title: Evaluating the genomic and sequence integrity of human ES cell lines; comparison to normal genomes.
abstract: 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.
authors.affiliation: BioTime, Inc., Alameda, CA, USA. wfunk@biotimemail.com
authors.forename: Walter D
authors.initials: WD
authors.lastname: Funk
authors.forename: Ivan
authors.initials: I
authors.lastname: Labat
authors.forename: Janani
authors.initials: J
authors.lastname: Sampathkumar
authors.forename: Pierre-Antoine
authors.initials: PA
authors.lastname: Gourraud
authors.forename: Jorge R
authors.initials: JR
authors.lastname: Oksenberg
authors.forename: Elen
authors.initials: E
authors.lastname: Rosler
authors.forename: Daniel
authors.initials: D
authors.lastname: Steiger
authors.forename: Nadia
authors.initials: N
authors.lastname: Sheibani
authors.forename: Stacy
authors.initials: S
authors.lastname: Caillier
authors.forename: Birgit
authors.initials: B
authors.lastname: Stache-Crain
authors.forename: Julie A
authors.initials: JA
authors.lastname: Johnson
authors.forename: Lorraine
authors.initials: L
authors.lastname: Meisner
authors.forename: Markus D
authors.initials: MD
authors.lastname: Lacher
authors.forename: Karen B
authors.initials: KB
authors.lastname: Chapman
authors.forename: Myung Jin
authors.initials: MJ
authors.lastname: Park
authors.forename: Kyoung-Jin
authors.initials: KJ
authors.lastname: Shin
authors.forename: Rade
authors.initials: R
authors.lastname: Drmanac
authors.forename: Michael D
authors.initials: MD
authors.lastname: West
mesh_terms: D000017:ABO Blood-Group System / Q000235:genetics; D000483:Alleles; D001057:Apolipoproteins E / Q000235:genetics; D001483:Base Sequence; D002460:Cell Line; D056915:DNA Copy Number Variations / Q000235:genetics; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D005091:Exons / Q000235:genetics; D015894:Genome, Human / Q000235:genetics*; D006680:HLA Antigens / Q000235:genetics; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D007621:Karyotyping; D018895:Microsatellite Repeats / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D016615:Telomere / Q000235:genetics
chemical_list: D000017:ABO Blood-Group System; D001057:Apolipoproteins E; D006680:HLA Antigens