TY - JOUR

T1 - Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells

AU - Abyzov, Alexej

AU - Mariani, Jessica

AU - Palejev, Dean

AU - Zhang, Ying

AU - Haney, Michael Seamus

AU - Tomasini, Livia

AU - Ferrandino, Anthony F.

AU - Rosenberg Belmaker, Lior A.

AU - Szekely, Anna

AU - Wilson, Michael

AU - Kocabas, Arif

AU - Calixto, Nathaniel E.

AU - Grigorenko, Elena L.

AU - Huttner, Anita

AU - Chawarska, Katarzyna

AU - Weissman, Sherman

AU - Urban, Alexander Eckehart

AU - Gerstein, Mark

AU - Vaccarino, Flora M.

N1 - Funding Information: Acknowledgements We acknowledge support from the National Institutes of Health (NIH) and from the AL Williams Professorship fund and the Harris Professorship fund. We also acknowledge the Yale University Biomedical High Performance Computing Center and its supportteam(inparticular,R.BjornsonandN.Carriero).Wethank A.Klin for help with family recruitment. We thank M. V. Simonini for technical help, I.-H. Park for advice in the characterization of iPSC lines and the gift of the iPSC PGP1-1, and S. A. Duncan for the gift of the K3 iPSC line. We acknowledge the following grant support: NIMH MH089176 and MH087879, the Simons Foundation (SFARI 137055 F.V.) and the State of Connecticut, which funded the hiPSC generation and characterization; and NIH grant RR19895, which funded the instrumentation. We acknowledge the Yale Center for Clinical Investigation for clinical support in obtaining the biopsy specimens. We thank J. Overton for advice in carrying out DNA and RNA sequencing. Finally, we thank M. O’Huallachain and J. Li-Pook-Than for their advice on planning, carrying out and analysing the ddPCR experiments.

PY - 2012/12/20

Y1 - 2012/12/20

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84871410004&partnerID=8YFLogxK

U2 - 10.1038/nature11629

DO - 10.1038/nature11629

M3 - Article

C2 - 23160490

AN - SCOPUS:84871410004

VL - 492

SP - 438

EP - 442

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7429

ER -