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Genetics 2 > Arrays, NGS and Epigenetics > Flashcards

Arrays, NGS and Epigenetics Flashcards

exam 2

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1
Q

method to screen specimens for genome wide variation

A

Arrays

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2
Q

identify difference between the test DNA and the control DNA

A

Comparative Genomic Hybridization array

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3
Q

velocardial facial syndrome

A

DiGeorge syndrome

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4
Q

Di George is a

A

microdeletion disorder 22q11.2

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5
Q

SNP array asks

A

which SNPs are present

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6
Q

measure changes in gene regulation via gene expression levels

A

expression arrays

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7
Q

characterize tumors; used to guide tx. based on resistance or response of tumors with similar expression patterns

A

expression arrays

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8
Q

when do we use arrays?

A

used pretty often when we don’t have a clear clinical picture and can be used to identify genes

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9
Q

limitations of arrays (3)

A

(1) may not detect low level mosaicism
(2) only look at quantity, not location
(3) can not detect: translocations or inversion

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10
Q

known translocation or inversion should be followed up with an

A

array

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11
Q

gold standard for validation of variants found in NGS

A

sanger sequencing

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12
Q

sequencing:

I Kb read length

A

sanger

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13
Q

sequencing:

30-400 bp read length

A

Next generation sequencing (NGS)

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14
Q

predominantly on a research basis, but is coming to clinical practice

A

WGS

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15
Q

capture DNA fragments which contain exons prior to sequencing

A

Whole Exome sequencing (WES)

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16
Q

sequencing for a specific list of genes associated with the clinical phenotype

A

panel

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17
Q

NGS potential results: what is it and what sign is it?

Benign

A

(-)

  • does not affect gene function
  • not included in clinical report
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18
Q

NGS potential results: what is it and what sign is it?

variant of uncertain significance (VUS)

A

(?)

  • must meet threshold of evidence
  • not enough evidence to determine if change is pathogenic or benign
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19
Q

NGS potential results: what is it and what sign is it?

Pathogenic

A

(+)

  • disrupts gene function
  • potential to cause health effects
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20
Q

what are medically actionable genes?

A

pathogenic mutations

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21
Q

can patients opt-out of receiving this information of secondary findings?

A

yes

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22
Q

medically actionable genes are those that have

A
  • high penetrance

- established interventions

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23
Q

Potential results:

focused (4)

A

(1) mutations definitely related to phenotype
(2) variants possibly related to phenotype
(3) medically actionable mutations (secondary findings)
(4) carrier status for Mendelian disorders (AR or X-linked)

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24
Q

limitation of NGS;

can not detect (4)

A

(1) triplet repeat expansions
(2) methylation /imprinting
(3) structural rearrangements
(4) copy number variation- not as reliable as other methods

25
Q

True or False:

WES/WGS is a “one size fits all” tests

A

false, it is not

26
Q

modification of gene expression without alteration of underlying DNA sequence

A

epigenetics

27
Q

Epigenetics changes (3)

A

(1) methylation
(2) nucleosome positioning
(3) Histone Modification

28
Q

evidence for epigenetic modifications

A

concordance (or not) of disease between monozygotic twins

29
Q

evidence for epigenetic modifications

A

concordance (or not) of disease between monozygotic twins

30
Q

high throughout sequencing

A

Next Generation Sequencing

31
Q

modification of gene expression without changing DNA sequence

A

Epigenetics

32
Q

Level of resolution:

2-3 Mb

A

karyotype

33
Q

Level of resolution:

120-400 kb

A

FISH

34
Q

Level of resolution:

500bp

A

Array

35
Q

Level of resolution:

1 bp

A

NGS

36
Q

may or may not result in a change of the aa sequence

A

SNP

37
Q

SNPs observed in groups =

A

haplotype

38
Q

can be used for gene mapping

A

SNP

39
Q

CGH array:

Red=more of the patient DNA

A

duplication

40
Q

CGH array:

Green= more of the control

A

deletion

41
Q

one thing we need to assume with SNPs

A

that all SNPs occur with similar frequency

42
Q

for SNP array we should expect _____ and to have ____ copies at each position

A

for SNP array we should expect heterozygosity and to have two copies at each position

43
Q

How can we determine UPD/IBD vs deletion?

A

Both have drop out of the AB trace and we need to see the log-ratio data

44
Q

provide more information than CGH arrays

A

SNP

45
Q

SNP arrays reports on ___________, with ___________ being more easily recognized

A

SNP arrays reports on amount of DNA with deletions being more easily recognized

46
Q

SNP arrays can identify _____ of heterozygosity or _______

A

SNP arrays can identify loss of heterozygosity or uniparental disomy

47
Q

with SNP arrays we can only identify _______ (meiosis 2 error) and _____can’t be identified (meiosis 1 error)

A

with SNP arrays we can only identify isodisomy (meiosis 2 error) and heterodisomy can’t be identified (meiosis 1 error)

48
Q

why do we care about loss of heterozygosity? (4)

A

(1) Uniparental disomy UPD
(2) Imprinting
(3) consaguinity
(4) autosomal recessive conditions

49
Q

Arrays are valuable for assessing for _______ in apparently ________ rearrangements found on karyotype

A

Arrays are valuable for assessing for small deletions in apparently balanced rearrangements found on karyotype

50
Q

NGS that takes into about 180,00 exons, 3% of the genome

A

WES

51
Q

NGS that takes in from one to a few thousand genes

A

Panels

52
Q

secondary findings

A

when you find something that you were not looking for

53
Q

ACMG recomendations (3)

A

(1) 1 of the 59 genes
(2) high penetrance
(3) interventions in place

54
Q

Potential Results: Expanded (3)

A

(1) mutations in genes unrelated to phenotype
(2) variants in genes unrelated to phenotype
(3) deleterious mutations in genes with no disease association

55
Q

what is a variant of uncertain significance (VUS)

A

A change in a gene for which there is not enough information to determine its health effect

56
Q

epigenetic modifications lead to changes in the _______ of genes

A

expression

57
Q

Epigenetic modifications _____ over time and are ______

A

Epigenetic modifications change over time and are reversible

58
Q

can affect the adult human methylome

A

early gestation changes in methylation

Genetics 2 (7 decks)

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