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fall 2022 > molecular exam 3 > Flashcards

molecular exam 3 Flashcards

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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
large scale screening of a population for a diseases to ID ppl who probably do and probably do not have a disease not diagnostic
population screening
26
population screening for a gene that can cause disease in carrier of offspring
genetic screening
27
goals of screening
early detection prevent or reverse disease process allow informed reproductive decision
28
principles of screening for a disease
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 5. sources of dx and treatment should be accessible
29
the ability of a test to correctly identify those with the disease
sensitivity
30
the ability of a test to correctly identify those without the disease
specificity
31
guidelines for heterozygote screening
screen should be voluntary and confidential informed consent must be given education and counseling must be available quality control of test equal access
32
genetic testing performed to ID people w/ a disease causing gene before symptoms develop
aid in repro decision improve health currently universal pre-symptomatic screening is impractical
33
limits of genetic testing
not 100% accurate reveals mutations not disease may not detect all disease causing mutations can lead to complex ethical considerations
34
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
benefits of prenatal diagnosing
35
maternal age >35 previous child w/ aneuploidy family history of genetic defects increased NT defects
all indicate prenatal screening by amniocentis
36
preformed 10-11 weeks post LMP risk of fetal loss approx 1% mosaicism can confuse Dx some evidence of increased limb deficiencies
chorionic villus sampling
37
applications of cordocentisis
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
lower sensitivity than using amniotic methods non-invasive helps detect NTDs and trisomies
maternal serum screening
39
1 in 10^3 -- 10^7 nucleated cells in maternal blood are
fetal, proportion decreases with increasing maternal BMI
40
fetal cell analysis
FISH, chromosome specific DNA probes uses cell sorting less invasive can be done as early as 7 wks
41
accurate detection of increased gene dosage due to trisomies can be done with
digital PCR (relative chromosome dosage)
42
curves that delimit decision boundaries in accepting or denying child is aneuploid
sequential probability ratio test
43
analysis of fetal-specific differentially methylated regions using methylated DNA immunoprecipitation
MeDiP, also uses qPCR to assess fetal chromosome dosing assessment higher sensitivity compared to RNA-SNP method
44
cffDNA in health adults comes from
hematopoietic cells undergoing apoptosis increased cffDNA can indicate several pregnancy-related disorders
45
non-invasive prenatal testing methodologies
WGS, SNP, target capture, microarray based
46
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
WGS
47
a panorama simultaneously targets 19,000 SNPs
SNP based targeted sequencing
48
T21 detection by F-S* ratio
euploid is higher ratio
49
SNP based methods for microdeletions can Dx
digeorge angelman prader-willi cri-du-chat
50
microdeletion risk is reported using
Odds of being Affected given a Positive Result
51
OAPR takes into account
clinical incidence of disease % cases caused by deletion of entire covered region
52
Digital Analysis of Selected Regions
selected analysis of cell-free DNA in maternal blood for evaluation of fetal trisomy
53
factors that affect NIPT results
fetal fraction maternal BMI
54
fetal fraction increases
by 0.1% in the first 21 weeks by 1% in weeks 22-40
55
twins show
increased ff but not doubled
56
steps for visualizing metaphase chromosomes
1. culture patient cells 2. add PHA to stimulate division 3. colcemid stops cells in metaphase 4. methanol and acetic acid fixes chromosomes
57
dye that binds to AT rich DNA and G band segments
quinacrince
58
how are R bands visualized
87 Celsius for 10 mins then add Giemsa stain
59
how to visualize centromeres
alkali treatment
60
Euchromatin rich areas high in GC content are
R bands
61
types of fish probes
chromosome painting (whole chromosome) centromere probes, locus specific probes,
62
locus specific probes detect
gene rearrangements, microdeletions, and amplifications used to detect aneuploidies and tumors
63
types of structural chromosome abnormalities
translocation, inversion, deletion, insertion, ring, isochromosome
64
chromosome 22q11.2 deletion
DiGeorge
65
chromosome 7q11.23 deletion
williams syndrome
66
deletion on chromosome 4 4p16
wolf-hirschhorn
67
amplification copy number variation is the most common change seen in malignancies
true
68
what does comparative genomic hybridization do
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
limits of CGH
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
applications of micro CGH
classify tumors, tumor progression, genomic changes at various stages
71
applications of CGH reproductive genetic diagnosis
evaluation of fetal abnormalities/stillbirths, can ID chromosome abnormalities smaller than seen karyotyping, submircroscopic deletions detected,
72
Benefits of pre-natal CGH
no tissue culture needed automated better resolution/detects small rearrangements
73
first tier test when structural malformations are seen on an ultrasound
chromosomal micro-arrays
74
cell free fetal DNA is derived from
trophoblast 140-180 bp
75
massively parallel genomic sequencing is used to
detect aneuploid fetus, gives higher Z-score
76
who should be considered for whole exome sequencing
patients w/ genetic disease that hasn't been ID'd or diagnosis is unclear if testing many genes is cost prohibitive
77
chromosome structure abnormalities
translocation, deletion, inversion, isochromosome, derivative chromosome, insertion, ring chromosome

fall 2022 (6 decks)

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