Molecular Genetics Tests

Question 1

Which test is used for fragile X syndrome?

Answer 1

PCR/Fragment analysis

Question 2

What is a test looking for in Fragile X?

Answer 2

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

Question 3

Which test is used for spinal muscular atrophy?

Answer 3

Copy number analysis (MLPA)

Question 4

What is a test looking for in SMA?

Answer 4

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

Question 5

Which test is used for Huntington Disease?

Answer 5

PCR/Fragment analysis

Question 6

What is a test looking for in HD?

Answer 6

CAG repeat expansion in exon 1 of HTT gene

Question 7

Which test is used for myotonic dystrophy type 1?

Answer 7

PCR/Fragment analysis

Question 8

What is a test looking for in DM1?

Answer 8

CTG repeat expansion in the DMPK gene

Question 9

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

Answer 9

Methylation study

Question 10

What is a test looking for in PWS/AS?

Answer 10

abnormal methylation pattern in critical region 15q11-q13

Question 11

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

Answer 11

PCR/Fragment analysis

Question 12

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

Answer 12

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

Question 13

What do microsatellite markers look for?

Answer 13

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

Question 14

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

Answer 14

Copy number and methylation study (MS-MLPA)

Question 15

Adapter ligation-based library construction

Answer 15

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

Question 16

Transposon-based library construction

Answer 16

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

Question 17

PCR-related problems in NGS

Answer 17

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

Question 18

coverage

Answer 18

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

Question 19

mapping

Answer 19

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

Question 20

paired-end read

Answer 20

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

Question 21

variant calling

Answer 21

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

Question 22

WES

Answer 22

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

Question 23

4 channel sequencing imaging cycles

Answer 23

HiSeq, MiSeq

Question 24

2-channel sequencing imaging cycles

Answer 24

NextSeq, MiSeq

Question 25

primary analysis (sequence generation)

Answer 25

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

Question 26

econdary analysis (sequencing processing)