 1:300 live borns
1:50 lifetime prevalence
87
How many genes are in the human genome?
~20,000 protein coding
~20,000 noncoding RNA
88
what are the componnents of the nucleo some complex?
4 core histones (H2A, H2B, H3, H4)
~140bp DNA
Histone H1 bind to DNA at edge of nucleosome in spacer region.
89
How much genetic variation is between 2 randomly selected individuals?
~0.5%
90
What is G0 in cell cycle?
Permanently arrested phase for cells that have stopped dividing. (neurons, RBCs)
91
What are the 5 phases of mitosis
Prophase - DNA condense, centromere form
Prometaphase - Nuc membrane dissolves
Metaphase - Chromosomes align
Anaphase - Separation
Telophase - Decondence/cytokinesis
92
When does crossing over occur?
Prophase 1 of meiosis
- Zygotene = homologous choromsomes align in "synapsis"
- Pachytene = meiotic crossing over
93
When is meiosis I compelted for Oocytes?
Just before ovulation (pause at metaphase II until fertilization
94
What enzymes initiates trancription at start site?
RNA polymerase II
95
What sequence specifies the location of polyadeenylation on 3' end of mRNA
AAUAAA
96
Which two amino acides are only specified by a single unique codon?
Met (AUG) - start codon - **establishes reading frame**
Trp (UGG) - UAA, UAG, and UGA are STOP codons
97
What are the stop codons?
UAG, UGA, UAA
98
What strand of DNA is used as the template for Transcription?
Noncoding/antisense in 3'-\>5' direction
## Footnote
**Sense/coding strand is identical to mRNA transcript but NOT used as template**
99
What is the TATA box
region rich in A and T ~25bp upstream of start codon ipmoratnt for initiation.
-CAT box further upstream
100
What are CpG islands?
CG rich areas found in promoter regions that are sites for methylation
101
What are enchancers, promotors, and locus control regaions?
Promoters: regulate transcription initiation for small distance upstream; **same orientation as gene, 5' UTR**
Enchancer: regulate from a distance (can be any orientation/location)
Locus control: regulate **chromatin context** needed for expression
102
What chemical reaction happens in dna methylation
Cytoseine -\> 5-methylcytosine
103
Which allele is XIST expressed in?
Only the inactivated X
104
What are the 2 classes of splicing mutations?
Mutations that interfere w/ normal RNA splicing (donor/acceptor site)
Mutations that creat alternative splice site
105
What is the mutation rate in a dominant gene?
affected cases/ (total births x2)
- x2 for both parent alleles
106
Average genome has ___ of de novo mutations? LOF variants? inactivated genes?
75 de novo, 200 LOF, 25 inactivated genes
107
What is the resolution of karytyping w/ banding?
~1 million bp
108
What is the most commonly used tissue for karyotyping? Why?
T lymphocytes
Accessible, can be culture and stimulated to divide, then arrested in metaphase
3-4 days
109
What is the incidence of chromosome abnormalities among livebirths? Stillbirths? Infant deaths?
Livebirths \<1%
Stillbirth, Infant death ~10%
110
What FISH probes are used to ID chromosome copy number?
α-satellite family of centromere repeats
111
What are the 5 acrocentric chromosomes?
13, 14, 15, 21, 22
112
What are 2 diadvantages to microarray?
1) VUS
2) does not reveal structure (ie translocation)
113
What kind of inversion is more likely to result in abnormal offspring?
Pericentric
114
What causes partial hydatidiform mole?
Triploidy with extra paternal chromosome set - abnormal degenerative placenta
115
Aneuploidy is seen in ___ % of recognized pregnancies?
5%
116
What is the most common autosome aneuploidy?
Trisomy 16
117
What is the most common aneuoploidy?
45 X
| (Trisomy 16 is second)
118
In a balanced translocation, what kind of segregation results in normal phenotypic offspring?
Alternate
119
What is the most common type of chromosome arrangement?
Robertsonian
rob(13;14)(q10;q10) and rob(14;21)(q10;q10) are first and second
120
What is i(X)q(10)
isochromosome X
Most common isochromosome, seen in Turner syndrome often
121
Which type of inversion involved in centromere
Per**_I_**centric -\> **_I_**ncludes the centromere
122
What causes terminal deletion and duplication within the same chromosome
Per**_I_**centric inversion
123
What is the most common abnormalitity in abortuses?
45, X
- 20% of chromosomally abnormal abortuses
\<1% chromosomally abnormal liveborns
Trisomy 16 is #2
124
What are the most common chromosomal abnormalities in liveborns?
1) Balanced rearrangement
2) extra sex chromosome (XXY, XYY, XXX)
3) trisomy 21
125
What are the most common chromosomal abnormalities in abortuses?
1) 45X
2) Trisomy 16
3) Trisomy 21
126
Who should you screen for aneurysms in ADPKD?
People with a positive family history (Aneurysms cluster in familites)
127
What is the most common mechanism for the second hit in RB1
Deletion or isodisomy
128
When is the high risk age for developing retinoblastoma in RB1
Until age 7
Most patients develope in first 3 years
129
What type of SRY variant is seen in 46XX males? 46XY females?
80% of 46XX males (translocation to X chromosome) - tx with androgens to complete virilization
30% of 46XY females (deletion/mutation - LOF) - tx with estrogen at 14, progesterone for periods, remove gonads to avoid gonadoblastoma
130
What do breakpoints of aneusomies (segmental duplicatons/deletions) cluster?
Low copy repeated sequences (aka segmental duplications)
131
Microcephaly, hypertelorism, epicanthal folds, low set ears, micrognathia, high pitched cry
Cri Du Chat
5p15 deletion syndrome
132
What are the 3 most common mechanisms of Prader Willi syndrome?
1) Pat 15p11 del - 70%
2) Mat UPD - 25%
3) Imprinting defect
133
What are the 5 most common mechanisms for Angelman syndrome?
1) Mat 15q11 deletion - 70%
2) UBE3A point mutation - 10%
3) Pat UPD - 7%
4) imprinting defect - 3%
5) Unknown - 10%
134
Which X chromosome is preferentially inactivated when a balanced translocation involving X is present? What about an unbalanced offspring?
Balanced: normal X preferentially inactivated -\> this allows for the other translocated part to be expressed.
Unbalanced: Normal X active
135
Which autosomal gene is the effector (up-regulated) by SRY?
SOX 9 (causes campomelic dysplasia)
136
What is the offspring prognosis for a male with an X-Y translocation involving SRY?
All children will have sex reveral:
XY offsping will look female (SRY deleted)
XX offspring will look male (SRY present)
137
Male with infertility, hypotonia, decreased bone density, low-normal IQ, androgen deficiency
Klinefelters
47 XXY
Many can look normal. ALWAYS infertile (germ cell does not develope)
138
What are the most common chromosomal abnormalites in oocytes and sperm?
Oocytes: aneuploidy (~20% of total)
Sperm: Sturctural rearrangement (~10% of total)
139
What is the most common error (stage of meiosis and parent) that leads to aneuploidies?
Maternal meiosis 1
140
Which anueploidy is usually a maternal meiosis II error
Trisomy 18
141
Which aneuoploidies are most likely to be due to paternal meiosis error?
XXY - 50% pat MI
X - 75% pat
XYY - 100% pat MII
142
What is the predominant mechanism of aneuoploidy in females?
Premature separation of sister chromatids (BEFORE anaphase) during M1
Males have more classic nondysjunction
143
What is the most common autosomal trisomy in a SAB?
Trisomy 16 (30% o f SABs)
25% of all SABs are due to autosomal aneuploidy
144
What are the most common karyotype findings in Down syndrome?
95% trisomy
4% Robertsonian translocation - t(14:21) usually
1% mosaic/structural rearrangements
145
What are the most common Karyotype findings in Edwards syndrome
97% maternal nondisjunction (usually **Meiosis II**)
146
What are the most common karyotype findings in Patau syndrome?
75% trisomy 13
20% robertsonian translocation - **der (13;14)**
5% mosaic
147
What is anaphase lag?
Failure of chromosome to attach to spindle or migrate to pole during meiosis -\> thus not included in nucleus of daughter cell
Mechanism of chromosomal mosciacism in addition to nondysjunction
148
Isochromosome 12p
Pallister Killian
isochromosome -\> tetrasomy 12 p
- Always mosaic (can be detected on amnio, but not always CVS)
- DD, seizures, high hairline, diaphgramatic hernia
149
Which Chorionic villus tissue is MOST likely to have save genetic makeup as fetus? (least likely to be confined moasicism)
- Cytotrophoblast
- Syncythiotrophoblast
- Mesenchymal core
Mesenchymal core (in cultured prep only)
150
What does finding confined placenta mosiacism mean for fetus?
- most like normal
- high risk for iUGR, pregnancy loss
- 2% risk for UPD
151
What do Chromosomes 6, 7, 11, 14, 15, 20 have in common?
Imprinted
152
What is the most common interpretation for trisomy 16 seen on CVS vs amnio
CVS - usually confined placental mosiacism
Amnio - usually fetus is mosiac
True trisomy 16 not viable
153
What is the most common chromosomal abnormalities in SABs
Monosomy X
154
Which 45X patients are at risk for gonadoblastoma?
When there is mosaic 46XY cells
155
What causes partial hydatiform mole?
Paternal triploidy (2 sperm, 1 egg)
- AFP, hCG elevated
- Hydropic villi + normal villi + small fetus
156
Maternal triploid fetus
Small placenta, small fetus with large head
- AFP, hCG low
157
What is the difference between maternal (digyny) and paternal (dispermy) triploidy?
Paternal -\> partial mole, large villi, small fetus, **high AFP, hCG**
Maternal -\> small plaenta, small fetus w/ **large head**, **low AFP, hCG**
158
What is the difference between partial and compelte hydatiform mole?
Partial = triploid w/ 2 paternal chromosome sets -\> large villi w/ **small fetus**
Complete = diploid w/ 2 paternal chromosome sets (**NO mat chromosomes**) -\> **NO fetus**
159
Which X chromosome will be nonrandomly inactived if a structually abnormal X is present?
abnormal X
160
Which X will be nonrandomly inactived if there is a balanced translocation?
normal X
161
Which X chromosome will be nonrandomly inactivated when there is an unbalanced tranlsocation involving X?
Abnormal X
162
Which X is usually missing in Turner syndrome?
paternal
163
What are the 3 more common karyotypes in Turner Syndrome?
45, X - 15%
46, X, i(Xq) - 15% - missing most PAR genes in Xp
45X/46,XX mosaic - 15%
164
Why is it important to look for marker chromosomes in Turner syndrome?
Marker Y -\> risk for gonadoblastoma
165
What are the most common robertsonian translocations?
t(13:14) - 75% - can cause patau syndrome if unbalanced
t (14:21) - 8%
166
What is a trivalent
3 aligned chromosomes due to a robertsonian translocation carrier
167
In a trivalent, which segregation leds to normal offspring?
Alternate
168
What is the difference between adjacent 1 and adjacent 2 segretation?
Adjacent 1 -\> chromosomes with **different centromeres** go together in daughter cell -\> more common
Adjacent 2 -\> chromosomes with **same centromere** go together in daugher cell -\> very rare
169
What segregation might produce offspring with down syndrome if a parent is a carrier for t(14:21)?
Adjacent 1 -\> different centromeres go together, more common and more likely to be viable
170
What are the clinical consequences of having a balanced X-autosome translocation?
Females: **decreased fertility** (oogenesis needs both X); may also lead to abnormal offspring due to skewed inactivtion in oogenesis
Male: almost always **infertile**
171
What is the most common isochromosome?
Xq (seen in turners) - NOT Xp because p is where most PAR genes are
172
What type of inversion is most likely to lead to abnormal offspring?
Pericentric -\> del and dup in terminal ends of same chromosome
173
Which type of inversion will almost always result in normal offspring?
Paracentric -\> recombinant version acentric or dicentric -\> not viable
174
How does size of inverion affect offspring risk in pericentric inversions?
Small inversions are not likely to cross over-\> low risk of viable abnormal offspring
**Large inversion** -\> more like to cross over AND del/dup are smaller -\> **more likely to have viable abnormal offspring**
175
What does ring chromosome look like on microarray?
if normal chromosome number: terminal deletions on both ends
If additional ring: partial trisomy in middle but not the ends of chromosome
176
Name the following syndromes:
5q35 del
7q11 del
15q11 del
17p11 del
17p12 del
17p12 dup
22q11 del
5q35 del - Sotos
7q11 del - Williams
15q11 del - PWS/Angelman
17p11 del - Smith Magenis
17p12 del - HNPP
17p12 dup - CMT type 1A
22q11 del - VCF/Digeorge
177
What is the mechanism for recurrent chromosomal rearrangements?
non-allelic homologous recombination in **low copy repeat** (LCR; aka **segmental duplications**)
178
What is the mechanism for non-recurrent structural chromosomal rearrangements?
Nonhomologous end joining
179
How many copies of each alleles are present in isodicentric chromosomes?
2x in most cases
180
When is there risk to fetus after a marker chromosome is found?
If parent is phenotypically normal, non-mosaic, and a carrier
181
idic(22)
Isodicentric 22 -\> if present patient has tetraploidy of ch 22
Cat eye syndrome: Iris coloboma, CHD, ear tags, anal atresia w/ normal intellect
182
what is r(20) associated with?
Ringed chromosome 20
- usually mosiac
May be fused at telomere so no loss of termianl DNA - need to do FISH/karyotype
-intractable epilepsy
183
What is a haplotype
A set of alleles at two or more neighboring loci on ONE of two homologous chromosomes
184
What is the difference between penetrance and expressivity
Penetrance is chance ANY phenotype is expressed
Expressivity is the severity of phenotype
185
Semidominant (incompete dominant) vs codominant
Semidominant: Homozygotes are more severely affected than heterozygotes
Codominant: both alleles expressed togehter in compound heterozygotes
186
What is the genetic risk of offpring of first cousin marriages?
3-5% (background 2-3%)
187
What is reprodutive fitness?
(# Offspring of affected individuals that survive to reproductive age)/(#Offspring of unaffected)
188
For X linked disorder with fitness of 0, what % of cases should be de-novo?
\<50%; since allele is partially protected from selection in female carriers
189
For an AD disorder with fitness of 0, what % of cases should be de novo?
100%
190
In HD, which parent is more likely to pass along an expanded allele?
Father
191
In Fragile X, which parent is more likely to pass along an expanded allele?
Mother
192
What is allelic heterogeneity?
Different **Mutations** (same gene) -\> same phenotype
193
What is locus heterogeneity?
**Different genes** -\> same phenotype
194
What is clinical/phenotypic heterogeneity?
same gene (different mutations) -\> **different phenotype**
195
What is the difference between allelic, locus, and clinical heterogeneity?
Allelic: **Different variants** (same gene) -\> same phenotype
Locus: **DIfferent genes** -\> same phenotype
Clinical/phenotypic: Same gene (different variants?) -\> **different phenotypes**
196
What is the relative risk ratio?
Measure of familiam aggregation
Lamda = prevalence in relatives of affected/prevalence if general population
197
What does a Heritabilty (H2) of 1 mean?
Heritability = fraction of phenotypic variance of quantitative trait due to allelic variance
1 means completely attributed to genetics
198
How is Heritability (H2)calculated?
Subtracting coefficient of correlation in dizygotic twins (50% IBD) from monozygotic twins (100% IBD) and multiplying by 2
199
What is the difference between ascertainment and recall bias?
Ascertainment bias = affected more likely to come to researcher's attention
Recall bia = affected more likely to be aware of disease than controls
200
Name 2 modifier genes for cystic fibrosis.
1) MBL2 - mannose binding lectin (binds pathogens) - lower levels -\> worse outcome
2) TGFB1 - cytokine transforming growth factor B (promotes scarring) -high level -\> worse outcomes
201
What is the most common gene seen in Hirschsprung?
RET
202
Which gender is at higher risk for dementia?
females
203
How does the APOE gene modify alzheimer risk?
3 alleles (E2, E3, E4)
Baseline risk 10% by age 80
If one E4 risk is 40% by age 80
If 2 E4 risk is 60% by age 80
204
Which chromosomes cannot be distinguished by centromeric FISH?
13, 14, 21, 22 -\> common robertsonian translocations; too similar sequences
205
What is the advantage of using FISH to test for aneuoploidy?
Fast - only 1-2 days vs weeks for CMA/karyotype
Often used prenatally
206
When would you want to do interphase instead of metaphase fish?
when looking for tandem duplications (easier to see when stuff is less condensed)
207
When would you use Dual-fusion FISH vs Break-apart FISH?
Dual fushion - when both translocation breakpoints are known
Breakapart- when looking at loci with multiple rearrangement partners
208
What are reasons to use FISH after a CMA
- confirm result with different modality
- Find locations of duplications
- Help find structural rearrangements
209
ΔCCR5 allele
Resistance to AIDS - CCR5 = cytokine receptor that in entry point for HIV. Deletion prevents expression
210
What are the Hardy Weinberg Assumptions?
- random mating
- large population
- no new mutation
- same fitness
- no migration
211
How is observed allele frequency calculated?
(2x homozygotes + 1x heterozygotes)/ Total possibilities
212
What is hardy weinberg for X- linked cases?
Males: p+q=1
Females p2+2pq + q2
213
What is stratification? How does it affect HW allele frequencies?
- non fandom mating where subgroups remain genetically separated (ie culture, religion, class, etc)
- It results in excess of homozygotes
- does NOT affect autosomal dominant disease frequencies
214
Which type of disorders are most affected by new mutations?
Dominant and X linked
215
What is fitness (*f*)
Likelihood of affected individual's offspring to survive to reproductive age
216
What is coefficient of selection? (s)
s = 1-f
f = fitness
217
Which type of disorder is LEASE susceptible to selection?
Autosomal recessive -\> since only homozygotes (usually small portion) are exposed to selective pressure
218
How are mutation rates, selection, and allele frequency related in autosomal dominant diseases?
allele frequency = mutation rate/selection
u=sq, q=u/s
Mutation rate must accound for all cases that are lose due to selection
219
How are mutation rates, selection, and allele frequency related in X linked diseases?
u=sq/3 (only 1/3rd of q is in males, the rest are in unaffected females at equilbirum)
## Footnote
**If s is 1 (fitness is 0) new mutation rate is 1/3q**
220
How do you tell if an allele is under selective pressure?
Compared observed allele frequencies to hardy weinberg frequences.
221
What gene protects against trypanosomiasis (t brucei) in heterozygotes but cause increased risk for FSGS (nephropathy) in homozygotes?
APOL1 (apolipoprotein 1)
222
What are AIMS (ancestry infromative markers)
alleles that show large differences in fequency among populations from different parts of the word -\> used to track migration
223
Whats the difference between CGH array and SNP array?
CGH: control + patient sample with oligos - you choose coverage
SNP: patient hybridize to 2 sets of SNPs representing alleles
Most CMAs now do both
224
What an SNP arrays detect that CGH arrays cannot?
Can get genotype information such as runs of homozygosity and triploidy
- But SNPs are not evenly distributed and you cannot control where they are
225
What are the advantages of microarray vs karyotype?
- higher resolution (5KB)
- does NOT need metaphase/culturable cells (useful in products of conceptrion)
- Can detect UPD (isodisomy)
226
What are the major limitations of CMA
- No structural infromation
- does not locate extra material
- cannot detect uniparenal heterodisomy
227
In CGH array, what does a log 2 ratio of infinity mean?
Nullizygous deletion (CN = 0)
228
In CGH array, what does a log 2 ratio of -1 mean?
heterozygous deletion (CN = 1)
Log2 of 1/2
229
In CGH array, what does a log 2 ratio of 0 mean?
normal
Log2 of 2
230
In CGH array, what does Log 2 ratio of 0.6 mean?
Duplication
Log2 of 3/2
231
In CGH array, what does a Log 2 ratio of 1 (or more) mean?
amplification
Log2 of \>4
232
What is the difference between SNP allele difference track and B allele frequency track?
Different ways to look at SNP array data
Allele difference: arbitrary flourescence of haploid locus set to 0 (AA = 1, AB = 0, BB = -1)
B frequency: arbitrary floursecence of haploid locus set to 0.5 (AA = 0, AB = 0.5, BB =1)
233
What is the output of the CGH array?
A Log2 ratio since it compares hybridization of patient vs control
234
What is the output of a SNP array?
Allele difference or B allele frequency tracts
235
What is the difference in output of a CGH array vs SNP array?
CGH = Log 2 ratio
SNP = Allele difference or B allele frequency track
236
What does duplication and deletion look like on SNP array?
Duplication: 4 combinations instead of 3
Deletion: 2 combination instead of 3
237
What is the difference between coefficient of consanguinity and coefficienct of inbreeding?
Coefficient of consanguinity = % genome shared between the parents
Coefficient of inbreeding = % homogyzous genome in offspring
**Parents are consanguinous, Offspring are inbred**
238
What percent of genome is expected to be IBD in offspring of a first cousin mating? What is the coefficient of inbreeding? What is the coefficient of consanguinity?
6.25% IBD
Co of Inbreeding = 1/16
Co of consanguinity = 1/8
239
If you see loss of heterozygosity on CMA, when should you think about UPD instead of inbreeding?
Think about UPD when:
- ROH (runs of homozygosity) is blocked (in inbreeding ROH are interspersed throughout genome)
- ROH is large - entire chromosome or arm
- ROH is terminal and \>10MB or interstitial \> 20MN
240
What should you do next if you see many ROH interspaced throughout genome in a CMA?
Likely inbreeding, look for AR disorders on exome
241
What should you do if you suspect UPD in a non-imprinted chromosome on CMA?
= exome for AR disorders
- karyotyping to rule out robertsonian translocation or isochromosome
242
What should you do if you suspect UPD in chromosomes 6, 7, 11, 14, 15, or 12?
These are chromosomes with imprinted regions
- MS-MLPA (methylation specific) can determing parental origin without parental samples
- Get trio data to determine parent of origin
243
What does triploidy look like on CGH and SNP array?
CGH array - normal (data gets normalized)
SNP array - 4 lines of probes instead of 3 (every locus has 3 possible combinations instead of 4)
244
According to ACOG, when should you use CMA
- Replace karyotype if there is an US abnormality
- karyotype OR array if there are no US abnormalities
- NOT age-related - can offer to anyone
- Recommend in POC, IUFD, or stillbirth
245
What features make CMA abnormalities more likely to be pathogenic?
- Del \> duplications
- Larger (\>1MB)
- gene density
- OMIM genes
- Evidence of dosage sensitivity
- De novo
246
What does this CMA depict?
Supernumery Ring 20
- Pericentromeric duplication
247
What does this CMA depict
Ring X (replaced normal X)
- Distal monozomy of pter and qter
248
What does this CMA show?
Unbalanced translocation
- Terminal gain and loss in **different** chromosomes
249
What does this CMA show?
recombinant chromosome from parental pericentric inversion
- Terminal gain/loss in the **same** chromosome
250
What is del(5)(p15.3)
Terminal deletion in p arm of ch5
251
What is del(13)(q21.3q33)
interstitial deletion in Ch 13
252
What is dup(15)(q11.2q13.1)
Interstitial duplication in Ch 15
253
What is inv(9)(p11q13)
Pericentric inversion in Ch 9
254
What is inv(9)(q11q13)
Paracentric inversion in Ch 9
255
What is 46,XX,t(11,22)(q23.3;q11.2)?
46,XX,t(11,22)(q23.3;q11.2)
**Balanced** translocation (**no Der**) between Ch 11 and 22. Breakpoint 11 at first locus, breakpoint 22 at second locus
256
What is 47,XY,+der(22)t(11;22)(q23.3;q11.2)
47,XY,+der(22)t(11;22)(q23.3;q11.2)
47 chromosomes, extra chromosome contains centromere of c22 -\> this extra chromosome is the result of a 11;22 translocation
- Remaining 22 and 11 assumed normal
257
What is 45,XY,der(13;14)(q10;q10)
45,XY,der(13;14)(q10;q10)
Robertsonian translocation - **balanced**
- derivative chromosome that is the result of 13:14 translocation where p arms are lost is present
258
What is 46,XY,+13,der(13;14)(q10;q10)
46,XY,+13,der(13;14)(q10;q10)
Robertsonian translocation - unbalanced
- EXTRA material from 13 is present; a derivative 13;14 is present
- Assume 2 normal ch13s in addition to derivative since extra material is from 13
259
What is ish 17p13.3(RP11-806J5x2)
ish 17p13.3(RP11-806J5x2)
ish = metaphase FISH
- probe RP11-806J5 which targets 17p13.3 was seen x2
- This is NORMAL result
260
What is nuc ish (RP11-806J5x2)
nuc ish (RP11-806J5x2)
Nuc ish = interphase FISH (done in nucleus, not during mitosiss)
- Proble RP11-806J5 was seen twice
- This is NORMAL FISH result
261
What is ish del(17)(p13.3)(RP11-806J5-).nuc ish(RP11-806J5x1)
ish del(17)(p13.3)(RP11-806J5-).nuc ish(RP11-806J5x1)
- On metaphase (ish) FISH probe RP11-806J5 (which targets 17p13.3) is missine one copy; this means there is a deletion
- On interphase (nuc ish) FISH the same probe is seen only once
- These results are concordant and both point to missing genetic material at that locus
262
What is ish t(X;16)(q28;q12.1)(RP11-811K14-,RP11-368M4+; RP11-368M4-,RP11-811K14+)
ish t(X;16)(q28;q12.1)(RP11-811K14-,RP11-368M4+; RP11-368M4-,RP11-811K14+)
- Metaphase FISH
- Translocation of X and 16 detected
- RP11-811K14 probe which targets Xq28 is missing on copy in chX and gained one copy in ch16
- RP11-368M4 probe which targets 16q12.1 gained a copy in chX and is missing a copy in ch16
263
What is nuc ish(ABL,BCR)x2
nuc ish(ABL,BCR)x2
On interphase (nuc ish) FISH both ABL and BCR probes were seen twice
- this is a normal result
264
What is nuc ish(ABL,BCR)x2(ABL con BCRx1)
nuc ish(ABL,BCR)x2(ABL con BCRx1)
On Interphase FISH both BCR and ABL are each seen twice, a ABL connected to BCR is seen once
- This represents a BCR/ABL fushion found using a **dual-fusion** probe
265
What is nuc ish (p1,p2)x2(p1 sep p2x1)
nuc ish (p1,p2)x2(p1 sep p2x1)
Interphase FISH saw each of two probes seen twice. One P1 probe was separated from one P2 probe
- This represents a translocation found using a **break apart** probe
266
arr(X,Y)x1,(1-22)x2
arr(X,Y)x1,(1-22)x2
Normal Male
267
arr(X)x2,(Y)x1
arr(X)x2,(Y)x1
XXY -\> klinefelters found on CMA
268
arr(X)x2,(Y)x1,(1-22)x3
arr(X)x2,(Y)x1,(1-22)x3
Triploidy seen on CMA
269
arr[GRCh37]17p13.3(6160\_2054122)x1
arr[GRCh37]17p13.3(6160\_2054122)**x1**
CMA using genomce ref 37 showing deletion of 17p13.3
270
arr[GRCh37] 8p23.3p23.1(190822\_6735381)x1,8p23.1p11.21(12580131\_40802481)x3
arr[GRCh37] 8p23.3p23.1(190822\_6735381)**x1**,8p23.1p11.21(12580131\_40802481)**x3**
Array using ref genome 37 whoing both a deletion and duplication on ch8
271
arr[GRCh37] Yp11.32p11.2(100002\_10045809)x2,20q13.3(62328478\_62907526)x1
arr[GRCh37] Yp**11.32p11.2**(100002\_10045809)**x2**,20q13.3(62328478\_62907526)**x1**
- CMA using ref genome 37 showing interstitial (2 breakpoints) duplication in Y and terminal deletion in ch20
272
arr[GRCh37]13q11q34(19438806\_115095705)x2 hmz
arr[GRCh37]13q11q34(19438806\_115095705)x2 **hmz**
CMA using ref genome 37 showing homozygosity for segment of chromosome 13
273
rsa(X,Y)x1,(13,18,21)x2
rsa(X,Y)x1,(13,18,21)x2
**Region specific assay** showing normal results
274
seq[GRCh38] der(2)t(2;11)(p25.1;p15.2) NC\_000002.12:g.pter\_8247756delins[NC\_000011.10:g.pter\_15825272]
seq[GRCh38] der(2)t(2;11)(p25.1;p15.2) NC\_000002.12:g.pter\_8247756delins[NC\_000011.10:g.pter\_15825272]
Sequencing using ref genome 38 showed translocation between ch 2 and 11 with der2 sequence change in terminal P
- Delins = deletion then insertion = sequence change
275
What is the difference bewteen a parentl and nonparental gamete?
Parental gametes have the same combination of alleles of interest as one of the parents.
276
What does syntenic genes mean?
Genes that reside in the same chromosome (regardless of how far apart they are)
277
What conditions must be met in order to detect recombination events for linkage analyss?
1) A parent must be heterozygous
2) Phase of alelles must be known
278
What is recombination frequency?
θ = frequency of recombination/total
It is between 0 (no recombination) and 0.5 (independent assortment)
θ of 0.01 = 1 centimorgan
279
What is linkage disequilibirum? How is it calculated
Linkage disequilibrium is deveiation from predicted haplotypes based on allele frequencies
LD = freq of parental haplotypes - freq of recombinant haplotypes
If parental haplotypes are AS and as
LD = freq (AS)x Freq (as) - freq(As)xfreq(aS)
LD = 0 = alleles in linkage **equilibrium**
280
What determines the staying power of a new disease haplotype?
1) # of generations
2) Frequencing of recombination (θ) between disease and haplotype
3) Selection against the phenotype
281
What information do you need to perform linkage analysis in a family?
1) Recombination frequency (θ)
2) whether θ is significantly lower than 0.5 (expected for unliked loci)
- Result = LOD score (logarithm of the ODds)
282
What is the difference between a case control, cross sectional, and cohort study?
Case control: individuals with disease vs individuals without disease are compared; **best for super rare diseases where pop studies unlikely to find enough cases** -\> Odds ratio
Cross secton: Random sample of entire population analyzed for those with and without disease -\> Relative risk
Cohort: Random sample of entire population followed over time to see who gets disease -\> relative risk
283
What is the difference between Odds Ratio and Relative Risk
OR is for case-control studies: Odds of a carrier developing disease vs odds of a non-carrier developing disease
OR = (a/b)/(c/d) = ad/bc
RR is for cross-sectional or cohort studies: Ratio of proportion of those with disease to carry an allele vs those without
RR = (a/(a+b))/(c/c+d)
284
How does population stratification affect GWAS results?
Artifactual positive results since AIMs from a subpopulation with increased disease incidence will show up as associated to phenotype
285
Arg506Gln Factor V
Factor V leiden
- Resistance to protein C cleavage -\> continued activating prothrombin (FX)
286
What is Hb Kempsey?
B chain :Asp99Asn
β-globin allele that maintains the hemoglobin in a high oxygen affinity structure -\> causes polycythemia due to decreased peripheral O2
287
What is Hb A?
Normal adult Hemoglobin
α2β2
288
What is Hb F?
Fetal Hemoglobin
Hb F (α2γ2), the predominant hemoglobin throughout fetal life
- Expression decreases after birth to \<10% after 3 months
289
What is the LCR for B globin?
Locus control region -\> regulatory domain upstream of B-globin gene cluster that associates w/ binding proteins for form Active Chromatin hub and regulates B-globin gene expression
- Deleation of LCT = no B globin cluster expression
290
When does B thal become clinically apparent?
usually after 3 months -\> HbF drops off after birth.
(a-thal can have prenatal manifestations)
291
What is Hb E?
B chain: Glu26Lys
Abnormal Hb and decrased synthesis (abnormal splicing) -\> mild thalaseemia
- most common structually abnormal Hb in the world -\> **common in southeast Asia**
292
What is Hb Hyde Park?
B chain: His92Tyr
Hb resistant to methemoglobin reductase -\> cannot carry O2 -\> cyanosis
293
What is Hb Hammersmith?
B chain Phe425Ser
Unstable Hb -\> **hemolysis**/low O2 affinity
294
What is the strongest modifier for Sickle Cell Disease?
Hb F levels
- BCL11A and MYB (transcrption factors) and the γ-globin gene contribute to HbF levels
- BCL11A and MYB are therapeutic targets
295
What are Hb Bart?
Hb Bart = γ4 tetramer
Seen when all 4 a-globin genes are missing -\> Hydrops fetalis - gamma Hb (fetal) form tetramers
296
What is Hb H?
β4 tetramer seen in alpha Thal when only 1 of 4 a-globin genes is present
- moderate/severe hemolytic anemia
297
a-thal + Intellectual disability
ATR-X syndrome
- Alpha-that retardation syndrome
- X linked ATRX gene encodes chromatin remodeling protein that activates α-globin genes in trans; when missing macro H2A histones accumulate and prevent transcription
298
What is the modifier for B thalasemia?
alpha-Thal
- Unbound a-globin is toxic, so if alpha chains are also missing phenotype is milder
299
What kinds of mutations cause B-thal?
Anything that leads to decreased expression
1) Splicing (destroy splice site, cryptic splice site, intronic new splice site) - may be synonymous
2) Nonsense -\> leads to nonsense mediated decay if \>50bp upstream of final exon-exon junction
3) Frameshift.- nonfunctional product
4) PolyA tail variants -\> decaps in capping
300
short stature, macrocephaly, chronic otitis media, rhizomelia, metaphyseal dysplasia, **small sacrosciatic notches,** short broad cone-shaped proximal and middle phalanges
Achondroplasia
FGFR3 Gly380Arg
- main worry is small foramen magnum -\> cervical compression +central sleep apnea
301
Short stature, cleft palate, hearing loss, myopia, odontoid hypoplasia
- No pubic bone ossification
Spondyloepiphyseal dysplasia
Collage type II spectrum (more severe and stickler)
COLII, IX, Xi
302
Normal birth -\> rhizomelia, genu valgus AND varus (windswept), small irregular epiphysis, flat beaked vertebral, **arthritis**
Pseudochondroplasia
COMP (AD)
303
Short stature, club foot, hithhiker thumb, cauliflower ear, short braod fingers w/ ulner deviation
Diastrophic dysplasia
SLC26A2 (sulfate transporter)
304
Devits in distal long bones
Loose teeth early and **w/ root**
High urine phosphoethanolamine, pyrophosphate, and pyridoxal 5- phosphate (B6)
Hypophosphatasia
TNSALP - tissue nonspecific alkaline phosphatase
Adult w/ alk phos \<40
- **ERT Asfotase Alfa**
**- avoid bisphosphonates**
305
Dysgerminoma
Craniosynostosis, polysyndactyly of hands and feet (mitten hands), fused cervical vertebral
Apert syndrome
FGFR2 (AD)
306
Craniosynostosis, normal IQ/hands/feet
+ Proptosis, prognathism, beaked nose
Couzon syndrome
FGFR2 (AD de novo)
FGFR3 if acanthosis nigricans present
307
Craniosynostosis, fused calcaneocuboid bones, borad great toes, 2/3 toe syndactyly
Jackson-Weiss
FGFR2, amish
- think foot anomalies - fused calcaneocuboid bones, borad great toes, 2/3 toe syndactyly
308
craniosynostosis, carpal-tarsal fushion, heaing loss
Muenke
FGFR3 Pro250Arg - AD **w/ variable expressivity**
309
Craniosynostosis, broad thumbs/toes, proptosis
Pfeiffer
FGFR2 (95%)
FGFR1 (5%)
- may have cloverleaf skull
310
craniosynostosis, radioulnar synostosis, virilization (fetus AND pregnant mother)
Antley-bixler
POR (Cytochrome P450 Reductase)
311
Craniosynostosis, 2/3 syndactyly, duplicated great toe, radioulnar synostosis, pointed chin
Saethre-Chotzen
TWIST1 (downstream transcription factor to FGFR1, 2 and 3) -\> upstream of RUNX2 (cleidocranio)
312
How does **IFNGR2** missense variants cause mendelian susceptibility to mycobacterial disease?
Creates novel N-glycosylation site on interferon-gamma receptor 2 -\> loss of protin function due to **excess glycosylation**
313
What is the mechanism of disease in α1AT deficiency?
SERPINA1 = protease inhibitor
Novel property (aggregation) -\> trapping in rough ER of hepatocytes -\> Liver disease
Inability to get to lungs -\> deficiency of protease activity -\> lack of elastase inhibition -\> COPD
314
Xanthona, Arcus cornea, hypercholetersolemia, early MI
Name 3 genetic causes
Familial Hypercholesterolemia
LDLR = incomplete dominant.- 300 in hets, 600 in homo
ApoB100 (AR) - binds cholesterol ester (forms ligand for LDLR)
PCSK9 superactivity (AD) - targets LDLR for degradation
\*PCSK 9 LOF is protective
315
How does ΔF508 affect CFTR?
Misfolded protein cannot leave ER -\> never makes it to cell surface
316
Aside from CFTR, what gene can lead to high sweat chloride, lung infections, and intestinal disease?
SCNN1 -\> epithelial Na channel
- non-classic CF phenocopy
317
How do variants in TGFβ1, IL8, and IFRD1 affect CF?
They modify severity of lung disease.
Increased TGFB1 expression -\> more severe inflammatory response
318
Which phenotype in CF correlated w/ genotype?
pancreatic function
319
Which types of mutations in COL type 1 cause the worst disease?
- missense that replace glycine residue \> deletion (difficult to assemble chain)
- COL1A1 \> COL1A2 -\> 2 copies of a1 chain, only 1 copy of a2 chain; thus more likely to incorporate at least one abnormal a1 chain (3/4) into assembly
- carboxyl end glycine -\> start of assembly slowed, distal end can get extra-modified post-translationally and be harder to secrete
320
Name 3 genes that cause AD Alzheimer's
PSEN1, PSEN2, APP
- PSEN1 and 2 help drive cleavage of beta amyloid precursor protein into Aβ40 (non-toxic) rather than Aβ42 (aggregates)
- APP is on chromosome 21
321
homoplasmic substitution of 1178A.G in ND4 subunit of complex 1
Leber's hereditary optic neuropathy
Incomplete penetrance -\> affects 50% males and 10% females
322
Heteroplasmic MtATP6 mutations
Leigh syndrome
Neurodegeneration, DD, optic atrophy, respitaroy abnormalities
323
Heteroplasmic tRNAleu (3243A\>G)
MELAS
**- Diabetes, deafness**
- Myopathy, encephalopathy, lactic acidosis, stroke like episodes
- May also cause CPEO
324
Heteroplasmic tRNAlys (8344A\>G)
MERRF
myoclonic epilepsy, RR ribers, myopathy, ataxia, SNHL, dementia
325
homoplasmic mutations in 12S rRNA
Hearing loss induced by aminoglycosides
nonsyndromic hearing loss
326
Large sporadic heteroplasmic 5mb deletion
Kearns-Sayre
myopathy, external ophthalmoplegia, cardiomyopathy, ptosis, RP, ataxia, diabetes
327
What is the mechanism of mitochondrial depletion syndrome?
Reduction in number of copies of mtDNA both per mitochondria and per cell due to inability to maintain nucleotide pools/metabolize nucleotides in mitochondria
328
Where is fragile X repeat expansion?
What is the mechanism of disease?
CGG in 5'UTR
- transcription silencing
329
Where is Frataxin repeat expansion? what is the disease mechanism?
GAA in intron
- impaired transcription elongation
330
Where is Huntingons repeat expansion? what is the disease mechanism?
CAG in exon
- novel **protein** property
331
Where is myotonic dystrophy type I repeat expansion? what is the disease mechanism?
What about DM2?
CTG in 3' UTR of DMPK
- novel RNA property
DM2 = CCTG in intron of ZNF9 -\> also novel RNA property
332
Compare mechanisms of fragile X syndrome vs FXTAS
**Trasncription silencing:** 200+ repeats -\> methylation -\> no FMRP protein expression
**Toxic GOF**: 60-200 repeat -\> increased FMRP RNA transcripts -\> intranuclear neuronal inclusions
333
Name the following head shapes. Which one most likely syndromic?
Coronal most likely syndromic
334
What happens to patients with GALT and PKU deficiency long term treated with diet?
GALT and PKU: learning disability
GALT -\> ovarian faiure in females
335
What is the mechanism of acter for lumacaftor? Ivacaftor?
Lumacaftor: Chaperone for CF: Stabalizes 3D structure of mutant ΔF508 CFTR -\> normalizes trafficking
Ivacaftor: Enhances Cl transport through mutatnt CFTR
- Use in combo for ΔF508
- Use Ivacaftor for Gly551Asp
336
Half of homocystrinura patients respond to this supplement
Pyridoxine (B6)
337
What is danazol used to treat?
Hereditary Angioedema
C1 esterase inhibitor deficiency
- Danazol increases expression of C1 Esterase inhibitor by modulating transcription
338
How does decitabine help treat sickle cell disease or Beta Thal?
It is incorporated into DNA instead of cytidine -\> inhibits methylation of the CpG island in promotor region of γ-globin -\> incread HbF expression
339
What is an episome?
Stable nuclear but non chromosomal DNA molecule
- ie formed by AAV vector for gene therapy
- useful in target cells that are long-lived so expression can be long term
340
What makes lentivirus a good vector for gene therapy?
It is a **retrovirus** that **integrate into non-dividing cells** and does not show preferential integration (less likely to activate oncogene)
341
What traits allow AAV to be good gene therapy vector?
- can form stable episode
- Does **not** elicit strong immune response (safer than adeno-derived viruses)
342
When is intertional mutagenesis in gene therapy a problem?
- activate proto-onco gene
- Inactive tumor suppressor
- Inactivate an essential gene in germline (not likely to affect enough somatic cells to affect patient, but may create germline mosaicism
343
How did the first gene therapy for SCID work?
XL SCID - IL2RG -\> **γc-cytokine receptor** subunit of several interleukin receptors
Retroviral vector used to infect ex-vivo bone marrow stem cells -\> expressed the γc cytokine subunit cDNA
- must monitor for leukemia due to insertional mutagenesis
344
What is a malformation?
Intrinsic abnormality in genetic program -\> abnormal phenotype
345
What is a deformation?
extrinsic factor -\> abnormal physical phenotype
346
Malformation vs deformation
Malformation = problem w/ intrinsic developmental programming
Deformation = problem caused by extrinsic factors
347
What is a disruption?
birth defect resulting from **destruction** of irreplaceable tissue
348
Deformation vs disruption
Deformation - abnormality caused by extinsic factors physically affecting fetal development
Disruption: Destruption of irreplaceable fetal tissue
349
syndrome vs sequence
syndrome: multiple abnormalities caused in parallel by an underlying insult
Sequence: multiple abnormalities secondary to an initial single system abnormality
350
Homologous structurs vs analagous structures
Homolog = same function due to common ancestor
Analog = same function that evolved in parallel
351
When does the inner cell mass rearrange into three germ layers?
Gastrulation - the most important day of your life - week 3 of embryogenesis
352
What tissues arise form each germ layer?
Endoderm - gut cavity, airways, rep (visceral)
Mesoderm - solid organs + vasculature + MSK
Ectoderm - Nervous system and skin
353
What is regulative development?
Removal of a part of an embryo result in compensation from other similar cells (prominent in early embryogenesis)
354
When does cleavage have to occur to lead to dichorionic, monochorionic, and monoamniotic monozygotic twins?
Dichorionic - 4 cell stage
monochorionic - inner cell mass
monoamniotic - later
Later embryo -\> conjoined
355
What does CREB binding protein do?
- CREBB (Rubenstein Taybi) is a transcriptional activator for GLI3 (Pallister hall and greig cephalopolysyndactyly)
- GLI3 and PTCH1 (Gorlin) are part of SHH pathway (holoprosencephaly)
356
What is an oncomir?
noncoding miRNA that impract gene expression and contribude to oncogenesis
357
What is a proto-oncogene?
normal gene that when mutated to **increase activity** level become drive genes for cancer
activated proto-oncogene = activated oncogene
358
What is a tumor suppressor gene?
genes in which loss of expression -\> cancer
359
What does the RET gene do?
cell surface protein w/ extracellular binding domain and cytoplasmic tyrosine kinase.
- GOF -\> MEN2A
- LOF and GOF -\> Hirshsprung
360
What is the most common second hit in RB?
Loss of heterozygosity
- can occur by interstitial deletion of normal RB, mitotic recombination, or monosomy 13 due to nondysjunction
361
Breast, Ovarian, male breast, prostate, and pancreatic cancer
BRCA1 or 2 (double stranded DNA break repair)
- risk for most cancer higher in BRCA1 **except male breast and pancreas**
362
What is the lifetime risk of colon, endometrial, and ovarian/biliary/urinary tract ca in lynch syndrome?
Colon: 80%
Endometrial: 40%
Biliary/urinary/ovary: 20%
363
What does imatinib do?
Inhibit BCR-ABL (philadelphia chromosome 9:22) tyrosine kinase activity
- treat CML
364
Which proto-oncogene is activated in burkitt lymphoma?
MYC (ch 8, many translocation partners)
- Burkitt = B cell lymphoma
365
Which proto-oncogene is amplified in neuroblastoma?
MYCN
366
What environmental agent causes a G249T mutation in TP53?
**Aflatoxin** (From peanut mold) -\> causes **heptaocellular carcinoma**
367
How does aryl hydrocarbon hydroxylase (AHH) modify smoking risk?
Aryl Hydrocarbon Hydroxylase (CYP1A1 gene) is induced by smoke -\> increased cancer risk
- CYP2D6 alleles are protective
368
What is the probability of a random female in the population is a carrier for a lethal X-linked disorder?
4µ
- Calculated from bayes
369
When can amnio be performed?
16th - 20th week (just before halfway point)
370
What are possibel causes of high AFP?
NTD
fetal blood contamination
Twin pregnancy
Fetal death
Ventral wall defects
Overestimated gestational age
371
When can CVS be performed?
10-13 weeks (end of first trimester)
372
Which three prenatal ultrasound findings in isolation are most likely associated with abnormal karyotype?
Cystic hydroma, duodenal atresia, nuchal edema
373
How early can US determine fetal sex?
13 weeks (Start of 2nd trimester)
374
When are 1st and 2nd trimester screens done?
12 weeks and 16 weeks
375
What does extremely low levels of estriol mean in quad screen?
SLOS or steroid sulfatase deficiency
376
Triple screen: High nuchal translucency, low PAPP-A, high B-hcg
Trisomy 21
high hcg = trisomy 21
377
Triple screen: High nuchal translucency, low PAPP-A, low B-hcg
Trisomy 13 or 18
378
Quad screen: Low uE3, low AFP, high hCG, high inhibin
Trisomy 21
high hcg = trisomy 21
379
Quad screen: Low uE3, low AFP, low hCG, nl inhibin
Trisomy 13 or 18
380
What is the first line test after prenatal US detects an anomaly?
CMA (not karyotyping)
- All women having invasive testing should be given option for CMA (regardless of US findings)
381
What are the 3 levels of mosiacism in amniotic fluid or CVS cell cultures?
1) multiple colonies from **different primary cultures** -\> true mulsaicism
2) mosiacism involving several cells or colonies from a **single primary culture** -\> usually pseudomosiacism, but report if unable to confirm this through other testing
3) mosiacism only in **a single cell** - pseudomosaicism, disregard
382
What is the detection rate for fetal 10% mosiacism on CMA?
Unreliable when 10 cells are examing, 99% when 50 cells examined
Segmental mosiacism \<20% is difficult to detect
383
Compare analytical validity, clinical validity, and clinical utility?
analytical validity - is a rapid/economic test available
clinical validity - is the test senstitive/specific? What is PPV?
clinical utility - Is knowing the test result helpful? (affect outsomes)
384
How are most metabolic diseases screening for on NBS?
Tandem mass spec
385
What is the difference between pharmacokinetics and pharmacodynamics?
Pharmacokinetics - **rate** at which body absorbs/transports/metabolize/excretes drug
Pharmacodyamics - **how** body responds to drug
386
What gene converst codeine to morphine (active form)
CYP2D6 - predicts pharmacogenomic response
387
What does HLA B\*5701 and HLA B\*1502 predict?
SJS/TEN risk after drug exposure
HLA B\*5701 - abacavir (5% europeans)
HLA B\*1502 - carbamazepine, (10% SE Asians)
388
Compare strength's/weaknesses of cohort, cross sectional, and case control studies
Cohort - most accurate and complete, but expensive and time consuming (phenotype may take long time to compare, rare diseases take lots of subjects) - RR
Cross-sectional - underestimate disease prevalence (Some affected have died or are pre-symptomatic) - RR
Case-control - cannot detect population prevalence - OR
389
What is the difference between Odds Ratio and Relative Risk?
Odds ratio = (A/B) / (C/D) = AD/CB - use in case-control studies (no population data available)
relative risk = (A/(A+B))/(C/(C+D)) - use in cohort or cross section studies (when pop data is available)
390
in what situation does GINA apply?
Genetic info cannot be used:
- Company of **15 or more employees** cannot make employmend decision
- Health insurance
391
What is reproductive compensation
Prenatal diagnosis and termination means couples that are carriers for recessive conditions will have more carrier children than they otherwise would -\> increase allele frequency for recessive conditions
392
What should you check for before starting abacavir therapy?
HLB\*5701 status
50% PPV for SJS/TEN
100% NPV for SJS/TEN
393
HLA B\*1502
HLA B\*5701
HLA B\*5801
What drugs do these antigens interact with?
HLA B\*1502 - Carbamazepine
HLA B\*5701 - Abacavir
HLA B\*5801 - Allopurinol
- SJS/TEN
394
What does FGFR3 do?
Transmembrane tyrosine kinase receptor that binds fib fibroblast growth factors
RUNX2 = master downstream effector (Cleidocranial dysplasia)
395
What does Tyr402His in CFH do?
What about CFB and C2?
RIsk for age-related macular degeneration
CFH (complement factor H) Y402H = polymorphic variant -\> increase risk
CFB (complement factor B) p.L9H and C2 (complement component 2) p.E308D = protective
396
When and why do patients with down syndrome get Alzheimer's?
By age 40
βAPP gene is on chromosome 21
397
16p11.2 microdeletion syndrome
Susceptibility to ID/DD/ASD
- increase risk for obesity, epilepsy, midor dysmoprhic features
- Reciprocal 16p11.2 duplication -\> schizophrenia risk
**- Low Copy Repeats** = mechanism of recurrent del/dups
398
What phenotypes does LOF in CDKN1C and IGF2 cause?
CDKN1C (Normally maternally expressed, suppresed by paternal KCNQOT1) -\> represses growth -\> mutations -\> BWS
IGF2 (normally paternally expressed, suppressed by maternal H19) -\> promote growth -\> mutations -\> RSS
399
Which cancers are more common in BRCA2 than BRCA1?
male breast, pancreatic
400
What does 17p12 Duplicaton cause?
CMT1A
- PMP22 is in 17p12
401
Name the major phenotypic features of chromodomain Helicase DNA-binding protein 7 haploinsufficiency
CHD7 = CHARGE
**C**oloboma of the iris, retina, optic disc, or optic nerve
**H**eart defects
**A**tresia of the choanae
**R**etardation of growth and development
**G**enital abnormalities
**E**ar anomalies
Facial palsy
Cleft lip
Tracheoesophageal fistula
402
der(22)t(9;22)(q34;q11.2)
Philadelphia chromosome in CML
ABL = tyrosine kinase invovled in cell cycle, stress response, integrin signaling, and neural development
BCR = phophoprotein
BCR-ABL -\> Constitutive activation
403
Variants in what gene increase risk for Crohn's?
NOD2 (aka CARD15)
- binds to gram negative bacterial cell walls -\> activated NF-κB - regulates inflammatory response in monocytes of intestinal cell wall to gut bacteria
- Risk from baseline \<0.1% to 2% in homozygotes
404
chronic respiratory illness, meconeum ileus, FTT, decreased pancreatic function, azoospermia, pulmonary HTN
Cystic fibrosis
CFTR
405
What is the mode of inheritance for hearing loss in GJB2?
GJB2 = connexin 26
- LOF/frameshift -\> AR (majority)
- 35delG in Caucasians
- 235delC in Chinese
Rare missense mutations can cause dominant hearing loss
406
How does duchennes affect IQ?
average IQ is 1SD below mean
407
What are the rates of de novo and germline mosiacism in DMD?
De- novo ~30%
Germline mosiacism ~15%
408
Congenital hypertrophy of the retinal pigmented epithelium is associated with what gene?
APC - regulates transcription, cell adhesion, microtubules, cell migration, apoptosis, and proliferation
- APC LOF -\> increased free β-catenin -\> inappropriate gene activation
Disease:
- FAP (100+ polyps)
- Gardner (polyps, osteoma, soft tissue tumors)
- Turcot (Polyps, medulloblastoma)
409
What is attenuated FAP and what gene should you look for?
Attenuated FAP = \<100 polyps
- If no germline **APC** change found, look for **MYH mutations (recessive FAP2)**
410
Polyarthritis, tenosynovitis, arcus cornea, xanthoma, coronary artery disease
Familial hypercholesterolemia
LDLR, ApoB100, PCSK9 (GOF -\> increased degradation of LDLR)
- LDLR most common, incomplete dominant (2 hits = present 1st decade of life, LDL levels \>600)
411
Fragile X accounts for _ % of ID in boys?
3-6%
412
What is the fragile X premutation?
5' UTR CGG repeat expansion in FMR1
59-200 repeats -\> causes ovarian failure/tremor-ataxia syndrome -\> can expand (especially during **maternal transmission**) into full
413
What is correlated with abnormal genetic testing results in cases of male infertility?
Decreased sperm count -\> increased chance of abnormal genetic test (up to 25% in azoospermia)
414
What are the most common genetic causes for male infertility?
1) 47 XXY (Klinefelters) - Testicular atrophy/fibrosis
2) AZF insufficiency - structural abnormalities (SRY translocation, Y microdeletion, etc)
3) CBAVD (CFTR), Kallman, androgen insensitivity, congenital adrenal hypoplasia (NROB1, aka DAX1)
415
Which genetic anomaly should you not do testicular sperm extration on?
AZFa or AZFb mutations -\> zero chance of sperm recovery
416
What is the most common cause of non obstruction azoospermia?
Klinefelter syndrome
47 XXY
- low testosterone (Decreased Leydig cell funciton) -\> low sperm count
417
CFTR -\> IVS8 5T + F508Del
5T in IVS8 affects splicing of exon 9
- Associated with CBAVD when in trans with classic variant
418
What gene should you test for in CBAVD if CFTR is normal?
ADGRG2
XL CBAVD
accounts for 20% of CBAVD (CFTR is most common)
419
What is the only viable monosomy?
45X
- risk unrelated to pat or mat age
- 80% **paternal nondysjunction**
420
What is the risk of a trisomy 21 fetus when mother is 35?
1:353
421
Where do cfDNA come from?
apoptotic placental trophoblast cells
422
What factors can alter cfDNA levels?
Gestational age (increase)
high maternal BMI (decrease - more maternal apoptosis, dilutes fetal DNA)
Anueoploidy (decrease)
Twin pregnancy (decrease)
423
What is the next step after abnormal NIPT?
Diagnostic testing -\> amnio (preferred) or CVS
424
4 reasons for false positive NIPT
1) Vanishing twin
2) maternal sex-chromosome aneuploidy (undiagnosed mom)
3) maternal cancer
4) placental mosaicism
425
What is the phenotype of confined placental mosiacism?
IUGR (placental unhealthy)
426
Why might NIPT be false negative?
Mosaicism with normal placenta and abnormal fetus
427
Reasons for "no-call" NIPT? What do you do next?
- low fetal fraction (\<4%)
- eatly gestation
- high maternal BMI
- **Aneuploidy**
- if no call -\> get diagnostic testing because aneuoploidy may be reason
428
What % of embryos is aneuploid at maternal age 38?
50/50
429
When is embryo biopsied for pre-implanataion diagnosis?
5 days -\> 5 cells taken
430
Who should be offered preimplantation genetic testing?
- women \>35 years
- History of multiple miscarriages or implantation failure
- hig hrisk for single gene disorder
431
What is allele dropout?
When one allele is preferentially amplicied in PCR such that end result falsely showed homozygosity/deletion
- Common issue in preimplantation genetic testing due to low amount of starting DNA
432
What is PGT-A?
Preimplantation genetic testing - **A**neuploidy
AKA PGS - Preimplantation genetic **S**creening
- offer to all IVF patients, standard protocol
433
What is PGT-M
Preimplantation genetic testing - **M**onogenic
AKA PGD - preimplantation genetic **D**iagnosis
Offer to high-risk couples
- Requires personalized test/probes
- Allele dropout is a problem -\> false positives
434
What genetic changes are most common in IVF created embryos?
- Chromosomal mosiacism.- may be technique/lab issues (cells damanged during processing) - **do not transfer viable aneuoploidy**
- imprinting defects
435
Why should PGT not be offered for mitochondrial mutations?
Heteroplasmy -\> results at 5 cell stage does to predict phenotype because heteroplasmy levels vary with each cell division, so future levels will be different/tissue specific
436
What percent of Beckwith Wiedemann Cases are caused by UPD in general? IVF?
BWS
General: 50% maternal imprinting defect
IVF: 90% maternal imprinting defect
437
Angiofibroma + seizures
TSC
Tuberin and Hamartin
+ Heart/Renal/Lung neoplasms
438
What do you see in ARPKD that's not present in ADPKD?
LIver fibrosis
- Hepatic (and other) cysts present in ADPKD
439
Important gene in 22q11 deletion region
TBX1
440
periorbital edema, stellate irises, hypercalcemia, hypercalciuria
Williams
7q11. 23del (ELN)
- Supravalvular AS
441
5p deletion vs 5q35del
5p del = cri du chat
5q35 = sotos (NSD1)
442
Abnormal teeth, cleft lip/palate (bilateral), ectrodactyly, ankyloblepharon
TP63
443
Which syndrome is adrenocortical carcinoma seen in?
Li Frameni
TP53
444
Radial ray defect with preservation of thumb
Thrombocytopenia absent radius syndrome
RMB8A, 1q21.1del
445
Characteristic limb anomaly in CDLS
ulnar hypoplasia \> radial defect
NIPBL, cohesin complex (HDAC8, RAD21, SMC1A, SMC3)
446
RUNX2
Cleidocranial dysplasia
+ supernumery teeth, open fontanelles
447
Brachycephaly, medial deviation of thumbs/toes
Pfeiffer
FGFR2, FGFR1
448
Ear tags, imperforate anus
Townes Brock
SALL1
+ limb anomalies
449
If 2 parents with achondroplasia have children, what are expected offspring phenotypes?
1/3 normal
2/3 achondroplasia
- Recessive = lethal
450
Lip Pits, midline cleft
Van der Woude
IRF6
451
What dysmorphic features are associated with diffuse gastric cancer syndrome?
CDH1
- Cleft lip/palate
452
Cleft L/P, flat face profile
Stickler
Col 2, 9, 11
+ ophtho, hearing, MSK
453
What are T cell receptor excision circles? (TRECs)
Remnants of VDJ recombination in T cells -\> used for SCID NBS
Actin = control for DNA amplification
454
NBS: Low TREC
TREC = T cell receptor excision circle (VDJ recombination remnant)
Concern for SCID -\> repeat TREC assay w/ actin control
if TREC normal or actin low -\> false positive NBS
if TREC still low and actin normal -\> get immune profile
455
High adenosine, 2-deoxyadenosine, and deoxyadenosine triphosphate
T, B, and NK cell lymphopenia
SCID
ADA deficiency
+ SNHL, skeletal changes
456
What gene causes XL scid?
IL2RG - IL2 receptor gamma
- somatic reversion -\> late onset phenotype
457
What percentage of 22q11del patients will have normal FISH results?
5%
- Deletion may be outside of probe coverage retion
- Get microarray
458
Frequent bacterial infections or chronic viral infections.
Small lymph nodes
**Absent/small tonsils**
Bruton's agammaglobinemia (XL)
- BRK gene (necessary for B cell maturation)
- normal response to acute viral illnesses
459
**Micropenis**, microphthalmia, renal hypoplasia
BMP4
- Could be microphthalmia, aniopthalmia, or coloboma (spectrum)
460
Anophthalmia, **esophageal atresia**, hypopituitarism, short stature
SOX2
- Could be microphthalmia, aniopthalmia, or coloboma (spectrum)
461
Coloboma, **XY Sex reversal**, skeletal dysplasia
SOX9
Campomyelic Dysplasia
- Could be microphthalmia, aniopthalmia, or coloboma (spectrum)
462
What teratogens can cause eye malformations?
**Vitamin A** and fetal alcohol
463
Posterior embryotoxon, iris atrophy, iridogonoidysgenesis, dental hypoplasia, maxillary hypoplasia, redundant peri-umbilical skin
Axenfeld-Rieger Syndrome
PITX2, FOXC1 - AD
- Posterior embryotoxon + Iris + dental + failure of involution of periumbilical skin
464
Match eye findings with disease:
1. Lisch Nodule
2. Brushfield Spots
3. Heterochromia
4. Starburst Irides
1. Lisch Nodule - NF1
2. Brushfield Spots - Down Syndrome
3. Heterochromia - Wardenburg
4. Starburst Irides - Williams
465
Which hereditary vision loss has FDA approve gene therapy?
RPE65 - AAV therapy
466
Where are ribosomal RNA genes located in the genome?
p-arms of acrocentric chromosomes
467
What is advanced paternal age?
35 (same for mothers!)
468
is recombination rate higher in males or female?
females
- females have more genes on X /more centimorgans (4400cM vs 2700cM)
469
How many base pairs in human genome?
6 billion (diploid)
1 haploid set = 3 billion
470
How long is the humna genome?
Average 3700 cM
4400 cM females
2700cM males
471
What is leading strand vs lagging strand?
In DNA replication, leading strand is synthesized in 1 direction
Lagging strand is synthesized in pieces (Ookazaki fragments) and joined together
472
Which polymerases catalyze DNA replication?
Leading strand = polymerase delta
Lagging strand = polymerase alpha
473
Which RNA polymerase started transcription?
Polymerase II
474
Which RNA polymerase transcribes tRNA?
Polymerase III
- also 5S rRNA
475
Which RNA polymerase trasncribes most rRNA?
Polymerase I (not 5S)
- 5S rRNA transcribed by pol III
476
Where is CAAT box? What does it do?
-80 to -70 upstream of gene, regulates **amount of transcription**
477
What is TATA box?
-30 to -25 upstream, regulates **transcription start site**
478
Where are enhancers located? how to to act?
Within 1Mb of start site (can be up or downstream)
- **Cis acting**
479
What are silencers? How do they act?
Repress transcrtiption, **cis acting**
**-** Usually up to 2000bp upstream of gene, but can be downstream or within
480
What are genetic insulator?
DNA that blocks an enhancer when located between enhancer and gene
481
What modification is seen in histones being actively transcribed?
Acetylation
482
What modification is seen in histones being inactive?
methylation
483
What promoter modification means inactive?
CpG island methylation
484
What does H3K27Ac mean?
Histone 3, lysine 27 is acetylated -\> transcription enhanced
485
What does H3K27Me3 mean?
Histone 3, lysine 27 is tri-methylated - represses transcription
486
AAUAAA
Poly A signal sequence -\> tells endonuclease to cleage 1-15 beases downstream and RNA polymerase adds poly-A tail
487
What are splice site consensus sequences?
Donor: GU
Acceptor: AG
Branch site -. 20-50bp upstream of aceptor -\> CUPuAPy
488
What are the components of spliceosome?
U1 - binds donor site
U2 - binds branch site
U5 - binds both donor and acceptor site
489
What distinguishes an AUG as a start codon rather than a methionine in the middle of a protein?
Kozak sequences - GCCPuCC**AUG**G - signals translation initiation
490
What type of mutation does CpG methyluation cause?
C -\> T transitions due to spontaneous deaminiation of 5-methylcytosine
491
What does p.Ter807LeuextTer101 mean?
Stop-loss variant resulting in externsion of protein another 101 amino acids
492
Which SCAs are repeat expansion but not CAG in exon?
SCA 12 - CAG in 5'UTR
SCA 10 - intronic ATTCT
1,2,3,6,7,17 are CAG
493
Where is C9ORF72 expansion located?
Intronic GGGGCC
494
Common mechanism of UPD in PWS
Trisomy rescue
495
Common mechanism of UPD in Angelman
Monosomy Rescue
- maternal nondysjunction (no c15 in egg) -\> paternal duplication -\> AS
496
Common mechanism of UPD in BWS
Post-zygotic somatic recombination
497
What does dominant negative mean?
Mutant protein interferes w/ WT protein function
498
how many PCR cycles does it take to make a million copies of DNA?
20
499
What is the cofactor to Taq DNA polymerase in PCR?
Magnesium
500
What is the most common single nucleotide substitution?
C to T
- 2/3rds of SNPs are due to C methylation, then deamination to form T
501
What method is standard to detect repeats?
PCR + capillary electrophoresis
502
How do you calculate maternal cell contamination is a sample?
MCCarea/(Fetalarea + MCCarea)
503
What should you do if maternal cell contamination is detected in a sample?
Use back up culture of resample specimen
504
Large deletions account for how much DMD?
60%
505
What is a junctional fragment in DMD?
A fragment on multiplex PCR electorphoresis that does not match any known exon size -\> means it was generated by probes up/downstream of a deletion
- Only carriers have it
506
What is MLPA used to find?
Use specific probe pairs that only ligate if both bind -\> see specific result length
1) specific deletion
2) Copy number variant
3) methylation
507
Most mutable nucleotide in human genome
FGFR3 1138 G\>A
Gly380Arg
- Achon
508
Classic test for achondroplasia
RFLP analysis
- mutations cause restriction site
- Normal: 164bp (no digestion)
- G\>A: 55bp and 109bp
- G\>C: 57BP and 107bp
509
Classic test for Sickle Cell
RFLP
Common mutation creates restriction site
- Digest + southern blot
510
2 tests to detect changes in DNA length
Southern blot or PCR + capillary electrophoresis
511
What does full fragile X expansion look like on southern?
Smear \> 5.8kb
- Unstable
512
What does methylated fragile X look like on southern?
5. 2kb
- methylated -\> **not digested** by restriction enzyme
513
What does normal active (unmethylated) fragile X look like on southern?
2.8kb (digested by restriction enzyme)
514
What does fragile X premutation look like on southern?
Slightly above normal (2.8 or 5.2kb) depending on whether it is methylated (lyonized)
515
What phenotype do you expect in someone with R117H in cis with 7T and a severe mutation w/ 5T?
Mild CF or CBAVD
- 5T means severe allele is barely expressed while R117H with 7T = mild allele
516
What % of genome is exons?
~2%
517
What does treatment with bisulfite do to PCR reaction?
Methtylation sensitivity
Bisulfite converst unmethylated C to U
