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MI and Genomics > GM 03: Testing > Flashcards

GM 03: Testing Flashcards

1
Q

Genetic tests often performed on (X) material that’s purified from patient’s (Y) samples.

A 
X = DNA 
Y = blood
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2
Q

T/F: Only blood samples can be used for genetic tests.

A

False - some cases require other tissues to be examined

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3
Q

Abnormal events during (X) can cause disruption of normal (Y). These are gross structural/numerical changes that are detected with techniques that (Z).

A 
X = meiosis;
Y = chromosome number and structure;
Z = image whole chromosomes
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4
Q

List techniques that detect abnormalities in whole chromosome number/structure.

A
  1. Karyotype (and spectral karyotyping (SKY))
  2. (Interphase) FISH
  3. Chromosomal microarray
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5
Q

Karyotype allows visualization of (X), stained with (Y).

A 
X = metaphase chromosomes
Y = Giemsa dye
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6
Q

(X) imaging technique paints each chromosome a different color. (Y) probes are used to target (Z).

A 
X = Spectral Karyotyping (SKY)
Y = DNA
Z = specific chromosomes
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7
Q

In SKY, you would expect to see (X) number of each colored (Y) in a diploid sample.

A 
X = 2
Y = chromosome
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8
Q

Name one key benefit to using SKY. Which abnormality is visually obvious?

A

Contrasting colors make presence of translocation obvious

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9
Q

(X) chromosomal test(s) require both harvesting and amplification of patient’s cells.

A

X = karyotyping

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10
Q

T/F: Interphase FISH technique requires neither harvesting nor amplification of patient cells.

A

False

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11
Q

List the main characteristics that can be visualized/identified in karyotyping.

A
  1. Number
  2. Size/structure
  3. centromere position
  4. Banding pattern
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12
Q

To avoid the need to harvest and amplify patient cells for chromosomal testing, which method(s) can be used?

A
  1. (Interphase) FISH

2. Chromosomal microarray

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13
Q

Interphase FISH uses probes directed toward:

A

Particular chromosomal region

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14
Q

Interaphse FISH technique primarily used to ID changes in:

A

Chromosomal copy number

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15
Q

How can Interphase FISH be used to ID a translocation?

A

Two probes from different chromosomes are found to co-localize

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16
Q

T/F: Interphase FISH test results should always be verified with full karyotyping.

A

True

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17
Q

Key disadvantage of microarray.

A

Only able to pinpoint changes in copy number, not spatial organization

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18
Q

Microarray can’t detect (X) rearrangement/translocation due to its inability to detect (spatial/numerical) changes in chromosomes.

A

X = balanced;

Spatial

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19
Q

PCR and (X) blotting techniques are primarily used to detect changes in (Y) of (Z).

A 
X = Southern;
Y = size
Z = genes
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20
Q

T/F: Generally, PCR will not detect subtle change in DNA sequence.

A

True

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21
Q

How can a PCR-based approach, aka (X) approach, be modified to identify specific changes to gene sequence?

A

X = allele-specific PCR

The expected mutation is known

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22
Q

How would you design the PCR (X) in allele-specific PCR to detect subtle change?

A

X = primers;

Complementary to either wild-type or mutant allele sequence

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23
Q

In allele-specific PCR, what tells you the patient has mutant (X)?

A

X = allele;

If you use primer complementary to mutant allele and the target amplification proceeds

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24
Q

Aside from allele-specific PCR, a similar method is allele-specific (X). This method uses which part of genetic information?

A

X = hybridization;

Full genomic DNA

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25
Q

Allele-specific hybridization. (X) is hybridized to (Y). Which tool is used to then detect (Z)?

A

X = complete genomic DNA;
Y = spot on nylon membrane
Labeled oligoNT probe
Z = either normal or mutant allele

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26
Q

T/F: Allele-specific hybridization allows you to skip electrophoresis step of allele-specific PCR.

A

True

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27
Q

T/F: DNA separated by size in allele-specific hybridization.

A

False

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28
Q

How could disease exhibiting allelic heterogeneity be detected via allele-specific PCR/hybridization?

A

Can’t - a more unbiased approach needs to be implemented

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29
Q

A preferred testing method in cases of allelic heterogeneity is to directly ID (X) through (Y). What’s the classical method for doing this?

A 
X = the single BP sequence changes
Y = DNA sequencing

Dideoxy (Sanger) sequencing

30
Q

Sanger sequencing is a method similar to (X), using mixture of (Y).

A 
X = PCR
Y = dNTPs and (labeled) ddNTPs
31
Q

T/F: Sanger sequencing allows you to skip electrophoresis step.

32
Q

Why is Sanger sequencing a (good/poor) method for detecting mutation causing cystic fibrosis?

A

Poor;

If not caused by delta(F508) mutation, limited by read length (can’t sequence entire CFTR gene to find mutation)

33
Q

How can Sanger sequencing be improved for detecting mutation causing disease with high allelic heterogeneity (like cystic fibrosis)?

A
  1. Sequence only the exons (harbor most predictable mutations)
  2. Test for most common mutations
34
Q

Detection of a “variant of unknown significance” can occur with (X) testing, such as (Y).

A 
X = sequence-based;
Y = Sanger sequencing method
35
Q

What does it mean to detect variant of unknown significance?

A

Identifying sequence change that hasn’t been previously characterized and don’t have predictable effect on gene product

36
Q

The two key limitations to sequence-based testing (i.e. Sanger) can be worked around via which approach?

A

Test affected family members first (even if not the patient)

37
Q

If patient exhibits disease pathology suggestive of particular disorder, but mutations can’t be ID’d by exonic sequencing methods, which test is offered next?

A

Linkage tests

38
Q

T/F: The same types of DNA markers used in linkage analysis can also be used for linkage testing.

39
Q

In linkage testing using RFLPs, what could you do with the patient’s (mRNA/DNA)?

A

DNA;

  1. Digest then Southern blotting
  2. PCR, digest, electrophoresis
40
Q

In linkage testing using SSLPs, what could you do with the patient’s (mRNA/DNA)?

A

DNA;

Just amplify (PCR) and electrophoresis

41
Q

In linkage testing using SSLPs, what is the (mRNA/DNA) digested with?

A

No need to digest - sequence lengths vary already, so just amplify and electrophoresis

42
Q

What’s uniparental disomy?

A

Individual actually enherited both copies of chromosome from same parent

43
Q

Uniparental disomy can be detected as (X) on karyotype.

A

X = normal

44
Q

T/F: Uniparental disomy can cause unaffected parent to pass on recessive disorder.

A

True - if carrier

45
Q

Which methods can be used to detect uniparental disomy?

A

Linkage testing

46
Q

What’s a haplotype?

A

Group of genes in that are inherited together from a single parent

47
Q

You’re use (X) testing to verify suspicions of uniparental disomy. If you’re correct, you expect all (Y) to match (Z) from (one/both) parents.

A

X = linkage
Y = marker loci
Z = haplotype(s)
One parent

48
Q

In uniparental disomy, heterodisomy means the individual inherited (X) from (one/both) parent(s). Where did the (Y) error occur?

A

X = non-identical chromosomes;
One
Y = nondisjunction
Meiosis I

49
Q

In uniparental disomy, isodisomy means the individual inherited (X) from (one/both) parent(s). Where did the (Y) error occur?

A

X = identical chromosomes;
One
Y = nondisjunction
Meiosis II

50
Q

You’re use (X) testing to verify suspicions of uniparental disomy. If marker alleles are homozygous for one parent’s alleles in a haplotype, which phenomenon is seen?

A

X = linkage

Isodisomy

51
Q

Name limitations to linkage genetic tests.

A
  1. Require samples from multiple (heterozygous and affected) family members
  2. Recombination can separate disease locus and marker
52
Q

(X) testing strategy to ID uniparental disomy (can/can’t) also ID imprinting defects.

A

X = haplotype;

Can, but only if derived from single parent via UPD or deletion

53
Q

List the methods that can lead to Prader-Willi Syndrome. Star the one overlooked by haplotype testing.

A
  1. Deletion of paternal 15q11-13 region
  2. Uniparental (maternal) disomy of same region
  3. Imprinting defect*
54
Q

List the methods that can lead to Angelman Syndrome. Star the one overlooked by haplotype testing.

A
  1. Deletion of maternal 15q11-13 region
  2. Uniparental (paternal) disomy of same region
  3. Imprinting defect*
55
Q

What’s a limitation to diagnostic tests (like sweat test for CF)?

A
  1. Can’t make conclusions about individuals who may not have developed disease yet
  2. Can’t yield insight about carrier status
56
Q

When testing a minor child, if the carrier state doesn’t affect his health but does affect future reproductive decisions, should carrier status be revealed to parents?

A

No - preferable to wait until adult years

57
Q

Describe isoelectrical focusing.

A

Separating different molecules by differences in their isoelectric point (pI)

58
Q

A biochemical testing for hemoglobinopathy analysis is (X), which is essentially protein electrophoresis that separates Hb subunits according to (Y), within (Z) gradient.

A 
X = isoelectric focusing
Y = size and charge properties
Z = pH
59
Q

List some situations in which profiling chromosomes may be appropriate/necessary.

A
  1. Problems in early growth/dev
  2. Infertility
  3. Older-age mother
  4. Neoplasia
  5. Still birth
  6. Family history
60
Q

In chromosomal microarray, (X) is labeled green and (Y) is labeled red. What are you comparing?

A 
X = normal/reference DNA
Y = fetal/patient DNA

Compare amount of genetic info between the two (to detect extra/missing copies)

61
Q

Chromosomal microarray: yellow spot indicates (X).

A

X = equal copy/copies between reference and fetal sample

62
Q

Chromosomal microarray: red spot indicates (X) and green spot (Y).

A 
X = extra copy/copies  in patient sample
Y = missing copy/copies  in patient sample
63
Q

Chromosomal microarray can detect (X) BP and karyotypes can detect (Y) BP.

A 
X = under 0.5 million
Y = 7-10 million
64
Q

(focused/expanded) panel of mutations is better testing strategy for increasing allelic heterogeneity.

65
Q

(Gene/whole genome) sequencing is better testing strategy for increasing allelic heterogeneity.

A

Whole genome

66
Q

(Single mutation test/panel of mutations) is better testing strategy for increasing allelic heterogeneity.

A

Panel of mutations

67
Q

(Gene sequencing/expanded panel of mutations) is better testing strategy for increasing allelic heterogeneity.

A

Gene sequencing

68
Q

Which technique can be

used to measure the relative expression of many gene transcripts simultaneously?

A

Microarray

69
Q

(X) technique measures relative amounts of DNA

between two samples. This is well suited to measure (Y) in genome.

A 
X = Comparative genomic hybridization
Y = copy number variation
70
Q

Why is PCR a (good/poor) technique to use to detect a gene deletion?

A

Poor;
Better suited to identify small changes that can be contained within interval small enough for amplification by primers/Taq

MI and Genomics (16 decks)

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