Molecular Genetics Tests Flashcards

1
Q

Which test is used for fragile X syndrome?

A

PCR/Fragment analysis

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2
Q

What is a test looking for in Fragile X?

A

CGG repeat expansion in the 5’ UTR of the FMR1 gene

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3
Q

Which test is used for spinal muscular atrophy?

A

Copy number analysis (MLPA)

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4
Q

What is a test looking for in SMA?

A

Homozygous deletion of the SMN1 gene, including at least exon 7

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5
Q

Which test is used for Huntington Disease?

A

PCR/Fragment analysis

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6
Q

What is a test looking for in HD?

A

CAG repeat expansion in exon 1 of HTT gene

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7
Q

Which test is used for myotonic dystrophy type 1?

A

PCR/Fragment analysis

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8
Q

What is a test looking for in DM1?

A

CTG repeat expansion in the DMPK gene

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9
Q

Which test is used for prader-willi/angelman syndrome?

A

Methylation study

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10
Q

What is a test looking for in PWS/AS?

A

abnormal methylation pattern in critical region 15q11-q13

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11
Q

Which test is used for y-chromosome deletion (Y-del)?

A

PCR/Fragment analysis

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12
Q

What is a test looking for in y-chromosome deletion (Y-del)?

A

deletions in regions of the Y chromosome called azoospermia factor (AZF) A, B, or C

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13
Q

What do microsatellite markers look for?

A

uniparental disomy (UPD) and maternal cell contamination (MCC)

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14
Q

Which test is used for beckwith-wiedemann/Russell Silver syndrome (BWS/RSS)?

A

Copy number and methylation study (MS-MLPA)

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15
Q

Adapter ligation-based library construction

A

shear or enzymatically treat high molecular weight DNA to fragment OR derive fragments from other preparatory methods

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16
Q

Transposon-based library construction

A

transposons interact with genome and creates breaks in DNA and adds in unique adapter sequencing ends.

17
Q

PCR-related problems in NGS

A

PCR can introduce preferential amplification (jackpotting) of certain fragments, PCR also introduces false positive artifcats due to substitution errors by the polymerase, cluster formation is a type of pCR

18
Q

coverage

A

average number of times that nucleotides in aligned sequence reads at different genomic positions appear in a sequencing data set

19
Q

mapping

A

process of searching the sequence of a read against a reference genome sequence to locate its origin in the genome

20
Q

paired-end read

A

sequence read data obtained from the two ends of a library fragment

21
Q

variant calling

A

identification of sequence difference at specific positions of an individual genome (or transcriptome) in comparison with a reference genome

22
Q

WES

A

identifies variants across a wide range of applications; achieves comprehensive coverage of coding regions; provides a cost-effective alternative to whole-genome sequencing, produces a smaller, more manageable date set for faster, easier analysis compared to whole-genome approaches

23
Q

4 channel sequencing imaging cycles

A

HiSeq, MiSeq

24
Q

2-channel sequencing imaging cycles

A

NextSeq, MiSeq

25
Q

primary analysis (sequence generation)

A

signal analysis, base calling, base quality scoring, read generation

26
Q

econdary analysis (sequencing processing)

A