Genotyping by array

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

Getting the data

Complete lists of genotyping array data can be found under the files tab of the cell lines and data browser or in the dataset indexes on the FTP site.

  • Signal intensity data – Distributed in Illumina idat file format. This binary file can be read by Illumina software.
  • Genotyping array calls – Distributed in vcf file format and in Illumina’s genotyping console gtc format. These are the genotypes called directly from the signal intensities, before phasing or imputation. We distribute a single-sample vcf and a single-sample gtc file for each cell line.
  • Imputed and phased genotypes – Distributed in vcf file format. These contain the output from SHAPEIT and IMPUTE2. We distribute a single-sample vcf file for each cell line, containing genotypes imputed to the 1000genomes and UK10K reference panels.

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.