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

Alexej Abyzov, Jessica Mariani, Dean Palejev, Ying Zhang, Michael Seamus Haney, Livia Tomasini, Anthony F. Ferrandino, Lior A. Rosenberg Belmaker, Anna Szekely, Michael Wilson, Arif Kocabas, Nathaniel E. Calixto, Elena L. Grigorenko, Anita Huttner, Katarzyna Chawarska, Sherman Weissman, Alexander Eckehart Urban, Mark Gerstein, Flora M. Vaccarino

Research output: Contribution to journalArticle

251 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)438-442
Number of pages5
JournalNature
Volume492
Issue number7429
DOIs
StatePublished - Dec 20 2012

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    Abyzov, A., Mariani, J., Palejev, D., Zhang, Y., Haney, M. S., Tomasini, L., Ferrandino, A. F., Rosenberg Belmaker, L. A., Szekely, A., Wilson, M., Kocabas, A., Calixto, N. E., Grigorenko, E. L., Huttner, A., Chawarska, K., Weissman, S., Urban, A. E., Gerstein, M., & Vaccarino, F. M. (2012). Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells. Nature, 492(7429), 438-442. https://doi.org/10.1038/nature11629