Comparative genomics studies in primates are restricted due to our limited access to samples. In order to gain better insight into the genetic processes that underlie variation in complex phenotypes in primates, we must have access to faithful model systems for a wide range of cell types. To facilitate this, we generated a panel of 7 fully characterized chimpanzee induced pluripotent stem cell (iPSC) lines derived from healthy donors. To demonstrate the utility of comparative iPSC panels, we collected RNA-sequencing and DNA methylation data from the chimpanzee iPSCs and the corresponding fibroblast lines, as well as from 7 human iPSCs and their source lines, which encompass multiple populations and cell types. We observe much less within-species variation in iPSCs than in somatic cells, indicating the reprogramming process erases many inter-individual differences. The low within-species regulatory variation in iPSCs allowed us to identify many novel inter-species regulatory differences of small magnitude.

This work was supported by NIH grant GM077959 to YG as well as by grants from the California Institute for Regenerative Medicine (CIRM)/nCL1-00502 and TR01250 to JFL, and ERC Starting Grant 260372 and MICINN (Spain) BFU2011-28549 to TM-B. IGR is supported by a Sir Henry Wellcome Postdoctoral Fellowship; IHH is supported by FI Generalitat Catalunya; MCW is supported by an EMBO Long-Term Fellowship (ALTF 751-2014) and the European Commission Marie Curie Actions; NEB is supported by an NIH training grant (GM007197) and an NIH pre-doctoral award (F31 AG 044948); LCL is supported by a WRHR Career Development award (NIH K12 HD001259) and the UCSD Department of Reproductive Medicine; TRL and KS are supported by the UCSD Department of Reproductive Medicine; CLK is supported by a CTSA TL1 pre-doctoral fellowship (TR 432-7). We also acknowledge the generous support of the Yerkes Primate Center through their grant ORIP/OD P51OD011132.