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

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...

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Bibliographic Details
Published in:	PloS one Vol. 11; no. 5; p. e0155014
Main Authors:	Danecek, Petr, McCarthy, Shane A, Durbin, Richard
Format:	Journal Article
Language:	English
Published:	United States Public Library of Science 13-05-2016 Public Library of Science (PLoS)
Subjects:	Abnormalities Algorithms Aneuploidy Arrays Biology and Life Sciences Biotechnology Cell lines Cells, Cultured 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 United Kingdom United Kingdom > UK
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Summary:	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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Conceived and designed the experiments: PD RD. Performed the experiments: PD. Analyzed the data: PD SM. Wrote the paper: PD RD SM. Competing Interests: The authors have declared that no competing interests exist. A full list of participants and their affiliations is available in S1 Text.
ISSN:	1932-6203 1932-6203
DOI:	10.1371/journal.pone.0155014