title: Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells.
abstract: Reprogramming somatic cells into induced pluripotent stem cells (iPSCs) has been suspected of causing de novo copy number variation. To explore this issue, here we perform a whole-genome and transcriptome analysis of 20 human iPSC lines derived from the primary skin fibroblasts of seven individuals using next-generation sequencing. We find that, on average, an iPSC line manifests two copy number variants (CNVs) not apparent in the fibroblasts from which the iPSC was derived. Using PCR and digital droplet PCR, we show that at least 50% of those CNVs are present as low-frequency somatic genomic variants in parental fibroblasts (that is, the fibroblasts from which each corresponding human iPSC line is derived), and are manifested in iPSC lines owing to their clonal origin. Hence, reprogramming does not necessarily lead to de novo CNVs in iPSCs, because most of the line-manifested CNVs reflect somatic mosaicism in the human skin. Moreover, our findings demonstrate that clonal expansion, and iPSC lines in particular, can be used as a discovery tool to reliably detect low-frequency CNVs in the tissue of origin. Overall, we estimate that approximately 30% of the fibroblast cells have somatic CNVs in their genomes, suggesting widespread somatic mosaicism in the human body. Our study paves the way to understanding the fundamental question of the extent to which cells of the human body normally acquire structural alterations in their DNA post-zygotically.
authors.affiliation: Program in Neurodevelopment and Regeneration, Yale University, New Haven, Connecticut 06520, USA.
authors.forename: Alexej
authors.initials: A
authors.lastname: Abyzov
authors.forename: Jessica
authors.initials: J
authors.lastname: Mariani
authors.forename: Dean
authors.initials: D
authors.lastname: Palejev
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhang
authors.forename: Michael Seamus
authors.initials: MS
authors.lastname: Haney
authors.forename: Livia
authors.initials: L
authors.lastname: Tomasini
authors.forename: Anthony F
authors.initials: AF
authors.lastname: Ferrandino
authors.forename: Lior A
authors.initials: LA
authors.lastname: Rosenberg Belmaker
authors.forename: Anna
authors.initials: A
authors.lastname: Szekely
authors.forename: Michael
authors.initials: M
authors.lastname: Wilson
authors.forename: Arif
authors.initials: A
authors.lastname: Kocabas
authors.forename: Nathaniel E
authors.initials: NE
authors.lastname: Calixto
authors.forename: Elena L
authors.initials: EL
authors.lastname: Grigorenko
authors.forename: Anita
authors.initials: A
authors.lastname: Huttner
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Chawarska
authors.forename: Sherman
authors.initials: S
authors.lastname: Weissman
authors.forename: Alexander Eckehart
authors.initials: AE
authors.lastname: Urban
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
authors.forename: Flora M
authors.initials: FM
authors.lastname: Vaccarino
mesh_terms: D002454:Cell Differentiation; D002478:Cells, Cultured; D065150:Cellular Reprogramming; D002999:Clone Cells; D056915:DNA Copy Number Variations / Q000235:genetics*; D005347:Fibroblasts / Q000166:cytology; D020869:Gene Expression Profiling; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism*; D008297:Male; D009030:Mosaicism; D009474:Neurons / Q000166:cytology; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D012867:Skin / Q000166:cytology / Q000378:metabolism*