Table 1.

Genetic Terminology

Gene - An ordered sequence of nucleotide bases that, via mRNA, encodes one polypeptide chain. The gene includes leader and trailer untranslated regions (UTR) preceding and following the coding region respectively, as well as intervening sequences (introns) between individual coding segments (exons). The ends of an individual strand of DNA are designated as 3' prime and 5' prime based on the position on the deoxyribose sugar.

Polymorphism - One of two or more alternate forms (alleles) of a chromosomal locus that differ in nucleotide sequence or have variable numbers of repeated nucleotide units

SNP - Single Nucleotide Polymorphism - DNA sequence variations that occur when a single nucleotide in the genome sequence is altered. These are designated by abbreviations for the possible amino acids before and after the position on the protein, for example Gly16Arg.

Synonymous SNP - a change in the SNP that does not alter amino acid coded for in the sequence.

Non-synonymous SNP - a change in the SNP that does alter the amino acid coded for in the sequence

Haplotype - A set of closely linked genetic polymorphisms present on one chromosome.

Coding Region Polymorphisms - Alterations in the genetic code of the area of a gene that encodes the polypeptide chain

Non-coding Region Polymorphisms - Alterations in areas in the genetic code that are not translated into the final protein but may affect the type or degree of transcription of the gene

Copy Number Variant - Deletions and duplications of DNA segments that are present in variable copy number compared with a reference genome

Insertion - Addition of one or more nucleotide base pairs into a DNA sequence.

Deletion - Genetic aberration in which a part of a chromosome or a sequence of DNA is missing.

Candidate Gene Studies - Studies of a specific gene in which variation might influence the risk of a specific disease or response to medication, usually because the gene is part of a biological pathway that is plausibly related to the disease.

Family-based Studies - Study of genetic variations between an affected individual and his parents or siblings in an attempt to identify the aberrant gene. This allows to account for the confounding environmental effects.

Pathway Studies - Simultaneous study of polymorphisms in multiple genes involved in a biological pathway

Genome-Wide Association Studies (GWAS) - An approach to gene mapping that involves scanning markers across the entire genome to find associations between a particular phenotype and allelic variation in a population. This methodology relies on the fact that the markers will be in linkage disequilibrium (see next) with polymorphisms truly associated with the phenotype.

Linkage Disequilibrium - The occurrence of combinations of genetic variants at different loci at a frequency that varies from what would be accounted for by chance. Also known as “allelic association” For example if variants A and B occur at one locus and X and Y occur at another. If each time X is detected, A is detected, these variants X and A are in linkage disequilibrium.