Molecular Genetics Tests Flashcards
Which test is used for fragile X syndrome?
PCR/Fragment analysis
What is a test looking for in Fragile X?
CGG repeat expansion in the 5’ UTR of the FMR1 gene
Which test is used for spinal muscular atrophy?
Copy number analysis (MLPA)
What is a test looking for in SMA?
Homozygous deletion of the SMN1 gene, including at least exon 7
Which test is used for Huntington Disease?
PCR/Fragment analysis
What is a test looking for in HD?
CAG repeat expansion in exon 1 of HTT gene
Which test is used for myotonic dystrophy type 1?
PCR/Fragment analysis
What is a test looking for in DM1?
CTG repeat expansion in the DMPK gene
Which test is used for prader-willi/angelman syndrome?
Methylation study
What is a test looking for in PWS/AS?
abnormal methylation pattern in critical region 15q11-q13
Which test is used for y-chromosome deletion (Y-del)?
PCR/Fragment analysis
What is a test looking for in y-chromosome deletion (Y-del)?
deletions in regions of the Y chromosome called azoospermia factor (AZF) A, B, or C
What do microsatellite markers look for?
uniparental disomy (UPD) and maternal cell contamination (MCC)
Which test is used for beckwith-wiedemann/Russell Silver syndrome (BWS/RSS)?
Copy number and methylation study (MS-MLPA)
Adapter ligation-based library construction
shear or enzymatically treat high molecular weight DNA to fragment OR derive fragments from other preparatory methods
Transposon-based library construction
transposons interact with genome and creates breaks in DNA and adds in unique adapter sequencing ends.
PCR-related problems in NGS
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
coverage
average number of times that nucleotides in aligned sequence reads at different genomic positions appear in a sequencing data set
mapping
process of searching the sequence of a read against a reference genome sequence to locate its origin in the genome
paired-end read
sequence read data obtained from the two ends of a library fragment
variant calling
identification of sequence difference at specific positions of an individual genome (or transcriptome) in comparison with a reference genome
WES
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
4 channel sequencing imaging cycles
HiSeq, MiSeq
2-channel sequencing imaging cycles
NextSeq, MiSeq
primary analysis (sequence generation)
signal analysis, base calling, base quality scoring, read generation
econdary analysis (sequencing processing)
