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fall 2022 > molecular exam 3 > Flashcards

molecular exam 3 Flashcards

1
Q

alternative form of a genetic locus

A

allele

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2
Q

any heritable change in DNA sequence

A

mutation

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3
Q

genetic variants occurring in >1% of a population

A

polymorphism

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4
Q

insertion, deletion, duplication, repeating patters of DNA that vary in number

A

copy number variation

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5
Q

the most common polymorphism

A

SNP

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6
Q

coding region plus 10kb upstream is

A

a gene

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7
Q

a set of associated SNP alleles in a region of a chromosome

A

haplotype

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8
Q

factors effecting gene penetrance

A
  1. importance of the function of the protein encoded by the gene
  2. functional important of the mutation
  3. interaction with other genes
  4. onset of somatic mutations
  5. interaction with the environment
  6. existence of alternative pathways to substitute for LOF
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9
Q

diseases with high penetrance

A

SCD, thalassemias, huntingtons, CF, color blindness

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10
Q

most diseases are multifactorial and of low penetrance

A

true

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11
Q

type 1 and 2 diabetes
RA, chrohn’s, CHD, and asthma are

A

multifactorial (Low Penetrance)

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12
Q

studies that find correlations of genes with disease by comparing frequency of gene variation with frequency of disease

A

case control study

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13
Q

a population based study where diseased and non-diseased individuals are unrelated

A

GWAS

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14
Q

the tendency of genes or other DNA seqences at specific loci to be inherited together as a consequence of their physical proximity to one another on a single chromosome

A

Linkage disequilibrium

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15
Q

gives strength of association

A

relative risk

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16
Q

direct causation
epistatic effect
population stratification
linkage disequilibrium

A

causes of associations

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17
Q

linkage disequilibrium focuses on

A

two alleles/SNPs

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18
Q

occurs when a set of alleles on one copy of a chromosome stay associated with each other at a higher frequency than would be expected if recombination were completely random

A

linkage disequilibrium

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19
Q

SNPs are the marker of choice for

A

Linkage studies, bc they are abundant, have low rate of mutation, and are easy to genotype on a larger scale

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20
Q

association throughout the whole genome of SNPs with diseases or phenotypes

A

GWAS

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21
Q

provide individuals with info about their risk of developing disease or trait and/or their odds of responding in a particular way to a drug

A

direct to consumer testing

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22
Q

multiple hypothesis testing

A

p=0.5 there is a 5% chance for (hypothesis) to occur randomly and a 95% chance the association is real

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23
Q

the failure to detect an allele in a sample or failure to amplify the allele

A

allele drop out

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24
Q

repeated telomeric breakage and instability of fusion of sister chromatids, as a result they are broken apart during anaphase

A

breakage fusion bridge cycles

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25
Q

large scale screening of a population for a diseases to ID ppl who probably do and probably do not have a disease
not diagnostic

A

population screening

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26
Q

population screening for a gene that can cause disease in carrier of offspring

A

genetic screening

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27
Q

goals of screening

A

early detection
prevent or reverse disease process
allow informed reproductive decision

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28
Q

principles of screening for a disease

A
  1. disease should be serious and common
  2. disease should be well understood
  3. there should be effective treatment available
  4. test should be easy and cheap
  5. test should be valid/reliable
  6. sources of dx and treatment should be accessible
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29
Q

the ability of a test to correctly identify those with the disease

A

sensitivity

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30
Q

the ability of a test to correctly identify those without the disease

A

specificity

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31
Q

guidelines for heterozygote screening

A

screen should be voluntary and confidential
informed consent must be given
education and counseling must be available
quality control of test
equal access

32
Q

genetic testing performed to ID people w/ a disease causing gene before symptoms develop

A

aid in repro decision
improve health
currently universal pre-symptomatic screening is impractical

33
Q

limits of genetic testing

A

not 100% accurate
reveals mutations not disease
may not detect all disease causing mutations
can lead to complex ethical considerations

34
Q

provides reassurance when normal, provide risk info in pregnancy planning, allows psychological preparation if baby affected, prepares health care team, allows for informed decision making about termination

A

benefits of prenatal diagnosing

35
Q

maternal age >35
previous child w/ aneuploidy
family history of genetic defects
increased NT defects

A

all indicate prenatal screening by amniocentis

36
Q

preformed 10-11 weeks post LMP
risk of fetal loss approx 1%
mosaicism can confuse Dx
some evidence of increased limb deficiencies

A

chorionic villus sampling

37
Q

applications of cordocentisis

A

for studies when ultrasound shows structural abnormality and rapid Dx is needed
if hematological issues arise
helps make distinction between true and false mosaicism

38
Q

lower sensitivity than using amniotic methods
non-invasive
helps detect NTDs and trisomies

A

maternal serum screening

39
Q

1 in 10^3 – 10^7 nucleated cells in maternal blood are

A

fetal, proportion decreases with increasing maternal BMI

40
Q

fetal cell analysis

A

FISH, chromosome specific DNA probes
uses cell sorting
less invasive
can be done as early as 7 wks

41
Q

accurate detection of increased gene dosage due to trisomies can be done with

A

digital PCR (relative chromosome dosage)

42
Q

curves that delimit decision boundaries in accepting or denying child is aneuploid

A

sequential probability ratio test

43
Q

analysis of fetal-specific differentially methylated regions using methylated DNA immunoprecipitation

A

MeDiP, also uses qPCR to assess fetal chromosome dosing assessment
higher sensitivity compared to RNA-SNP method

44
Q

cffDNA in health adults comes from

A

hematopoietic cells undergoing apoptosis
increased cffDNA can indicate several pregnancy-related disorders

45
Q

non-invasive prenatal testing methodologies

A

WGS, SNP, target capture, microarray based

46
Q

relies on identifying and counting DNA fragments in maternal serum
only first 25-36 BP are sequenced (aka a Tag)
count and compare tags at a specific chromosome and compare to reference chromosome number

A

WGS

47
Q

a panorama simultaneously targets 19,000 SNPs

A

SNP based targeted sequencing

48
Q

T21 detection by F-S* ratio

A

euploid is higher ratio

49
Q

SNP based methods for microdeletions can Dx

A

digeorge
angelman
prader-willi
cri-du-chat

50
Q

microdeletion risk is reported using

A

Odds of being Affected given a Positive Result

51
Q

OAPR takes into account

A

clinical incidence of disease
% cases caused by deletion of entire covered region

52
Q

Digital Analysis of Selected Regions

A

selected analysis of cell-free DNA in maternal blood for evaluation of fetal trisomy

53
Q

factors that affect NIPT results

A

fetal fraction
maternal BMI

54
Q

fetal fraction increases

A

by 0.1% in the first 21 weeks
by 1% in weeks 22-40

55
Q

twins show

A

increased ff but not doubled

56
Q

steps for visualizing metaphase chromosomes

A
  1. culture patient cells
  2. add PHA to stimulate division
  3. colcemid stops cells in metaphase
  4. methanol and acetic acid fixes chromosomes
57
Q

dye that binds to AT rich DNA and G band segments

A

quinacrince

58
Q

how are R bands visualized

A

87 Celsius for 10 mins then add Giemsa stain

59
Q

how to visualize centromeres

A

alkali treatment

60
Q

Euchromatin rich areas high in GC content are

A

R bands

61
Q

types of fish probes

A

chromosome painting (whole chromosome) centromere probes, locus specific probes,

62
Q

locus specific probes detect

A

gene rearrangements, microdeletions, and amplifications
used to detect aneuploidies and tumors

63
Q

types of structural chromosome abnormalities

A

translocation, inversion, deletion, insertion, ring, isochromosome

64
Q

chromosome 22q11.2 deletion

A

DiGeorge

65
Q

chromosome 7q11.23 deletion

A

williams syndrome

66
Q

deletion on chromosome 4 4p16

A

wolf-hirschhorn

67
Q

amplification copy number variation is the most common change seen in malignancies

A

true

68
Q

what does comparative genomic hybridization do

A

CGH analysis software measures fluorescence intensity values along the length of the chromosomes and translates the ratios into chromosome profiles.

The ratio of green to red fluorescence values is used to quantitate genetic imbalances in tumor samples.

69
Q

limits of CGH

A

cannot detect less than 5-10 Mb changes
cannot differentiate between diploid, triploid, and tetraploid
cannot ID balanced structural xsome translocations
cannot distinguish mosaicism from trisomy

70
Q

applications of micro CGH

A

classify tumors, tumor progression, genomic changes at various stages

71
Q

applications of CGH reproductive genetic diagnosis

A

evaluation of fetal abnormalities/stillbirths, can ID chromosome abnormalities smaller than seen karyotyping, submircroscopic deletions detected,

72
Q

Benefits of pre-natal CGH

A

no tissue culture needed
automated
better resolution/detects small rearrangements

73
Q

first tier test when structural malformations are seen on an ultrasound

A

chromosomal micro-arrays

74
Q

cell free fetal DNA is derived from

A

trophoblast
140-180 bp

75
Q

massively parallel genomic sequencing is used to

A

detect aneuploid fetus, gives higher Z-score

76
Q

who should be considered for whole exome sequencing

A

patients w/ genetic disease that hasn’t been ID’d or diagnosis is unclear
if testing many genes is cost prohibitive

77
Q

chromosome structure abnormalities

A

translocation, deletion, inversion, isochromosome, derivative chromosome, insertion, ring chromosome

fall 2022 (6 decks)

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