HipSci assays for genotypes in all candidate iPS cell lines, typically two or three per donor, and in the somatic cell lines from which they were derived (e.g. fibroblasts). The assay is used as QC before one cell line from each donor is selected for banking. The assay uses the HumanCoreExome-12 v1 BeadChip Kit from Illumina.
HipSci’s QC procedure is to compare the called genotypes between the primary and derived cells of the same donor, to ensure genomic integrity in the derived lines. Aneuploidy and subchromosomal aberrations are detected from genotyping arrays by detecting differences in copy number between the original fibroblasts and iPSCs using a HMM algorithm detected for the purpose
For managed access cell lines, genptyping array data files are archived in the EGA. The data browser contains links to the relevant EGA dataset page, from where researchers can request access to the data.
For open access cell lines, the signal intensity data files are archived in ArrayExpress and the variant call files are archived in EVA Data are openly available to anybody, and the data browser contains direct links to the files on the ArrayExpression files download page and the EVA ftp site.