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

PLoS One. 2016 May 13;11(5):e0155014. doi: 10.1371/journal.pone.0155014. eCollection 2016.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cells, Cultured
  • Chromosome Deletion
  • Computer Simulation
  • DNA Copy Number Variations / genetics
  • Gene Duplication
  • Gene Frequency / genetics
  • Genome*
  • Genotyping Techniques / methods*
  • Humans
  • Polymorphism, Single Nucleotide / genetics*
  • Reproducibility of Results
  • Statistics as Topic*