Open AccessA Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data
Author(s) -
Petr Danecek,
Shane McCarthy,
Richard Durbin
Publication year - 2016
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0155014
Subject(s) - genotyping , snp array , biology , aneuploidy , copy number variation , snp genotyping , computational biology , snp , genetics , genome , comparative genomic hybridization , genomics , genotype , single nucleotide polymorphism , chromosome , gene
Genomic screening for chromosomal abnormalities is an important part of quality control when establishing and maintaining stem cell lines. We present a new method for sensitive detection of copy number alterations, aneuploidy, and contamination in cell lines using genome-wide SNP genotyping data. In contrast to other methods designed for identifying copy number variations in a single sample or in a sample composed of a mixture of normal and tumor cells, this new method is tailored for determining differences between cell lines and the starting material from which they were derived, which allows us to distinguish between normal and novel copy number variation. We implemented the method in the freely available BCFtools package and present results based on induced pluripotent stem cell lines obtained in the HipSci project.