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

Athanasia D. Panopoulos(Salk Institute for Biological Studies), Matteo D’Antonio(University of California San Diego), Paola Benaglio(University of California San Diego), Roy M. Williams(Scripps Research Institute), Sherin I. Hashem(University of California San Diego), Bernhard Schuldt(University Hospital Schleswig-Holstein), Christopher DeBoever(University of California San Diego), Angelo D. Arias(University of California San Diego), Melvin Garcia(University of California San Diego), Bradley Nelson(University of California San Diego), Olivier Harismendy(University of California San Diego), David Jakubosky(University of California San Diego), Margaret K. R. Donovan(University of California San Diego), William W. Greenwald(University of California San Diego), KathyJean Farnam(University of California San Diego), Megan Cook(University of California San Diego), Victor Borja(University of California San Diego), Carl A. Miller(University of California San Diego), Jonathan D. Grinstein(University of California San Diego), Frauke Drees(University of California San Diego), Jonathan Okubo(University of California San Diego), Kenneth E. Diffenderfer(Salk Institute for Biological Studies), Yuriko Hishida(Salk Institute for Biological Studies), Veronica Modesto(Salk Institute for Biological Studies), Carl Dargitz(Salk Institute for Biological Studies), Rachel Feiring(Salk Institute for Biological Studies), Chang Zhao(University of California San Diego), Aitor Aguirre(University of California San Diego), Thomas J. McGarry(University of California San Diego), Hiroko Matsui(University of California San Diego), He Li(University of California San Diego), Joaquin Reyna(University of California San Diego), Fangwen Rao(University of California San Diego), Daniel T. O’Connor(University of California San Diego), G Yeo(University of California San Diego), Sylvia Μ. Evans(University of California San Diego), Neil C. Chi(University of California San Diego), Kristen Jepsen(University of California San Diego), Naoki Nariai(University of California San Diego), Franz-Josef Müller(University Hospital Schleswig-Holstein), Lawrence S.B. Goldstein(University of California San Diego), Juan Carlos Izpisúa Belmonte(Salk Institute for Biological Studies), Eric Adler(University of California San Diego), Jeanne F. Loring(Scripps Research Institute), W. Travis Berggren(Salk Institute for Biological Studies), Agnieszka D’Antonio‐Chronowska(University of California San Diego), Erin N. Smith(University of California San Diego), Kelly A. Frazer(University of California San Diego)
Stem Cell Reports
April 1, 2017
10.1016/j.stemcr.2017.03.012
Cited by 198Open Access
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Abstract

Large-scale collections of induced pluripotent stem cells (iPSCs) could serve as powerful model systems for examining how genetic variation affects biology and disease. Here we describe the iPSCORE resource: a collection of systematically derived and characterized iPSC lines from 222 ethnically diverse individuals that allows for both familial and association-based genetic studies. iPSCORE lines are pluripotent with high genomic integrity (no or low numbers of somatic copy-number variants) as determined using high-throughput RNA-sequencing and genotyping arrays, respectively. Using iPSCs from a family of individuals, we show that iPSC-derived cardiomyocytes demonstrate gene expression patterns that cluster by genetic background, and can be used to examine variants associated with physiological and disease phenotypes. The iPSCORE collection contains representative individuals for risk and non-risk alleles for 95% of SNPs associated with human phenotypes through genome-wide association studies. Our study demonstrates the utility of iPSCORE for examining how genetic variants influence molecular and physiological traits in iPSCs and derived cell lines.

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