Chapter 22: Single Nucleotide Polymorphism Profiling

Single Nucleotide Polymorphism (SNP)

It constitutes a single-base-pair change originating from a spontaneous mutation that can be a base substitution, insertion, or deletion at a single site.

HLA-DQA1 gene

A a member of the human leukocyte antigen (HLA) family, which contains a large number of genes involved in the immune response in humans.

DQα AmpliType® kit

The first commercial kit, developed in the late 1980s by Cetus Corporation in Emeryville, CA.

allele-specific hybridization

In _______, allele discrimination is based on an optimal condition allowing only the perfectly matched probe–target hybridization to form.

Primer extension methods

These are based on the ability of DNA polymerase to incorporate specific deoxynucleotides (dNTPs) complementary to the sequence of the template DNA.

Allele-specific oligonucleotide ligation

It is based on the condition that only the allelic probe perfectly matched to the target is ligated.

invasive cleavage method

In the ______, allelic discrimination is based on DNA sequence-specific cleavage by endonucleases.

de novo genome sequencing

In _________, uncharacterized genomes or characterized genomes with substantial structural variations are sequenced.

resequencing applications

In ________, characterized genomes are sequenced. Sequence reads are assembled against an existing reference sequence to identify sequence polymorphisms.

Target resequencing

is a useful method of resequencing that can be utilized for forensic applications. The genomic regions of interest from a DNA sample are selectively isolated through a method known as enrichment.

Mate-pair library

It is often used in de novo sequencing applications.

Fragment Library

It is often used for resequencing and forensic applications.

emulsion PCR

In the ________, single-stranded DNA templates are bound to beads.

solid-phase PCR

In _______, both forward and reverse primers are attached to a slide.

Pyrosequencing Technology

During this method, each nucleotide substrate is introduced one at a time. Only the correct nucleotide corresponding to the template is incorporated, and a pyrophosphate is released.

coverage or the sequencing depth

The average number of times that each nucleotide in the genomic regions of interest is sequenced is known as the _______.