What is a “reference sequence” in the PharmGKB and how is it used?
The reference sequence is a DNA sequence of part, or all, of the gene of interest and is provided to PharmGKB by the data submitter. The location of polymorphisms or variants, gene features (e.g. exons, introns, etc.) and primer binding sites are reported by their position on this sequence. The reference sequence is used by PharmGKB primarily for two purposes. (1) It is used for alignment with the human genome sequence called Golden Path in order to provide chromosomal locations for variants. (2) It is used as a comparison sequence, and the default sequence for individuals, when reporting assay results as follows: If a sequencing assay (e.g. PCR) is performed, and no variants are reported for subject x, the genotype x same as reference sequence. If a position-specific genotyping assay (e.g. RFLP, TaqMan, pyrosequencing) is performed, and no variant is reported for subject x, the genotype for subject x at that position is the same as that of the reference sequence at that position. If a
