title: Whole-genome mutational burden analysis of three pluripotency induction methods.
abstract: There is concern that the stresses of inducing pluripotency may lead to deleterious DNA mutations in induced pluripotent stem cell (iPSC) lines, which would compromise their use for cell therapies. Here we report comparative genomic analysis of nine isogenic iPSC lines generated using three reprogramming methods: integrating retroviral vectors, non-integrating Sendai virus and synthetic mRNAs. We used whole-genome sequencing and de novo genome mapping to identify single-nucleotide variants, insertions and deletions, and structural variants. Our results show a moderate number of variants in the iPSCs that were not evident in the parental fibroblasts, which may result from reprogramming. There were only small differences in the total numbers and types of variants among different reprogramming methods. Most importantly, a thorough genomic analysis showed that the variants were generally benign. We conclude that the process of reprogramming is unlikely to introduce variants that would make the cells inappropriate for therapy.
authors.affiliation: Scripps Translational Science Institute and The Scripps Research Institute, Department of Molecular and Experimental Medicine. La Jolla, California 92037. USA.
authors.forename: Kunal
authors.initials: K
authors.lastname: Bhutani
authors.affiliation: The Scripps Research Institute, Department of Chemical Physiology, Center for Regenerative Medicine, La Jolla, California 92037 USA.
authors.forename: Kristopher L
authors.initials: KL
authors.lastname: Nazor
authors.affiliation: The Scripps Research Institute, Department of Chemical Physiology, Center for Regenerative Medicine, La Jolla, California 92037 USA.
authors.forename: Roy
authors.initials: R
authors.lastname: Williams
authors.affiliation: The Scripps Research Institute, Department of Chemical Physiology, Center for Regenerative Medicine, La Jolla, California 92037 USA.
authors.forename: Ha
authors.initials: H
authors.lastname: Tran
authors.affiliation: BioNano Genomics, San Diego, California 92121. USA.
authors.forename: Heng
authors.initials: H
authors.lastname: Dai
authors.affiliation: BioNano Genomics, San Diego, California 92121. USA.
authors.forename: Željko
authors.initials: Ž
authors.lastname: Džakula
authors.affiliation: BioNano Genomics, San Diego, California 92121. USA.
authors.forename: Edward H
authors.initials: EH
authors.lastname: Cho
authors.affiliation: BioNano Genomics, San Diego, California 92121. USA.
authors.forename: Andy W C
authors.initials: AWC
authors.lastname: Pang
authors.affiliation: The National Institutes of Health, Bethesda, Maryland 20892. USA.
authors.forename: Mahendra
authors.initials: M
authors.lastname: Rao
authors.affiliation: BioNano Genomics, San Diego, California 92121. USA.
authors.forename: Han
authors.initials: H
authors.lastname: Cao
authors.affiliation: Scripps Translational Science Institute and The Scripps Research Institute, Department of Molecular and Experimental Medicine. La Jolla, California 92037. USA.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Schork
authors.affiliation: The Scripps Research Institute, Department of Chemical Physiology, Center for Regenerative Medicine, La Jolla, California 92037 USA.
authors.forename: Jeanne F
authors.identifier: http://orcid.org/0000-0001-6226-9767
authors.initials: JF
authors.lastname: Loring
mesh_terms: D002454:Cell Differentiation; D004252:DNA Mutational Analysis / Q000379:methods*; D005347:Fibroblasts / Q000737:chemistry / Q000166:cytology*; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000737:chemistry / Q000166:cytology*; D009154:Mutation