Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany.
Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 6, Erlangen, Germany.
Sci Rep. 2018 Nov 21;8(1):17201. doi: 10.1038/s41598-018-35506-0.
Genetic integrity of induced pluripotent stem cells (iPSCs) is essential for their validity as disease models and for potential therapeutic use. We describe the comprehensive analysis in the ForIPS consortium: an iPSC collection from donors with neurological diseases and healthy controls. Characterization included pluripotency confirmation, fingerprinting, conventional and molecular karyotyping in all lines. In the majority, somatic copy number variants (CNVs) were identified. A subset with available matched donor DNA was selected for comparative exome sequencing. We identified single nucleotide variants (SNVs) at different allelic frequencies in each clone with high variability in mutational load. Low frequencies of variants in parental fibroblasts highlight the importance of germline samples. Somatic variant number was independent from reprogramming, cell type and passage. Comparison with disease genes and prediction scores suggest biological relevance for some variants. We show that high-throughput sequencing has value beyond SNV detection and the requirement to individually evaluate each clone.
诱导多能干细胞 (iPSC) 的遗传完整性对于它们作为疾病模型的有效性以及潜在的治疗用途至关重要。我们描述了 ForIPS 联盟的综合分析：来自神经疾病和健康对照供体的 iPSC 集合。特征分析包括多能性确认、指纹分析、所有细胞系的常规和分子核型分析。在大多数情况下，鉴定了体细胞拷贝数变异 (CNVs)。选择具有可用匹配供体 DNA 的亚组进行比较外显子组测序。我们在每个克隆中以不同的等位基因频率鉴定了单核苷酸变异 (SNVs)，突变负荷的变异性很高。在亲本成纤维细胞中低频率的变体突出了种系样本的重要性。体细胞变体数量与重编程、细胞类型和传代数无关。与疾病基因和预测评分的比较表明，一些变体具有生物学相关性。我们表明，高通量测序除了 SNV 检测之外还有价值，并且需要单独评估每个克隆。
