iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types

摘要

class="head no_bottom_margin" id="sec1title">IntroductionDue to their ability to differentiate into a variety of cell types, induced pluripotent stem cells (iPSCs) are a potentially powerful model system to study mechanisms underlying non-coding genetic variants associated with human traits, many of which lie in cell-type-specific regulatory regions (). However, because non-coding regulatory variants can have relatively small effect sizes, hundreds of lines from diverse individuals may be needed to measure genetic associations as opposed to the tens of different lines typically used to study disease-associated coding variants with strong effects (). To enable the study of genetic variants associated with complex diseases and cell-type-specific molecular phenotypes, we and others are establishing large systematically generated collections of iPSCs toward the goal of generating large genomic datasets that will be openly available to researchers (, , , ). Ongoing collections, including large disease-focused iPSC repositories (), however, are currently limited in sample diversity and in related individuals (e.g., pedigrees or twins), which would allow for the interrogation of population-associated genetic variation, rare variation, and family-based genetic study designs. Thus, the generation of a resource consisting of hundreds of systematically derived iPSCs with available genomic data including SNP arrays, RNA sequencing (RNA-seq), and whole-genome sequencing, and that includes a variety of familial architectures and individuals of multiple ethnicities, would further enable a wide variety of study designs to interrogate the genetic basis of phenotype and disease.There are a number of potential challenges to using iPSC and iPSC-derived cells 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 (, , ). 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) (, , ). 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 (, , href="#bib40" rid="bib40" class=" bibr popnode">Panopoulos et al., 2017, href="#bib43" rid="bib43" class=" bibr popnode">Rouhani et al., 2014, href="#bib51" rid="bib51" class=" bibr popnode">Thomas et al., 2015), but it is still unclear whether genetic background is associated with molecular phenotypes in iPSC-derived cells.Here, we describe the iPSCORE (iPSC Collection for Omic Research) resource, a systematically derived and characterized reference panel of iPSC lines. Participants were recruited to include families, twins, and individuals of diverse ethnicity to enable genetic studies investigating the segregation of traits. While the majority of the participants were generally healthy, 39 individuals with heart diseases were included to allow for investigations into heart disease using derived cell types. iPSCs were systematically reprogrammed from fibroblasts and analyzed for pluripotency and the presence and recurrence of somatic copy-number variants (CNVs). We differentiated a subset of iPSCs to cardiomyocytes and examined how the donor's genetic background is associated with gene expression variation in derived cell lines. Finally, we examined and annotated how individuals in the iPSCORE resource carry SNPs associated with diverse genome-wide association studies (GWAS) phenotypes. The iPSCORE resource provides a powerful tool to examine how genetic variants influence molecular and physiological traits across a variety of derived cell types, as well as to functionally interrogate variants underlying a variety of GWAS phenotypes.