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Vol 19 n° 1

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Glossary


Definitions useful in understanding pharmacogenetics; Author: D. Farkas http://www.aacc.org/AACC/members/nacb/LMPG/OnlineGuide/DraftGuidelines/Pharmacogenetics/

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allele - version of a gene at a given locus
amplicon - copy of a target DNA created by PCR or other amplification methods
central dogma (of molecular biology) - fundamental tenet of molecular biology stating that DNA is copied via replication, RNA is derived from DNA via transcription, and protein is derived from RNA via translation. The discovery of reverse transcription disrupted the central dogma of molecular biology by showing that genetic information could also flow from RNA to DNA, not just DNA to RNA.
complementary DNA (cDNA) - DNA produced using an RNA template via the enzyme reverse transcriptase
compound heterozygote - individual with two abnormal alleles at a given locus, each with a difference polymorphism or mutation.
deletion - mutation resulting from the removal of base(s)
DNase - enzyme that degrades DNA
DNA ligase - enzyme that joins two pieces of DNA
DNA polymerase - enzyme that uses DNA as a template to produce a complementary strand of DNA; cDNA is made with a type of DNA polymerase called reverse transcriptase (an RNA-dependent, DNA polymerase)
DNA sequencing - base-by-base determination of the exact sequence of target DNA
epigenetic - referring to heritable changes to the genome that do not alter the coding sequence
frame-shift mutation - insertion or deletion of base(s) that alters the reading frame of a coding sequence, thereby changing the amino acids encoded downstream and/or producing a stop codon
gel electrophoresis - separation of DNA by size via migration in an electric field in an agarose or polyacrylamide matrix
gene - segment of DNA transcribed into RNA that (i) is translated into a protein or (ii) forms structures such as ribosomes
genetic variant - alternative forms of a gene which may or may not lead to altered phenotype
genome - all the genetic material of an organism
genotype - the alleles at a given locus in an individual; see also phenotype
haplotype - analogous to genotype, haplotype is the set of alleles (or SNPs) on one chromosome or part of a chromosome that are linked and usually or often inherited together
heterogeneous - regarding PCR, requiring separate amplification and detection steps
homogeneous - regarding PCR, having combined amplification and detection steps
hybridization - process of forming a double-stranded molecule from a single-stranded probe and a single-stranded nucleic acid target
hybridization probe - type of fluorescently-labeled probe used in real-time PCR that produces signal following hybridization to a target DNA
missense mutation -base change resulting in coding of a different amino acid
molecular diagnostics - diagnosis of disease using nucleic acids as analytes, often used synonymously with molecular pathology
mRNA - messenger RNA, translated into protein
mutation - generally harmful DNA sequence change; compare to polymorphism
nucleic acids - deoxyribonucleic acid ( DNA ) and ribonucleic acid ( RNA ), the molecules containing the genetic code
nucleoside - nucleotide lacking a phosphate group
nucleotide - building block of nucleic acids composed of phosphate group(s), a five-sided sugar molecule, and a nitrogenous base
oligonucleotide - short sequence of nucleotides, often used as primers for PCR or DNA sequencing
penetrance - percent expression in a population of the phenotype of a given mutant genotype
pharmacogenetics - the hereditary basis for inter-individual differences in drug response
pharmacogenomics - the convergence of pharmacogenetics and genomics used to mean the influence of DNA sequence variation on the effect of a drug on an individual
phenotype - traits resulting from a given genotype
point mutation - mutation that changes a single base
polymerase chain reaction (PCR) - enzymatic in vitro nucleic acid amplification method using temperature cycling to produce repeated cycles of DNA replication
polymorphism - variant DNA sequence change, typically benign, found in 1% or more of individuals; compare to mutation
primer - oligonucleotide used in PCR or DNA sequencing to target an area of interest
primer-dimers - nonspecific products formed during PCR by the interaction of primers
probe - relatively small piece of DNA or RNA used to find or detect a specific piece of target nucleic acid
proteomics - study of the entire complement of proteins in organisms
quantification standard - synthetic nucleic acid standard spiked into samples before processing to serve as a reference in quantitative PCR
real-time PCR - PCR in which detection of product is simultaneous with amplification
replication - process of duplicating DNA with DNA polymerase
restriction endonuclease (RE) - enzyme purified from bacteria that recognizes and cleaves unique sequences
restriction fragment length polymorphism (RFLP) - polymorphism that changes the electrophoretic banding pattern of DNA fragments generated by digestion with a restriction endonuclease
single nucleotide polymorphism (SNP) - polymorphism that is a single base change
Southern blot hybridization - DNA detection method where digested sample is separated by electrophoresis, transferred to a membrane, and probed
transcription - process of producing mRNA from a DNA template
translation - process of converting the information contained in mRNA into protein
uracil-N-glycosylase - enzyme used to prevent amplicon carryover contamination that degrades any DNA containing uracil (uracil-containing DNA is not natural and is produced in vitro during some PCR protocols)
variant allele - specific alternative forms of a gene, generally causing a known alternative phenotype
wild-type - normal allele; compare to mutant or variant

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