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    • There are a number of

    2018-11-05

    There are a number of potential challenges to using iPSC and iPSC-derived Go 6983 cost to model human phenotype and disease. Somatic heterogeneity in iPSC lines that can occur during isolation and culture may interfere with examining genetic variants with subtle effects (Fusaki et al., 2009; International Stem Cell et al., 2011; Nazor et al., 2012). This heterogeneity can include copy-number alterations, which have been reported as occurring in recurrently altered regions in existing collections of pluripotent stem cells (both embryonic stem cells [ESCs] and iPSCs) (International Stem Cell et al., 2011; Laurent et al., 2011; Taapken et al., 2011). However, because many of these lines were not systematically generated and may have undergone prolonged passaging in culture, it is unclear how prevalent these hotspots are in limited passaged lines and/or if other hotspots could be uncovered as additional iPSC are examined. In addition, it is not yet known whether iPSC-derived cell types (cardiomyocytes, neurons, adipocytes) will be useful for functionally examining genetic variants. We and others have recently shown that genetic differences between individuals are associated with a variety of molecular phenotypes in iPSCs, including the transcriptome and epigenome (Burrows et al., 2016; DeBoever et al., 2017; Panopoulos et al., 2017; Rouhani et al., 2014; Thomas et al., 2015), but it is still unclear whether genetic background is associated with molecular phenotypes in iPSC-derived cells.
    Results
    Discussion Current large-scale collections of iPSCs generally have limited numbers of lines from people of non-European ancestry or individuals in multigenerational families. The iPSCORE collection includes 75 lines from people of Hispanic ethnicity, non-European ancestry, or multiple ancestries, which will aid in studies interrogating population-associated genetic variation or in fine-mapping using trans-ethnicity mapping. Additionally we include multigenerational families and monozygotic twins, which will enable interrogation of rare, family-specific variation, segregation analysis of molecular and physiological traits, and estimation of technical and environmental variation independent of genetic background. The 136 genetically unrelated individuals in the resource enable the derived cell lines to be used for genetic association studies that historically have required unrelated individuals; although with methods that account for sample structure (Kang et al., 2010), these studies can incorporate all 222 individuals. These association studies will be further augmented by the fact that whole-genome sequence data has been generated from somatic tissue (blood and in some cases fibroblasts) of the iPSCORE participants and is part of the resource (Table S1C). Because risk and non-risk alleles for the vast majority of GWAS SNPs are represented in the genomes of the 222 individuals, this resource will allow for the functional interrogation of these important predominantly regulatory variants in appropriate iPSC-derived cell types. Thus, the nature of the individuals who participated in the iPSCORE resource will allow for diverse experimental approaches to examine how genetic variation affects molecular and physiological traits. To efficiently characterize more than 200 iPSC lines, we incorporated genomic tools such as the HumanCoreExome BeadChip to examine genomic integrity, establish sample identity, and estimate genetic ancestry and familial relatedness; and RNA-seq to establish pluripotency. Overall, genomic integrity for these low-passage lines was high with almost half of the iPSCs in the iPSCORE resource showing no detectable abnormalities, and ∼90% showing less than 2 Mb of cumulative CNV coverage (in bp). It is important to note that genotype array assays are limited to the extent that they are unable to detect balanced chromosomal translocations or abnormalities occurring at a frequency lower than 20% (D\'Antonio et al., 2017 [this issue of Stem Cell Reports]); however, previous studies using genotype arrays have found higher ratios and frequencies of abnormalities in iPSCs (International Stem Cell et al., 2011; Laurent et al., 2011; Taapken et al., 2011) than we report, suggesting that a systematic approach to iPSC generation can result in significantly fewer abnormalities. We also used RNA-seq data to validate the quality of the iPSCORE lines by comparing them with publicly available RNA-seq data for stem cells previously shown to be pluripotent and performed pluripotency estimation using PluriTest-RNAseq. Thus, the adoption of high-throughput genomic methods can help reduce costs and enable effective and relatively rapid characterization of iPSC lines for genomic integrity and pluripotency.