Program in Neurodevelopment and Regeneration, Yale University, New Haven, Connecticut 06520, USA.
Nature. 2012 Dec 20;492(7429):438-42. doi: 10.1038/nature11629. Epub 2012 Nov 18.
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.
将体细胞重编程为诱导多能干细胞（iPSCs）被怀疑会导致新的拷贝数变异。为了探讨这个问题，我们使用下一代测序技术对来自 7 个人的原代皮肤成纤维细胞的 20 个人 iPSC 系进行了全基因组和转录组分析。我们发现，平均而言，一个 iPSC 系表现出两种在其来源的成纤维细胞中不明显的拷贝数变异（CNVs）。通过 PCR 和数字液滴 PCR，我们表明，这些 CNVs 中至少有 50%是以低频率体细胞基因组变体的形式存在于亲本成纤维细胞中（即每个相应的人 iPSC 系所源自的成纤维细胞），并且由于其克隆起源而在 iPSC 系中表现出来。因此，重编程不一定会导致 iPSCs 中出现新的 CNVs，因为大多数表现出来的 CNVs 反映了人类皮肤中的体细胞镶嵌现象。此外，我们的研究结果表明，克隆扩增，特别是 iPSC 系，可以作为一种发现工具，可靠地检测组织来源中的低频 CNVs。总体而言，我们估计大约 30%的成纤维细胞的基因组中存在体细胞 CNVs，这表明人体中广泛存在体细胞镶嵌现象。我们的研究为理解人体细胞在合子后获得 DNA 结构改变的程度这一基本问题奠定了基础。
