Genotyping

Johan T. den Dunnen, Dunnen, Johan T. den

DNA sequencing is usually performed to determine the sequence of a region of interest or even the entire genome of an individual. After sequencing, the sequence obtained is compared to a reference, all differences (the variants) are recorded, and the possible consequences of the changes identified, on both the RNA and protein level, are predicted. Finally, when available, a database containing previously reported variants is consulted to determine what other studies might have revealed about the variant or other variants in the same sequence (gene) and what the functional and phenotypic consequences were for the individuals carrying the variant.To facilitate the reporting and databasing of variants a standard was developed, the HGVS recommendations for the description of sequence variants. HGVS nomenclature contains specific formats to describe the basic variant types; substitution, deletion, duplication, insertion, inversion, and conversion. The basics of how to apply the recommendations to describe sequence variants will be explained here. An extensive description of the current HGVS guidelines (version 15.11) is available online at http://www.HGVS.org/varnomen .