Ch 3 - Definitions

allele

one of a number of alternative DNA sequences at a particular site in the DNA

allele detection

method used in a genotyping reaction to capture the information from the allele discrimination step

allele discrimination

method used in a genotyping reaction to differentiate between various alleles (wild vs polymorphic)

allele-specific oligonucleotide (ASO) hybridization

a common allele discrimination method used in genotyping procedures whereby probes are designed to bind complementary to specific DNA sequences and are used to interrogate the polymorphism of interest

assay

an analytical procedure used for qualitative or quantitative measurement of an analyte (molecule); a procedure or test used to determine a person’s genetic makeup or genotype

deoxyribonucleic acid (DNA)

a self-replicating material present in nearly all living organisms as the main constituent of chromosomes

genotype

an individual collection of genes; two alleles inherited for a particular gene

genotyping

determination of a person’s genetic makeup at a particular site in the DNA

massively parallel sequencing

a high-throughput sequencing approach in which many sequencing reactions (100-1000) can be run at the same time using the same platform (parallel); used in next-generation sequencing technologies

multiplexing

analysis of multiple polymorphisms in the same genotyping reaction

oligonucleotides

short fragments of single-stranded DNA that are designed to bind to specific DNA sequences via ASO hybridization; often referred to as primers or probes

polymorphism

the presence of two or more alleles for a gene or DNA sequence that exists in > 1% of the population

primer extension

a common allele discrimination method used in genotyping procedures where a single-stranded oligonucleotide is bound complementary to the sequence of interest, and the strand is extended over the polymorphism of interest

restriction enzymes

enzymes that recognize a specific short sequence of nucleotides in the DNA and cut the DNA at that site

restriction sites

short nucleotide sequences (4-8 base pairs length) that are present throughout the genome that are sites of cleavage for restriction enzymes; hallmark of RFLP

throughput

the number of samples or polymorphisms that can be genotypes with a particular genotyping method

wild type

the most prevalent (“normal”) DNA sequence for a given gene and/or allele within a species

target sequence

a specific region of DNA that contains the gene or polymorphism of interest

polymerase chain reaction (PCR)

method used to target and amplify a specific sequence of DNA within a genome

PCR-restriction fragment length polymorphism (PCR-RFLP)

method that uses bacterial restriction enzymes to discriminate between polymorphic and wildtype alleles; uses gel electrophoresis to separate DNA fragments and either radiolabeled or fluorescently labeled probes to detect alleles present in a given sample

ligand-based assays

aka oligonucleotide ligation assays (OLA); single strand breaks in DNA fused by DNA ligase enzymes that catalyze the reaction facilitating formation of PDE bond between two nucleotides

cytochrome P450 (CYP450)

superfamily of heme-containing monooxygenases involved in metabolism of drugs, xenobiotics, and endogenous compounds; primarily in liver and GI tract