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Gene 500 Flashcards

1
Q

What are the 3 most common chromosomal abnormalities in recognized pregnancies?

A

1) Triploidy (100% SAB)
2) 45, X (99% SAB)
3) trisomy 16 (100% SAB)

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2
Q

Large tongue, excess nuchal skin, auricular dysplasia, upslanting palpebral fissure, clinodactyly, hyperextensibility, single palmar crease, hypotonia

A

Down syndrome

47,XX,+21 (95%)

46,XX,rob(14:21) (4%)

Mosaic trisomy 21 (1%)

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3
Q

What are the complications of down syndrome?

A

Hearing problems (narrow ear canals)

Vision porblems

Cataracts, OSA

CHD

hypothyroidism

Leukemia

atlantoaxial instability

dementia

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4
Q

Small fingernails, short sternum, clenched hands (2 over 3, 5 over 4), micrognathia

A

Edwards Syndrome

Trisomy 18

  • look for CHD, horshoe kidney, cerebllar hypoplasia, microphthalmia, central apnea
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5
Q

Sloped forehard, cutis aplasia, hypoterloirsm, cleft L/P, omphalocere, polydactyly, HPE

A

Patau, Trisomy 13

  • Heart, CNS, renal, general anomalies
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6
Q

What are the most common karyotype findings for Turner Syndrome?

A

45,X - 50%

46, X, i(Xq) - 15%

45,X/46,XX mosiac - 15%

45X/46,X,i(Xq) - 5%

other

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7
Q

Low posterior hairline, renal anomalies, cardiovascular anomalies, short stature, edema in infancy

A

Turner Syndrome

+ gonadal dysgenesis, webbed neck, widely-spaced nipples

  • Lack of secondary sex characteristics/ammenorhea in puberty
  • Monitor for aortic root dilation
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8
Q

Hypogonadism, tall, gynecomastia, decreased muscle mass, osteopenia, low libido

A

Klinefelter

47 XXY (85%)

Mosaic 47XXY/46XY (15%)

  • Increased risk for learning disabilities
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9
Q

What is the phenotype for 47XYY

A

Not dysmorphic

Tall, at risk for langage delay/low verbal IQ

  • ~10-15 IQ points lower than siblings
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10
Q

What is 47XXX phenotype?

A

Tall, 70% have learning porblems

  • no dysmorphic features
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11
Q

How is gonadal sex determined?

A

SRY -> SOX9

  • established around 6 weeks gestation
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12
Q

When does X inactivation occur?

A

2 weeks post-fertilization

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13
Q

What gene is expressed in the inactive X but not active X?

A

XIST

in Xq13

  • produces large RNA molecules that coat inactive X
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14
Q

Which X is usually missing in 45X?

A

paternal 75%

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15
Q

Cystic hydroma, ovarian dysgenesis, low hairline, aortic root dilation

A

Turner Syndrome

Haploinsufficiency of PAR genes

  • 2 Xs needed for ovarian development -> inactive X is reactivated in oogoina during meiosis (starts in fetal life)
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16
Q

When are patients witt Turner Syndrome at risk for gonadoblastoma?

A

When mosaic for 45X and 46XY and external genetalia is female or ambiguous

- okay if external genetalia is male

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17
Q

What does a ringed chromosome in turner syndrome mean?

A

Need to do FISH to determine if X or Y and if XIST is present

  • if Y risk for gonadoblastoma
  • if X and XIST is present -> PAR haploinsufficiency -> Turner
  • if X and XIST is absent -> X disomy -> severe ID, OCD, dysmorhpic features, and congenital malformation

-

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18
Q

Xp21 deletion syndrome

A

DMD, RP, adrenal hypoplasia, ID, glycerol kinase

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19
Q

What does Xp duplication involving DAX1 do?

A

46XY females

  • increased DAX1 dose can overcome sry
  • w/ ID
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20
Q

In X-Autosome translocations, which X is inactivated?

A

If balanced; normal X nonrandomly inactivated

If unbalanced: abnormal X is nonrandomly inactivated

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21
Q

What is the reproductive consequence of X-autosome translocation?

A

Half of females infertile

All males infertile

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22
Q

Which chromosomes can be involved in robertsonian translocation?

A

Acrocentrics

13, 14, 15, 21, 22

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23
Q

What is the clinical consequence of balanced translocation?

A

Usually multiple miscarriages due to unbalanced offspring

  • Phenotype depends on size, genes involved, monosomy vs trisomy
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24
Q

What type of segregation is most common in a quadrivalent?

A

Adjacent 1 (chromosomes next to each other with different centromeres go together)

  • Alternate results in normal/balanced offspring
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25
Q

What are 3 mechanisms of isochromosome formation?

A

Centromere misdivision - isochromosome w/ identical arms

U-type exchange in meiosis 1 (most common) - isodicentric chromosome w/ homologous arms

U-type exchange in meiosis 2 -isodicentric chromosome w/ identical arms

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26
Q

Which type of inversion involves the centromere? Which type is more likely to result in abnormal offspring?

A

Pericentric involves centromere and is more likely to result in liveborn but abnormal offspring

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27
Q

What is the significance of segmental duplications?

A

Seg Dup = Low copy repeats

  • Non-homologous recombination -> recurrent Del/Dup syndromes
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28
Q

Name the syndrome associated with:

5q35 deletion

7q11 deletion

15q11q13 deletion

17p11. 2 deletion or duplication
22q11. 2 deletion

A

5q35 deletion - Sotos

7q11 deletion - Williams

15q11q13 deletion - PWS/AS

17p11. 2 deletion or duplication - Smith magenis, HNPP/ CMT
22q11. 2 deletion - DiGeorge

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29
Q

75% of chromosome rearrangements come form which parent?

A

father

Exceptions:

  • novo markers (associated w/ advanced maternal age)
  • De novo robertsonian (90% mom)
  • interstitial del/dup -> 50/50
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30
Q

What are alpha-satellites? Why are they relevant?

A

Alpha-satellite is a 171bp repeated region at centromeres -> different by 2-3% between chromosomes and allow chromosomes to be distinguished on FISH

- Exceptions: 13 and 21, 14 and 22

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31
Q

What are the advantages of interphase FISH?

A
  • Fast - no need to culture cells (takes 1-2 days vs 7-14 days for karyotypes)
  • better for Tandem duplications
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32
Q

What is the best FISH probe for philadelphia chromosome?

A

Dual fushion -> for when both tranlsocation breakpoints are known

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33
Q

What can SNP array tell that CGH array cannot?

A
  • UPD, loss of heterozygosity
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34
Q

Why would you follow up CMA results with FISH?

A
  • confirm finding
  • provide location of duplications
  • identify balanced translocations in parents (recurrence risk)
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35
Q

According to ACOG, when should a pregnant woman be offered CMA?

A
  • if U/S abnormal get CMA
  • if U/S normal can do karyotype or CMA
  • offer to women of all age groups (most findings are not AMA related)
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36
Q

What is the resoluation of:

  • Karyotype
  • high resolution karyotype
  • CMA/FISH
  • Sequencing?
A
  • Karyotype - 5-15MB
  • high resolution karyotype - 1-3MB
  • CMA/FISH - 20-250KB
  • Sequencing? - 1-100bp
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37
Q

What is the signfiicance of JAK2?

A

Driver mutations in essential thrombocytopenia and polycythemia vera

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38
Q

What is the significance of MYC ?

A

Burkitt lymphoma

Protooncogene on Ch8, multiple translocation partners

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39
Q

What is the significance of ALK, EGFR, and KRAS?

A

Amplified in lung cancer

  • ALK inversion is drug target
  • EGFR can betargered by Cetuximab
  • KRAS is downstream of ALK and EGFR and can negate effects of targeted therapy
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40
Q

Which aneuploidies are more likely to be paternal origin?

A

45X, and XYY

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41
Q

Which aneuploidies are more likely to be MII errors?

A

Trisomy 18, XYY

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42
Q

Which aneuploidy is 50/50 in parent of origin?

A

XXY

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43
Q

Most aneuploidies originate from which parent?

A

Maternal M1

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44
Q

Small placenta, high B-hCG, severe growth restriction, syndactyly, multiple congenital anomalies

A

Digynic triploidy

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45
Q

mild growth restriction, large cytic placenta, low B-hCH, syndacytly, multiple congential anomalies

A

Diandreic triploidy

  • Partial hydatiform mole
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46
Q

Which phase of cell cycle are cellular contents duplicated?

A

G1

  • chromosomes duplicated in S
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47
Q

Recombination occurs in what stage of meiosis?

A

Porphase 1 - Pachytene

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48
Q

When does meiosis start?

A

Males: after puberty

Females: 3rd month of gestation -> arrest at prophase 1 -> continue at menstration -> arrest at metaphase 2 -> complete if fertilized

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49
Q

TTAGGG repeat

A

Telomere cap sequence -> critical in meiotic pairing

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50
Q

In a karyotype G banding, which bands are GC rich?

A

Light bands = gene rich, GC rich, more euchromatic

Dark bands = gene poor, AT rich, more heterochromatin

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51
Q

What is the difference between a polymorphism and variant?

A

Polymorphism is >1% pop frequency

Variant is < 1% pop frequency - may or may not be disease causing

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52
Q

Locus vs alleleic heterogeneity

A

Locus heterogeneity = multiple genes -> same phenotype

Allelic heterogeneity = multiple variants in same gene -> same phenotype

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53
Q

Definte autosomal dominant

A

phenotype seen in heterozygotes

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54
Q

Definte autosomal dominant

A

Phenotype only seen in homozygotes

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55
Q

What does X-Linked mean?

A

If recessive: No father -> son transmission

If dominant: affected males have no affected sons but all affected daughters

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56
Q

Co dominant vs incomplete dominant

A

Codominant = both A and B show up (Ie ABO blood type)

Incomplete dominant = hets are intermediate to homozygotes

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57
Q

What does g.112931A>T mean?

A

genomic sequence change

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58
Q

What does c.112931A>T mean?

A

coding sequence change

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59
Q

What does r.112931A>T mean?

A

RNA sequence change

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60
Q

What does p.112931A>T mean?

A

Protein sequence change

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61
Q

What does m.112931A>T mean?

A

mitochondrial DNA sequence change

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62
Q

What does n.112931A>T mean?

A

noncoding RNA transcript change

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63
Q

What does c.9A>G, p.Lys3 mean?

A

synonymous A>G in DNA -> Lys 3 position

  • May still affect splicing
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64
Q

What does c.100+1G>T mean?

A

Intronic change 1 nucleotide downstream from nucleotide 100 in coding sequence

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65
Q

What does c.100-2A>T

A

Intronic change 2 nucleotides upstream from nucleotide 100 in coding sequence

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66
Q

LMNA c.1824 C>T, p.Gly608

A

Synonymous change in LMNA that creates cryptic splice site

-> Hutchinson-Gilford Progeria

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67
Q

FGFR3 p.G380R

A

Achondroplasia

C.1138G>A (98%) or G>C (2%)

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68
Q

Name the stop codons

A

UAA

UAG

UGA

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69
Q

When does a nonsense mutation result in a truncated protein?

A

When stop codon is downstream of the last 50bp of penultimate oxon (50bp from the last exon junction complex)

  • If stop codon is too early -> nonsense mediated decay
  • If gene has 10 exons, nonsense variant in exon 1-8 will trigger nonsense mediated decay -> no protein -> likely pathogenic
  • If nonsense if in exon 10 or last 50bp of exon 9 then it MIGHT NOT trigger decay and may make protein -> MIGHT have some function
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70
Q

What is the correct nomenclature?

c.locus is 1521-1523

A

p. Phe508del
c. 1521_1523delCTT
- > not delTCT because you push to the right

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71
Q

What is necessary to make a variant pathogenic?

A

1 very strong + 1 strong, 2 mod, or 1 mod + 2 sup

2 strong

1 strong + 3mod, 2mod +2 sup, 1mod + 4 sup

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72
Q

What evidence is necessary to classify variant at LPATH?

A

Very strong + mod

strong + 1-2 mod

strong + 2 sup

3 mod

2mod + 2 supporting

1 mod + 4 supporting

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73
Q

What evidence classified variant as benign?

A

1 stand alone strong OR 2 strong

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74
Q

What evidence classified variant as likely benign?

A

1 strong + 1 sup

2 supporting

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75
Q

Variant classification: allele frequency >5% in pop database

A

stand-alone benign

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76
Q

Variant classification:

  • allele frequency > expected for disease
  • observed in healthy individuals expected to have condition based on penetrance/age
  • not damaging in in-vivo funtional studies
  • no segregation
A

Strong Benign criteria

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77
Q

Variant Classification:

  • MIssense variant in gene where mostly truncating variants cause disease
  • Observed in trans with AD disease causing allele or in cis with known disease causing allel
  • in-frame del/dup in repetitive region
  • computations data -> benign
  • alternative molecular diagnosis found in case
  • reputable source reports variant as benign
  • synonymous variant not predicted to affect splicing
A

Supporting benign criteria

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78
Q

Variant Classification:

  • Same amino acid change as a previously established pathogenic variant regardless of nucleotide change
  • De novo (both maternity and paternity confirmed) in a patient with the disease and no family history
  • funcitonal studies support damaging effect
  • The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls
A

Strong pathogenic criteria

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79
Q

Variant interpretation:

  • Located in a mutational hot spot and/or critical and well-established functional domain without benign variation
  • Absent in controls (AD), rare (AR)
  • Detected in trans w/ pathogenic variant (AR)
  • Protein length changes as result in in frame del/dup
  • Novel missense in residue where missense has been seen before as disease causing
  • assumed de novo
A

Moderate pathogenic criteria

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80
Q

Variant Classification:

  • Cosegregation with disease*
  • Missense in gene w/ low missense frequency and where missense is common mechanism
  • Computational -> deleterious
  • Phenotype is specific for this gene
  • Reportable source interpreted this variant as pathogenic
A

Supporting pathogenic criteria

* segregation can become moderate/strong depending on size of pedigree

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81
Q

How do you detect variable number tandem repeat polymorphisms (minisatellites, microsatellites)?

A

Multiplex PCR

  • highly informative genomic variation since each locus has many possible alleles
  • Used in linkage and DNA fingerprinting
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82
Q

Which SCAs are repeat exapnsion disorders?

A

1, 2, 3, 6, 7, 17

  • CAG repeats
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83
Q

What are the 3 main types of non-random mating?

A
  • inbreeding
  • assortive mating
  • negative inbreeding (small population, people actively avoid kin)
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84
Q

What does identical in state mean?

A

Alleles that have the same phenotypic affect

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85
Q

How can heritability be estimated?

A

2x Parent-offspring correlation

h2=2Ppo

or

2(monozygotic twin concordance - dizogotic twin condordance)

h2=2(Pmz-Pdz)

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86
Q

How is relative risk (λ) calculated?

A

Frequency in relatives/ Freuqency in general population

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87
Q

What does a high λ mean?

A

High relative risk ratio = more heritable

λs>2 = significant (s= sibling)

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88
Q

What is the difference between linkage and association?

A

Linkage = cosegregation of phenotype with chromosome region in multiple families - best for finding rare alleles of large effect

Association: presence of phenotype with specific allele in many famlities in population -> more frequence in cases than controls - best for findings common alles with small effect

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89
Q

What does linkage dysequilibrium mean?

A

Behavior of 2 loci violates law of independent assortment

  • Excess of parental types (non-recombinants) in offspring
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90
Q

What needs to be true in order to perform linkage analysis?

A

One parent has to be hetrozygous and phase must be known

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91
Q

What is θ (recombination fraction)?

A

Prebability that a parent will produce a recombinant offspring (non-parental haplotype)

Recombinant haplotype/ total offspring

θ = 0 -> complete linkage

θ = 0.5 -> independent

θ < 0.5 = some linkage

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92
Q

What does θ = 0.5 mean?

A

50% of offspring have recombinant haplotype

  • Independent assortment -> no linkage
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93
Q

what does θ = 0 mean?

A

No offpsring have recombinant haplotype

  • complete linkage
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94
Q

Calculate θ

A

In generation 2 dad is heterozygote and we know phase (disease with A) -> linkage possible

Gen 3 unaffected AD daughter = recombination

θ = 1/8 = 0.125

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95
Q

Calculate θ

A

Gen 2 we know dad is BE. He is heterozygous and phase of disease is E -> linkage possible

  • Gen 3 son BE unaffected is recombinant

θ = 1/4

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96
Q

Calculate θ

A

Phase unknown -> cannot calculate

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97
Q

Calculate θ

A

Unable to tell who is recombinant in third generation because both C and D could have come from either mom or dad.

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98
Q

How do you tell if θ of <0.5 is statistically significant?

A

Calculate LOD score

LOD 3 = 1000:1 odds favoring linkage

LOD 3.4 = genome wide significant linkage

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99
Q

What is the definition of association?

A

Lack of independence between 2 things

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100
Q

how can association (between phenotype and allele) and linkage (marker and phenotype) be uncoupled?

A

Recombination

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101
Q

Breech position, hypotonia, low birth weight, Thick saliva, hypoplastic genetalia, almond shaped eyes, small hands/feet, ID

A

Prader Willi

Paternally expressed (maternally imprinted) genes in 15q11q13 - pat deletion > mat UPD > methylation defects

– hyperphagai, fair skin/hair in deletions (P gene in area)

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102
Q

Devlopmental delay, copious saliva, ataxia, happy demeanor, stereotypies, Large amplitude slow spike waves

A

Angelman

Maternally expressed (paternally imprinted) genes in 15q11q13 - UBE3A

  • Mat deletion > UBE3A mutationn > Pat UPD > methylation defects
103
Q

Is the imprinted allele silent or active?

A

Imprinted allele is silent

104
Q

How does methylation specific PCR (MS-PCR) work?

A
  • Treat DNA w/ bisulfite to convert unmethylated C -> Uracil
  • Maternallly C’s are methlated -> readout C
  • Paternal C’s are unmetylated -> readout U
105
Q

What is the recurrence risk for PWS/AS?

A

Deletion/UPD -> risk low (<1/1000)

Methylation defect, chormosome rearrangements, UBE3A mutations -> Up to 50%

106
Q

Which ETC complex is completely encoded by nuclear genome?

A

Complex 2 (FAD -> CoQ)

Succinate DH of TCA cycle

107
Q

Why does mito genome have high mutation rate?

A
  • Limited repair/proofreading (not part of G2 phase of cell cycle)
  • no histone
  • More free radicals
108
Q

Features of most cleft lip cases

A

Unilateral, L sided, male patient

109
Q

What disease can RFLP (restriction fragment length polymorphism) be useful?

A

Achondroplasia

Restriction enzyme + electrophoresis for a single disease causing variant at codon 380

110
Q

What is oligonucleotide ligation assay?

A

PCR with specific disease allele probes to see if they are present

  • good for testing for multiple disease alleles in same locus in parallel (ie CFTR)
111
Q

What is Multiple ligant-dependent probe amplification useful for?

A

MLPA for changes in size -> great for copy number variation/repeat expansions

112
Q

What are the repeat cutoffs for DMPK?

A

CTG expantion in DMPK = myotonic dystrophy type 1

Repeat in 3’UTR

<35 = normal

35-50 = premutation

50 - mild

100 - classic

2000 - congenital

113
Q

Repeat expansion in 5’UTR of DMPK more likely to expand in which parent?

A

Mother

114
Q

3 ways to find repeat expansions

A

MLPA, southern blot, triplet primed PCR (PCR using repeat as a proble -> result in ladder of different lengths)

115
Q

What is FASTQ file?

A

Initial output of next-gen sequencing - Raw data + quality scores

1) sequence identifier
2) raw read
3) optional description
4) quality value

116
Q

What is a BAM file?

A

Compressed FASTQ file from NGS -> usually the one that is saved/transported because it can be decompressed into FASTQ

117
Q

What is a VCF file?

A

Variant Call format

  • Shows points where sample is different from reference
118
Q

Totipotent vs Plauripotent cells

A

Toti can become anything -> zygote/blastomere

Pluri can become many, but not extra-embryonic membranes

119
Q

What is the different between chimera and mosiac?

A

Chimera started from 2 different zygotes, mosiac started as one

120
Q

What tissues come from endoderm

A

cells that line the lumen -> GI tract, Respiratory

121
Q

What tissues come from ectoderm?

A

Skin and Nervous system

122
Q

What tissues come from mesoderm

A

Blood, bone, connective, solid organs

  • includes mesenchyme
123
Q

What determines digit formation in embryogenesis?

A

SHH concentration and duration secreted by Zone of Polarizing Activity

124
Q

Which period of embryogenes is most critical for strucutural malformation?

A

3-8 weeks. After that difference tend to cause cellular level changes

125
Q

What is a deformation?

A

Abnormal shape/form caused by mechanical forces

  • Normally formed first -> usually changed in 3rd trimester
  • Ie Twinning, Uterine issues, low amniotic fluid
126
Q

Disruption vs deformation

A

Disruption -> destruction of normal tissue due to external factor (ie viral infections, ischemia, amniotic band)

Deformation -> Change in shape due to external factor

127
Q

Dysplasia

A

Structural defect results from abnormal cellular organization/function

  • often worse with age
128
Q

Malformation

A

Morphologic defect due to abnormal intrinsic programming

  • Often involves multiple tissue types
129
Q

Malformation vs dysplasia

A
  • Both intrinsic
  • Dysplasia = ongoing -> worse w/ age
  • Malformation = 1 time hit
130
Q

What is a complex?

A

Anomalies of several structures that lie in the same body region during embryonic develoment (developmental field)

  • example: OEIS complex (omphalocele, extrophy, imperforate anus, spinal defects)
131
Q

Short stature, webbed neck, low set ears, lymphedema

A

Noonan (hypertelorism, downslanting PFs, pulmonia stenosis)

or

Turner (Coarctation)

132
Q

Slender tapered fingers, cleft palate, TOF, hypotonia, tubular nose

A

22q11 Del

133
Q

What are the most common causes of Beckwith Weidemann Syndrome?

A

1) Loss of methylation in IC2 on maternal chromosome - normally repressed CDKN1C can be expressed (50%)
2) Paternal UPD 11p15.5 - CDKNiC expressed twice (20%)
2) Gain of methylation of IC1 on maternal chromosome - growth suppressor is suppressed (5%)
3) CDKN1C mutation (5%)

134
Q

postnata growth deficiency, persistent fetal fingertip pads, ITP, hypodonita, lateral aversion of lower eyelids

A

Kabuki

KMT2D, KDM6A

135
Q

Hemihypotrophy (limb length discrepancy), 5th finger clinodactyly, prominent forehead with small jaw

A

Russel Silver

136
Q

Upper seg/Lower seg ratio <0.85

Arm span/Height ratio > 1.05

A

Elongated limbs relative to body

  • Commony seen in Marfan
137
Q

Deep set eyes, downslanting PF, dolichocepahly, malar hypoplasia, micro/retrognathia, high narrow palate, striae

A

Marfan

FBN1

138
Q

What are the major diagnostic features of Marfan?

A
  • Ectopia Lentis
  • Aortic root dilation/dissection
  • Systemic score
  • FBN1 pathogenic variant
139
Q

What medications should be avoided by Marfan patients?

A

Calcium channel blockers and fluoroquinolones - worsen dilation

140
Q

Arachnodactyly, joint laxity, pectus, pes planus, club foot, malar hypoplasia, downslanting PF, micro/retrognathia, bifid uvula

A

Loeys Dietz

  • TGFB pathway
  • Club feet, bifid uvula, hypertelorism, arterial tortuosity, aneurysms are not seen in Marfan
  • no ectopia lentis
141
Q

What is the most common connective tissue disease?

A

Hypermobile EDS

  • Beighton score >5
  • Skeletal features or family history
  • Rule out alternatives
142
Q

Match each skin findings wtih EDS type

1) atrophic, widened scar
2) papyraceious (cigarette paper) hemosideric scar
3) thin translucent skin
4) hyperextensible skin with abnormal wound healing
5) mollusocoid pseudotumor

A

1) atrophic, widened scar - hypermobile
2) papyraceious (cigarette paper) hemosideric scar - classic
3) thin translucent skin - Vascular
4) hyperextensible skin with abnormal wound healing - Classic
5) mollusocoid pseudotumor - Classic

143
Q

What type of error occurs due to advanced maternal age?

A

Meiosis I errors

  • Meiosis I arrested at dictyotene of prophase 1 from 5 months of embyonic development until ovulation
144
Q

What maternal illnesses increase risk for fetal anomalies?

A

Diabetes, autoimmune disorders, early viral illness

145
Q

Macrocephaly, hypertelorism, overgrowth, synophrys, palmar/plantar pits, odontogenic keratocysts, BCC, ectopic calcifications, polydactyly

A

Gorlin

PTCH tumor suppressor (part of SHH pathway)

  • Also increased risk for medulloblastoma (avoid radiation), rhabdomyomas, and ovairan fibromas
146
Q

Tiger banded hair

A

Trichothiodystrophy

147
Q

What are key feaures of PTEN disorders?

A

Macrocephaly, Autism, Hamartomaous skin/breast, thyroid, mucusal lesions, Cancer risk

Cowden: Papillomas, Breast/Gyn/Thyroid Ca, lipoma

BRR: Penis freckline, thyroid/breast ca

148
Q

What is the function of PTEN?

A

Tumor suppressor gene

  • Part of PI3K, AKT, mTOR pathway
149
Q

Most common AD ichthyosis

A

Filaggrin

  • Incomplete Dominant
  • 7.7% of europeans
  • Ichthyosis, also atopic dermatitis
150
Q

Dark, scaly, tightly adherent skin most prominent on externsor surfaces and neck

+ Corneal opacities, cryptorchidism

Maternal E3 absent

A

Steroid Sulfatase Deficiency

AKA: Arylsultafase C

  • Abnormal cholesterol sulfate levels

-

151
Q

Keratitis, Ichthyosis, Deafness, SCC

A

KID syndrome

Connexin 26 (GJB2)

  • Missense variants
152
Q

Palmar-plantar hyperketaosis, nail dystrophy, alopecia, joint hyperpigmentation

A

Hidrotic ectodermal dysplaia

GJB6 - connexin 30 missense variants (AD)

Ectodermal dysplasia with normal sweating and teeth

153
Q

Hypotrichosis, anhidrosis, conical/pegged teetch, eczema, periorbital hyperpigmentation, absent dermal ridges

A

Hypohidrotic ectodermal dysplasia

EDA1 (XL), EDAR (AR)

  • No Sweat - avoid fevers!
154
Q

Split hand/feet, polysyndactyly, hypotrichosis, anodontia, hypohidrosis, pitted nails, cleft L/P, Blepharitis, Keratisis

A

Ectrodacylty-Ectodermal Dysplasia-Clefting syndrome

TP63 (AD)

155
Q

ichthyosis, spastic tetraplegia, glistening white dots in retina, leukodystrophy

  • high leukotriene B4 in urine
A

Sjorgren Larsson

ALDH3A2 (AR)

Fatty aldehyde dehydrogenase

156
Q

What is the most common α1-Antitrypsin Deficiency allel?

A

Pi*Z (Glu342Lys)

  • Homozygotes ->Dimerization -> aggregate in liver (cirrhosis), insufficient in lungs (lower lobe emphysema)
157
Q

What is the most common fatal AR disorder in whites?

A

Cystic Fibrosis

CFTR

1/25 carriers

158
Q

What does ivacaftor do?

A

Potentiates CFTR channel

  • Not useful as monotherapy for 508delF (mislocalization)
159
Q

What does lumacaftor do?

A

Improved localization of mutant CFTR

  • Used in combo with ivafactor for 508delF
160
Q

Pulmonary fibrosis, albinism, granulomatous colitis, bleeding diathesis

A

Hermansky Pudluck

HPS1-9 (AR)

Pale Bleeding Puerto Rican

+ pulmonary fibrosis, colitis, skin ca

161
Q

187delAG

5285insC

5946delT

999del5

156_157insAlu

A

Hereditary Breast and Ovarian Ca founder mutations

187delAG (BRCA1 - Ashkenazi Jew)

5285insC (BRCA1 -Ashkenazi Jew)

5946delT (BRCA2 - Ashkenazi Jew)

999del5 (BRCA2 - Iceland)

156_157insAlu (BRCA2 - Portuguese)

162
Q

PALB2

A

High risk breast ca gene

  • 50% lifetime risk

+ pancreatic, ovarian, male breast Ca

  • no melanoma (seen in BRCA)
163
Q

60% lifetime risk of lobular breast cancer

80% diffuse gastric cancer

A

CDH1

Hereditary diffuse gastric cancer

164
Q

Breast, Renal, Follicular thyroid, uterine cancer + autism

A

Cowden

PTEN- Hamartoma syndrome

165
Q

Breast, Brain, choroid plexus, adrenal, and GI cancers + sarcomas

A

LI Fraumeni

TP53

166
Q

Name 3 moderate risk breast Ca genes

A

ATM - also pancreatic; + ataxia/telangiectasia

CHEK2 - also colon ca

NF1 - neurofibromatosis

167
Q

Screening in Lynch Syndrome

A

Colonoscopy q1-2yrs - start at 20 or 5 yrs before earliest diagnosis in family

EGD q3-5 yrs - start at 40 or 5 yrs before earliest in family

168
Q

How does APC work?

A

Tumor suppressor in WNT signaling pathway

169
Q

Screening for FAP

A

APC gene

  • Colonoscopy at age 10 (Colectomy when adenoma burden cannot be managed by polypectomy)
  • EGD at 25

- Thyroid US annually in teens

- AFP/U/S for hepatoblastoma q6 months until age 7

170
Q

Small bowel obstruction, intussusception, pigmentation around lips, hands/feet

A

Peutz Jagher

STK11

  • Hamartomatous polyps
171
Q

Non-medullary thyroid, breast, endometrial cancer

Cerebelar dysplastic ganglicytoma

A

Cowden

PTEN

+ Macrocephaly, ID, hamartomas

172
Q

Management of MEN syndromes

A
  • Prophylactic thyroidectomy
  • Annual Pheo screening, and before any surgery (MEN2)
173
Q

Ovarian Sex-cord stromal tumors, pleuropulmonary blastoma, thyroid tumors

A

DICER1

174
Q

Fibrofolliculomas, lung cysts, renal cancer

A

Birt-Hogg-Dube

FLCN (folliculin) - AD w/ incompelte penetrance

+ angiofibromas, spontaneous pneumothorax

175
Q

Renal cell carinoma, Leiomyomatosis (fibroids)

A

Fumarase deficiency

Heterozygotes: RCC + fibroids

  • Homozygotes get fumaric aciduria, encephalopathy, FTT, seizures
176
Q

What is the most common gene associated with anophthalmia?

A

SOX2

  • Transcription factor that also interacts with PAX6 (aniridia)
  • May be associated with learning disablity, CNS malformations, SNHL
177
Q

What are the 4 major criteria for CHARGE syndrome?

A

All in head (Eye, nose, cranial nerve, ear)

1) Ocular coloboma
2) Choanal Atresia
3) Cranial nerve dysfunction
4) Ear changes

178
Q

What is the difference between type 1, 2, and 3 usher syndrome?

A

I: Hearing loss (congenital severe), Vestibular areflexia, early RP

II: Hearing loss (congenital moderate/severe), normal vestibular function, RP

III: Hearing loss (Progressive), sporadic vestibular function, variable RP

179
Q

How do you tell part a head shape deformity from craniosynostosis?

A

In deformity ears are the same height from the back, but different from the top

In craniosynostisis ears are different height from back and top

180
Q

What suture is most commonly affected in nonsyndromic craniosynostosis?

A

Saggital: 50-60%

Coronal: 20-30%

181
Q

craniosynostosis with toes pointing inward

A

Pfeiffer

182
Q

Craniosynostosis with toes pointing outward

A

Saethre-Chotzen

TWIST1

183
Q

brachycephaly, downslanting PF, proptosis, high arched palate, fused digits

A

Apert syndrome

FGFR2

  • Brachycephaly due to bicoronal craniosynostosis
184
Q

Cloverleaf skull, broad thumbs/toes

A

Pfeiffer Syndrome

FGFR2

  • Cloverleaf = pansynostosis
185
Q

Craniosynostosis with normal hands/feet

A

Crouzon

FGFR2

186
Q

Craniosynostosis with fused tarsal/carpal bones

A

Muenke

FGFR3

Most common syndromic craniosynostosis

187
Q

brachycephaly, hypertelorism with downslanting PF, grooved nasal tip and broad nasal root, short stature

A

Craniofrontonasal syndrome

EFBN1 -> efrin

  • X-Linked w/ cellular interference
  • Females more affected than males
188
Q

Which parent of origin do de novo FGFR craniosynostosis come from?

A

Almost exclusive paternal

189
Q

What caues trigonocephaly?

A

metopic craniosynostosis

190
Q

What does coronal synostosis look like?

A

Brachycephaly (bilateral)

Anterior plagiocephaly (unilateral)

191
Q

What causes posterior plagiocephay?

A

Lambdoid craniosynostosis

192
Q

What causes scaphocephaly (dolicocephaly)

A

Sagittal Craniosynostosis

193
Q

Most common monogenic causes of holoprosencephaly

A

1) SHH
2) ZIC2
3) SIX3 and TGIF

194
Q

What group of metabolic diseases commonly cause hearing loss?

A

MPS, biotinidase

195
Q

hearing loss + RP

A

Usher, cockayne, Refsum

196
Q

Hearing loss + goiter

A

Pendred (SLC26A4)

197
Q

Hearing loss + Long QT

A

Jervell and Lange Nielen

KCNQ1, KCNE1, SCN5A

198
Q

Hearing loss + albinism

A

Waardenburg (PAX3)

199
Q

Hearing loss + renal disease

A

Branchial-oto-reno syndrome (EYA1)

Alport (COL4)

200
Q

Hearing loss + skeletal findings

A

Stickler (COL 2, 9, 11)

Osteogenesis imperfecta (COL 1)

201
Q

Most frequent causes of nonsyndromic genetic deafness

A

GJB2 (connexin 26) - AR

GJB6 (Connexin 30)

202
Q

Genetic causes of adult onset deafness

A

Pendred syndrome (SLC26A4)

Aminoglycoside toxicity (mtA1555G) -12SrRNA

203
Q

12SrRNA

mtA1555G

A

Aminoglycoside ototoxicity

204
Q

All cardiac valves thickened w/ nodularity of leaflets, Coarctation of the Aorta

A

Trisomy 18

polyvalvular dysplasia

205
Q

Branched pulmonary artery stenosis, supravalvular AS

A

Williams syndrome

7q11 del

206
Q

Complete AV canal, TOF

A

Down syndrome

Trisomy 21

207
Q

All cardiac valves thickened w/ nodularity of leaflets, Arch hypoplasia

A

Trisomy 13

Polyvalvar dysplasia

208
Q

Coarctation of aorta, hypoplasic L heart, anomalous pulmonary venous return, Bicuspid AV

A

Turner Syndrome

209
Q

TOF, interrupted aortic arch, truncus arteriosis, pulmonary atresia

A

22q11

Conotruncal defects

210
Q

Peripheral pulmonic stenosis, coarctation of the aorta

A

Alagile syndrome (Jag1, Notch 2)

211
Q

ASD, VSD, conduction abnormalities, triphalangeal thumb

A

Holt Oram

TBX5

  • Upper limb + strucutural heart defect + conduction defect
212
Q

Pulmonic stenosis, AV valve thickening, hypertrophic cardiomyopathy

A

Noonan

213
Q

family history of sudden death during sleep or during fevers, nocturnal breathing, seizures, ventricular arrhythmias

A

Brugada syndrome

SCN5A LOF

214
Q

KCNQ2, KCNH2, SCN5A GOF

A

AD - romano ward - long QT

AR - Jervell and Lange Nielsen - Long QT + SNHL

215
Q

What is the significance of MYH7 and MYBPC3?

A

Account for 80% of familial hypertrophic cardiomyopathy

  • part of sarcomeric contractile apparatus
216
Q

LMNA, TTN

A

Familial dilated cardiomyopathy genes

217
Q

What is the most common severe neuromuscular disease of infancy?

A

SMA

Carrier frequency 1/40

218
Q

How do you distinguish types of SMA?

A

Type 0 - never flip/crawl

Type 1 - never sit

Type 2 - never stand

Type 3 - never walk

Type 4 - walk

219
Q

Vaginal atresia, craniosynostosis, choanal atresia, camptodactyly, renal anomlies

  • Maternal virizliation during pregnancy
A

Antley bixler

POR

220
Q

Vaginal atresia, RP, postaxial polydactyly, obesity, DD , hypogonadism

A

Bardel Biedl

Ciliopathy

221
Q

Vaginal atresia, enlarge clitoris and labia, cryptophthalmia, syndactyly, renal agenesis

A

Fraser syndrome

FRAS1, GRIP1, FREM2

222
Q

Postaxial polydactyly, CHD, hydrometrocolpos

A

McKusick-Kaufman Syndrome

MKKS (AR)

Ciliopathy

223
Q

Primary ovarian insufficiency + family hx tremor/ataxia

A

FMR1 related POI

POI = Premature ovarian failure

55-200 repeats, CGG 5’ UTR

224
Q

Primary ovarian insufficiency, low posterior hairline, short stature

A

Turner syndrome

45X, isoXq, mosaic

  • may have delayed breast development/menarche
225
Q

Primary ovarian insufficiency, liver disease, impaired executive function, speech apraxia

A

Classic Galactosemia

GALT

  • especially Q188R/Q188R
226
Q

2nd most common Ca in Lynch syndrome

A

Colon 80%

Endometrial (60% lifetime risk)

Stomach 13%

Ovarian 12%

227
Q

Macrocephaly, pipillomatous papules, trichilemmommas

+ what is risk of GYN cancer?

A

Cowden

PTEN

Breast CA 50%

Thyroid Ca 10%

Endometrial Ca 10%

228
Q

Besides GI hamartomas, what cancers are seen in Peutz-Jegher sydnrome?

A

STK11

  • Breast Ca 54%
  • Colon 39%

Pancreatic 36%

Stomach 29%

Ovarian 21%

229
Q

What do you need to look for in adults with a pathogenic variant in Fumarate Hydratase?

A

Leiomyomas and Renal Cell Carcinoma

230
Q

At what age should pubic bone be 1/2 mark between head and feet?

A

age 9

231
Q

Proportiate at birgh -> short limbs

Flat beaked vertebra

Arthritis

Small irregular epiphysis

Genu Valgus and varus

A

Pseudoachondroplasia

COMP (AD)

  • Genu valgus and varus = windswept
  • Normal at birth
232
Q

Cauliflower ear, hitchhiker thumb, club foot, short, broad fingers w/ ulner deviation

A

Distrophic Dysplasia

DTDST -> Sulfate transporter

  • Deplete intracellular sulfate -> softer cartilage/coarse collagen fibers
233
Q

High urine phosphoethanolamine, pyrophosphate, and pyridoxal 5 phosphate

Low alk phos

A

Hypophosphatasia

TNSALP

  • early fractures, poor heaing, osteoporosis, tooth loss, rickets

ERT: Asfotase alpha

Avoid bisphosphonates

234
Q

What is asfotase alfa used to treat?

A

ERT for hypophosphatasia

TNSALP

235
Q

meningioma, glioma, schwannoma, juvenile posterior subcapsular lenticular opacity, juvenile cortical cataract

A

NF2

Merlin

+ vestibular schwanomma, <6 CALS

236
Q

4 stages of incontinentia pigmenti

A

Blistering -> verrucous -> Hyperpigmented -> hypopigmented

IKBKG/NEMO gene (XL)

  • regulates NFkB
237
Q

GAA repeat expantion

Mitochondrial iron metabolism

A

Friedreich’s ataxia

FXN (frataxin) - AR (only AR repeat expansion)

Spasticity, ataxia, cardiomyopathy, deafness

238
Q

Which SCAs are caused by CAG repeats?

What about CTG?

A

CAG: 1, 2, 3, 6. 7, 17

CTG: 8

239
Q

Connective tissue dysfunction, macrocephaly, prominent ears, post pubertal macro-orchidism, DD

A

Fragile X

240
Q

Hyperintense signal in cerebellum (middle cerebellar peduncle sign), neuropathy, ataxia, parkinsonism, tremor

A

Fragile X tremor-ataxia syndrome

RNA toxic GOF

241
Q

agenesis of the corpus callosum, chorioretinal lacune, infantile spasms, upturned nose, prominent premaxilla, sparse lateral eyebrows

A

Aicardi Syndrome

XL -> Male lethal

242
Q

GNAQ mosiac gain of function

A

Sturge Weber syndrome

Quanine nucleotide binding protein (GNAQ) -> sporadic

  • Port wine stain, abnormal cerebral vasculature, seizures
243
Q

pectoralist hypoplasia

A

Poland anomaly

Male > Female

Right > Left

244
Q

Thrombocytopenia, absent radius

A

Thombocytopenia, absent radius syndrome

RMB8A

  • thumb preserved
245
Q

Anal atresia, thumb anomalies, ear anomalies

A

Towns Brock

SALL1 (AD)

246
Q

Triphalangeal thumb, VSD, conduction defect

A

Hold Oram

TBX5 (AD)

Thumb can be absent, small, or triphalangeal

  • Lower ext normal
247
Q

downslanting PF, convex nasal ridge, long columella, angulated/broad thumbs/halluces

A

Rubenstein Taybi

CREBBP, EP300 (AD)

248
Q

Name 2 GLI3 syndromes

A

Pallister Hall - AR - Polydacylty, hypothalamic hamartoma, bifid epiglottis,

Greig cephalopolysyndactyly - AD - Preaxial polydactyly, macrocephaly, hypertelorism, board nasal root

249
Q

Central/postaxial polydactyly, hypothalamic hamartoma, bifid epiglottis, laryngeal cleft, pulmonary segmental anomalies

A

Pallister Hall

GLI3 - AR

250
Q

CAG repeat in androgen receptor gene

A

SBMA

XL

>38 = pathogenic

35-37 = reduced penetrance

<34 = normal

251
Q

What are Ataluren, Eteplirsen, Golodirsen, and Viltolarsen used for?

A

DMD treatment

Ataluren = stop codon read through

Golodirsen/Viltolarsen = exon 53 skipping

Eteplirsen = exon 51 skipping

  • Also steroids might help
252
Q

What are the cutoffs for symptomatic myotonic dystrophy patients?

A

Type 1 - CTG in 3” UTR of DMPK - 50 = mild

Type 2 - CCTG in intron of ZNF9 - 75 = pathogenic

253
Q

How do nusinersen, resdiplam, and onasemnogene abeparvovec work?

A

SMA treatment

Nusinersen = ASO to normalize SMN2 splicing

Risdipal = small molecule (PO) that normalize SMN2 splicing

Onasemnogene abeparvovec = AA9 SMN1 repalcement

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