Table 1 Nomenclature and explanation of some terms in genetic epidemiology

Allele

Alternative form of gene

Epistasis

The interaction of two or more genes to influence a single phenotype

Exon

Part of the DNA that contains the code for producing the gene's protein

Haplotypes

Closely related variants that are inherited as a unit

Haplotype phase

Determination of which of the two chromosomes a series of markers or SNPs are present on

Intron

A non-coding sequence of DNA that is initially copied into the RNA, but is cut out of the final RNA transcript

Linkage disequilibrium

Non-random association of alleles at linked loci

Mutation

Change in DNA sequence with frequency ≤ 1%

Non-synonymous or missense SNPs

SNPs that are associated with change in amino acid in the transcribed protein

Polymorphism

Variation in DNA with frequency >1%

Recombination

Maternal and paternal chromosomes pair up and exchange segments of DNA in germ cells

Single nucleotide polymorphism (SNP)

Common, but minute variations in the DNA sequence

Synonymous SNPs

SNPs that are not associated with change in amino acid in the transcribed protein

Tag SNPs

There is a degree of redundancy when SNPs are in linkage disequilibrium with each other within a haplotype. A single or a group of SNPs can be used to identify the entire haplotype block and is called tag SNP

Transmission disequilibrium test

A family based study design using parents-affected child trios. This design tests for an association between a specific allele and disease in the child by testing whether heterozygous parents transmit this allele to affected children more frequently than expected