Journal Article

A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data

Danecek, Petr, Durbin, Richard, McCarthy, Shane A.

2016

Overview

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.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Abnormalities / Algorithms / Aneuploidy / Arrays / Biology and Life Sciences / Biotechnology / Cell lines / Cells, Cultured / Chromosome aberrations / Chromosome Deletion / Chromosomes / Computer Simulation / Consortia / Contamination / Copy number / Deoxyribonucleic acid / DNA / DNA Copy Number Variations - genetics / Gene Duplication / Gene Frequency - genetics / Genetic aspects / Genome / Genomes / Genotyping / Genotyping Techniques - methods / Humans / Identification methods / Medicine and Health Sciences / Methods / Mutation / Normal distribution / Physical sciences / Physiological aspects / Pluripotency / Polymorphism, Single Nucleotide - genetics / Quality control / Reproducibility of Results / Research and Analysis Methods / Single nucleotide polymorphisms / Statistics as Topic / Stem cells / Studies / Tumor cells