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Qbank Nuggets Flashcards

1
Q

What are G bands in a karyotype?

A

AT rich, relatively later replication, and gene rich regions of chromosomes

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2
Q

What are R bands in karyotype?

A

GC rich areas, gene poor, early replicating

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3
Q

Karyotype: G vs R bands

A

G positive (R negative) bands are AT rich, gene rich, late replicating, tissue specific genes

R positive (G negative) bands are GC rich, gene poor, early replicating, housekeeping genes

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4
Q

What percent of trisomy 21 conceptions result in birth?

A

20%

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5
Q

What is the most common non-robertsonian translocation seen in constitutional cytogenetics studies?

A

t(11:22)(q23,q11.2)

-

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6
Q

Which prenatal study can detect onfined placental mosiacism?

A

CVS (gets sample from placenta)

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7
Q

How many chiasma should be present during homologous recombination

A

1 per arm -> 2 per chromosome

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8
Q

which aneuploidy is 100% maternal meiosis error?

A

Trisomy 16

Trisomy 18 and 21 are 97% and 90% maternal

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9
Q

cancer associated with t(8;21)(q22;q22)

A

AML

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10
Q

cancer associated with t(15;17)(q22;q21)

A

Acute promyelocitic leukemia

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11
Q

Cancer associated t(12;21)(p13;q22) and t(4;11)(q21;q23)

A

B-ALL

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12
Q

3.7mb 17p11.2 duplication

A

Potoki-Lupuski syndrome

(duplication of RAI1)

neurodevelopmental, ASD, apraxia, sleep abnormalities, CHD, growth hormone deficiency

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13
Q

17p13.3 deletion

A

Miller-Dieker

LIS1 + dysmorphic featuers

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14
Q

Replication slippage

Fork stalling and template switching

Non-homologous end joining

A

Mechanisms of non-recurrent CNVs

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15
Q

What is the risk of CVS before 10 weeks?

A

Limb reduction defects and oromandibular hypogenesis

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16
Q

What is a common cause of death in CDLS?

A

GI malrotation/volvulus

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17
Q

high phytanic acid, low plasmalogens

A

RCDP type 1

PEX7

  • Other RCDPs have normal phytanic acid
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18
Q

What is a serum biomarker for ataxia telangiectasia?

A

AFP is elevated in 95% of patients

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19
Q

What phenotype is a patient with 2 null alleles for SERPINA 1 expected to have?

A

Emphysema

No liver disease -> cannot have toxic buildup

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20
Q

What does 5p deletion cause? 5q?

A

5p deletion = cri du chat (cat’s purr)

5q deletion = sotos (NSD1)

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21
Q

What aneuploidy is more likely to be a meiosis 2 error?

A

Trisomy 18

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22
Q

What does mosiac fragile X look like on southern blot?

A

A 2.8kb band (normal - unmethylated, unexpanded) and smear of methylated bands >6.6kb

  • expanded frm1 is unstable
  • methylated, nonexpanded alleles = 5.2kb
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23
Q

What does poly T tract in CFTR do?

A

T tract is in exon 8 and affect splicing of exon 9

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24
Q

What is the length of human genome in cM?

A

~3700cM on average

Female > male

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25
Q

Is SMN1 telomeric or centromeric to SMN2?

A

SMN1 is telormeric

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26
Q

How does UV light damage DNA?

A

Create pyrimidine dimers within strand

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27
Q

What is the most common mechanism of false positive MLPA result?

A

SNP at probe site -> poor binding of probe/ligation -> looks like a single exon deletion

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28
Q

What does 22q13del cause

A

Phelan Mcdermid

SHANK3 critical gene

terminal 22deletion

  • hypotonia, DD, large fleshy hands, dysplastic toenails
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29
Q

hypotonia, DD, large fleshy hands, dysplastic toenails

A

Phelan Mcdermid

SHANK3

22q13 (terminal) deletion

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30
Q

What can ringed chromosome 22 be associated with?

A

NF2

  • Unstable ring -> loss of ch22 (1 hit in 2 hit hypothesis)
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31
Q

What does arr(X)x1,(Y)x0[0.2] mean?

A

arr(X)x1,(Y)x0[0.2]

Array: Mosaic turner 45,X/46,X,Y with Y loss in 20% of cells

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32
Q

What does NM_002024.5:c.(-231_-20)ins(1800_2400) mean?

A

This is nomenclature for repeat expansion -> insertion of 600bp repeat -> 200 trinucleotide repeats

This might be consistent with fragile X

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33
Q

NM_0000511.3:c.[73-2A>G];[193del] mean? What about NM_0000511.3:c.73-2A>G[193del]?

A

NM_0000511.3:c.[73-2A>G];[193del] means 2 variants in trans

(;) = phase unknown

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34
Q

Flattened vertebrae, leukodystrophy, ID

+ high urine sulfatides

A

Multiple sulfatase deficiency

SUMF1

  • Combination of MPS + XALD symptoms
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35
Q

What gene impacts clopidogrel phamacogeneics?

A

CYP2C19

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36
Q

What is the mode of inheritance for malignant hyperthermia?

A

AD

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37
Q

What drug is indicated when someones has CF and G551D allele?

A

Ivacaftor (CFTR potentiator)

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38
Q

Cryptophthalmos, ear anomalies, midline nasal cleft, wide spaced nipples, cryptorchidism, syndactyly

A

Fraser syndrome

FRAS1

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39
Q

Natal teeth, extra frenula, ASD, narrow chest, postaxial-polydactyly

A

Ellis Van Crevald Syndrome

EVC

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40
Q

Multiple dislocated joints (hips, knees, etc), hypertelorism, flat nasal root, prominent forehead, cylindrical fingers, shorts stature

A

Larsen Syndrome

FLBN (filamin B)

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41
Q

Folded ears, VSP, imperforate anus, cryptorchidism, preaxial polydactyly

A

Towns brock

SALL1

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42
Q

What does HOXA13 mutations cause?

A

Hand-foot-uterus syndrome

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43
Q

What do Holoprosencephaly, Gorlin, Greig cephalopolysyndactyly, Saathre Chotzen, and Rubinstein Taybi have in common?

A

SHH signaling pathway

Holoprosencephaly (SHH)

Gorlin (PTCH1)

Greig cephalopolysyndactyly (GLI3)

Saathre Chotzen (TWIST)

Rubinstein Taybi (CREBB)

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44
Q

Lip pits, Cleft L/P

A

Van der Woude

IRF6

(severe form = popliteal pterygoid syndrome)

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45
Q

Cleft L/P, lower lip fistula, webbing of skin in back of legs, bifid scrotum, syndactyly, pyramidal fold of skin overline nail of hallux

A

Popliteal Pterygium syndrome

IRF6

(severe end of vanderwoude spectrum)

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46
Q

What repeat expansion is more likely to expand in mom?

A

Fragile X and Myotonic dystrophy

  • Most repeat expansions expand paternally
  • X = maternal
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47
Q

What is the mechanism of common achondroplasia mutation?

A

Gly380Arg

  • Methylation of G of CG dinucleotide results in readout of A -> leads to TG transition in forward strand
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48
Q

What drug can be used to treat KRAS negative tumors?

A

Imatinib - EGFR inhibitor - upstream of KRAS

  • would be useless if KRAS is mutated
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49
Q

What is 1-specificity?

What is 1-senstivity?

A

1- specificity = false positive rate

1-senstivity = false negative rate

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50
Q

What is the relationship between coefficient of inbreeding and coefficient of consanguinity?

A

Inbreeding = 1/2 of consanguinity

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51
Q

How do you calculate mutation rate from fitness and population frequency?

A

mutation rate = frequency x selection

Selection = 1 - Fitness

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52
Q

Which disorder of creatine metabolism is X linked?

A

Creatine transporter

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53
Q

What is the best screening modality for non ashkenazi jews at risk for Tay- Sachs?

A

Serum Hex A (WBC Hex A if pregnant)

  • Panels usually do not have non-jewish variants
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54
Q

Cathepsin A Deficiency

A

Galactosialidosis

PPGB

  • Lysosomal protease that processes precusors of sialidase and B-galactosidase
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55
Q

Cathepsin C

A

Papillon-Lefevre syndrome

CTSC

  • Removes N-terminal dipeptides from proteins
  • Keratosis palmoplanaris, periodontisis
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56
Q

Cathepsin K

A

Pycnodysotosis

CTSK

  • protease involved in bone resporption
  • Bone fragility, convex nasal ridge, small jaw, skeletal dysplasia
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57
Q

What is inheritance pattern for acute intermittent prophyria?

A

AD - incomplete penetrance

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58
Q

high stool isocoproporphyrin

A

Porphyria Cutanea Tarda

UROD

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59
Q

where is SURF1 located in genome?

A

Autosomal gene that encodes complex IV assembly

  • Most common cause of leigh
60
Q

What is CDG1b?

A

MPI -> phosphomannose isomerase; treat with mannose

61
Q

What finding is common on treated infantile Pompe?

A

Hearing loss and osteopenia

62
Q

high 3-Oh propionate, methylcitrate in UOA

A

PA

63
Q

Which syndrome is associated with absent radii but intact thumbs?

A

Thrombocytopenia absent radius

RMB8A

64
Q

What syndrome is rectal prolapse assocaited with?

A

Cystic Fibrosis

65
Q

What limb anomalies are associated with CDLS?

A

Ulnar defects

  • though can be anything
  • Upper > lower
66
Q

Most common mode of inheritance for hypohidiotic ectodermal dysplasia

A

XL

67
Q

What is mode of inheritance of Aarskog?

A

AD

FGD1

68
Q

Macrosomia, coarse facies, post-axial polydactyly

A

Simpson-Gobani-Behmel

Glypican 3 (XL)

  • Overgrowth + polydactyly

+ Conduction defects

69
Q

What is a pregnancy related complication of cleidocranial dysplasia?

A

RUNX2

Increased risk of needing C-section

70
Q

What % of pierre robin sequence is syndromic? What syndrome is most common?

A

50% syndromic

Half of syndromic = stickler

71
Q

Which clinical feature of non-accidental trauma is not seen in OI?

A

Retinal hemorrhages

72
Q

What does gefitinib target?

A

EGFR mutations

73
Q

What does MYO7A mutations cause?

A

AD -> Deafness

AR -> Deafness or Usher

74
Q

What is the common mutation in IKBKG?

A

Incontinentia pigmenti

80% deletions

75
Q

What causes XL SCID? AR SCID?

A

IL2RG - XL

ADA - AR

76
Q

What is the significance of TNFR5R13B?

A

Most common cause of common vairable immunodeficiency (CVID)

77
Q

Soft skin, myopia, hernias, normal joint mobility

A

Cutis Laxa

FBLN5

78
Q

abnormal teeth and nails

normal hair, skin, and sweat

A

Witkop syndrome

MSX1

ecterdermal dysplasia with normal hair/skin/sweating

79
Q

TSC + renal cysts

A

16p deletion

  • TSC2 + PKD1
80
Q

Most sensitive screening test for DMD in newborn?

A

CK levels

81
Q

What are the three most common recessive conditions in in Ashkenazi Jews?

A

1) Gaucher

2/3) Tay-sachs = CF

4) Familial dysautonomia
5) Canavan

82
Q

leukoplakia + bone marrow failure

A

Fanconi anemia

83
Q

rhabdomyosarcoma, pulmonary pleuroblasoma, multicystic goiter,

A

DICER1

84
Q

Leukoplakia, abnormal nails, marrow failure

A

Dyskeratosis Congenita

Most commonly XLinked, TER

  • Telomere shortening analysis
  • fanconi like + abnormal nails
85
Q

What syndromes predispose to hepatoblastoma?

A

FAP (APC) and Beckwith Weidemann

86
Q

What % of patients with unilateral retinoblastoma carry a germline mutation?

A

15%

87
Q

Chromophobe renal cancer

A

Seen in Birt-Hogg-Dube

Foliculin

Renal cancer + hair follicle cancers + pneumothorax

88
Q

Somatic mutation in which gene is founds in myeloproliferative disorder in down syndrome?

A

GATA1

89
Q

Crizotinib is used to treat tumors with what mutation?

A

Lung cancer with ALK inversion

90
Q

What is the significance of germline POLE mutations?

A

Colorectal cancer with hypermutated tumors

POLE = polymerase epsilon

91
Q

Most common cause of oligospermia, azoospermia, and obstructive azoospermia.

A

Oligospermia: balanced translocation

Azoospermia: Aneuploidy

Obstructive: CBAVD

92
Q

What is the increased risk over background of a major congenital malformation when IVF is used?

A

30%

93
Q

What congenital malformation is a fetus of obese mom at highest relative risk for?

A

NTD

  • also increased Cardiac and CL/P
94
Q

cryptophthalmos, midline nasal cleft, cryptorchidism, syndactyly

A

Fraser syndrome

FRAS1, REM, GRIP1

95
Q

What tissue are prominently affected by HOXA and HOXD genes?

A

Hands and genitals

96
Q

Spatula shaped fingers, multiple large joint dyslocations, hearing loss

A

Larsen Syndrome

FLNB

97
Q

dysplastic nails/teeth, heart defect, short limbs, amish

A

Ellis Van Crevald

EVC

98
Q

XL overgrowth w/ conduction defect and polydactyly

A

Simpson Gobani Behmel

OFD1

XL

99
Q

What are features of non-motile ciliopathies

A

Non-motile cilia = developmental signaling

  • Polydactyly, RP, renal, CNS

Motile cilia = respiratory/patterning -> heterotaxy

100
Q

What are features of motile ciliopathies?

A

Motile cilia = clearance and gradient patterning

Respiratory problems + patterning (kartageners/heterotaxy)

Nonmotile = BBS/Joubert/other named syndromic developmental stuff

101
Q

CFTR G551D

A

Treat with ivacaftor (keep channel open)

102
Q

What causes benign neontal seizures?

A

KCNQ2 and Q3

103
Q

Most common genetic cause of AD PTN

A

BMPR2

104
Q

TNFR5R13B

A

CVID

105
Q

OCRL

A

Lowe Syndrome

oculo-cerebral-reno

PI singaling

106
Q

Most common genes for : Eczema, hyper IgE, diarrhea

A

Hyper IgE syndrome

Stat3 (AD), Dock8 (AR, +viral infections)

107
Q

abnormal teeth/nails with normal hair/sweating

A

Witkop syndrome

MSX1

108
Q

what do you look for in urine of patients with hypophosphatasia?

A

High pyridoxal-5-phosphate (blood)

Phosphtidylethanolamine (urine)

109
Q

Epidermolysis bullosa with scarring below basement membrane

A

COL7A

Epidermolysis bullosa dystrophic

110
Q

Epidermolysis bullosa with scarring in epidermis

A

EB Simplex

Keratin 5, Keratin 14

AD

111
Q

Epidermolysis bullosa with scarring within basement membrane

A

Junctional EB

LAMB3, LAMC2, LAMA3

112
Q

Mito disease with arrhythmia, ptosis, gaze palsy

A

Kearns Sayre

Deletion

113
Q

Neonatal high MMA and HCy, resolves by 6 months

A

Maternal B12 deficiency

-> Transient MMA/ HCy

114
Q

metabolic acidosis + high ammonia

A

Organic Aciduria (IVA, MMA, PA)

115
Q

Suberylglycine in UOA

A

MCAD

116
Q

SMARCB1 (INI1) and LZTR1

A

Schwannomatosis

117
Q

posterior subcapsular cataracts

A

NF2

118
Q

Continguous gene deletion with ADPKD on Ch 16

A

TSC2

119
Q

CGG repeat

A

FMR1

200+ full mutation

55+ premutation

120
Q

alpha synuclein

A

Parkinsons

121
Q

what is biocytin?

A

Substrate for biotinidase, which removes lysine to form biotin

122
Q

SLC25A15

SLC25A13

A

25A15: Ornitine-citruline transporter (HHH)

25A13: Aspartate malate (citrin)

123
Q

Maroteux Lamy syndrome

A

MPS VI - ARSB/N-ACETYLGALACTOSAMINE-4-SULFATASE

DS

124
Q

Sly syndrome

A

MPS VII

B-glucoronidase

HS/DS

125
Q

when should breast MRI/mammo start in BRCA carriers?

A

MRI at 25

mammo at 30

126
Q

lifetime breast/ovarian cancer risk in BRCA

A

Breast ~80%

Ovarian ~40%

  • Both slightly lower in BRCA2 (70 and 20)
127
Q

Male breast ca risk in BRCA2

A

10% (2% in BRCA1)

128
Q

most useful indicator in working up short stature?

A

Growth velocity

129
Q

how do tell which chromosome centromere came from (derivative) in a translocation?

A

Deletion is usually on the derivative

130
Q

how do you tell apart AD and XL-D inheritance on pedigree?

A

no male-to-male transmission in XL-dominant

131
Q

oncogene in burkitt lymphoma

A

8:14 translocation

MYC - ig heavy chain

132
Q

what LOD cutoff shows no recombination in linkage analysis?

A

>3.0

133
Q

what is the empiric risk of a fetal sample with type 2 mosiacism (mosaic found in multiple cultures in same sample) having true mosaicism (vs lab artifact)?

A

20%

134
Q

what type of sequence do restriction endonucleases act on?

A

palindromic

135
Q

Which stage of meiosis are egg cells arrested?

A

diplotene of prophase 1

136
Q

Goiter, rhabdomyosarcoma, pleuropulmonary blastoma

A

DICER1

137
Q

Leukoplakia, abnormal nails, bone marrow failure

A

dyskeratosis congenita

Telomere shortening

138
Q

thyorid, colon, breast cancer

A

PTEN

139
Q

Embryonal Rhabdomyosarcoma

A

SMARCB1

+ schwannomatosis

140
Q

crizotinib

A

ALK inhibitor for nsclc with inversion

141
Q

Coefficient of inbreeding vs coefficient of consanguinity

A

Inbreeding = 1/2 * consanguinity

Consanguinity = (1/2)n

n= links in chain

142
Q

If woman has one affected child with X-linked lethal disorder, what is the chance she is a carrier?

A

2/3rd

143
Q

SURF1 mode of inheritance

A

AR -> Leigh syndrome, complex IV assembly

144
Q

KCNE1, KCNQ1

A

Jarvell and Lange Nielson

145
Q

SCN5A, KCNE5

A

Brugada

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