Evaluating the genomic and sequence integrity of human ES cell lines; comparison to normal genomes

• Published in: Stem cell research 2012-03, Vol.8 (2), p.154-164
• Main Authors: Funk, Walter D., Labat, Ivan, Sampathkumar, Janani, Gourraud, Pierre-Antoine, Oksenberg, Jorge R., Rosler, Elen, Steiger, Daniel, Sheibani, Nadia, Caillier, Stacy, Stache-Crain, Birgit, Johnson, Julie A., Meisner, Lorraine, Lacher, Markus D., Chapman, Karen B., Park, Myung Jin, Shin, Kyoung-Jin, Drmanac, Rade, West, Michael D.
• Format: Article
• Language: English
• Subjects: ABO Blood-Group System - genetics; Alleles; Apolipoproteins E - genetics; Base Sequence; Cell Line; DNA Copy Number Variations - genetics; Embryonic Stem Cells - cytology; Embryonic Stem Cells - metabolism; Exons - genetics; Genome, Human - genetics; HLA Antigens - genetics; Humans; In Situ Hybridization, Fluorescence; Karyotyping; Microsatellite Repeats - genetics; Polymorphism, Single Nucleotide - genetics; Telomere - genetics
• ISSN: 1873-5061; 1876-7753
• DOI: 10.1016/j.scr.2011.10.001

Copy number variation (CNV) is a common chromosomal alteration that can occur during in vitro cultivation of human cells and can be accompanied by the accumulation of mutations in coding region sequences. We describe here a systematic application of current molecular technologies to provide a detailed understanding of genomic and sequence profiles of human embryonic stem cell (hESC) lines that were derived under GMP-compliant conditions. We first examined the overall chromosomal integrity using cytogenetic techniques to determine chromosome count, and to detect the presence of cytogenetically aberrant cells in the culture (mosaicism). Assays of copy number variation, using both microarray and sequence-based analyses, provide a detailed view genomic variation in these lines and shows that in early passage cultures of these lines, the size range and distribution of CNVs are entirely consistent with those seen in the genomes of normal individuals. Similarly, genome sequencing shows variation within these lines that is completely within the range seen in normal genomes. Important gene classes, such as tumor suppressors and genetic disease genes, do not display overtly disruptive mutations that could affect the overall safety of cell-based therapeutics. Complete sequence also allows the analysis of important transplantation antigens, such as ABO and HLA types. The combined application of cytogenetic and molecular technologies provides a detailed understanding of genomic and sequence profiles of GMP produced ES lines for potential use as therapeutic agents. ► Cytogenetic, array and complete genome sequence were used to assess the integrity of human ES cell lines. ► FISH methods can detect low level contamination of cultures by genomically aberrant cells. ► Copy number variation assessment shows the vast majority of CNVs occur in regions common to normal human genomes. ► Complete genome sequence ensures integrity of key gene families (tumor suppressors/oncogenes). ► Sequence analysis can identify ABO blood type, HLA and disease-associated alleles.