Department of Human Genetics, University of Chicago, Chicago, United States
Bryan J Pavlovic
Department of Human Genetics, University of Chicago, Chicago, United States
Irene Hernando-Herraez
Institut de Biologia Evolutiva (CSIC/UPF), Barcelona, Spain
Xiang Zhou
Department of Biostatistics, University of Michigan, Ann Arbor, United States
Michelle C Ward
Department of Human Genetics, University of Chicago, Chicago, United States
Nicholas E Banovich
Department of Human Genetics, University of Chicago, Chicago, United States
Courtney L Kagan
Department of Human Genetics, University of Chicago, Chicago, United States
Jonathan E Burnett
Department of Human Genetics, University of Chicago, Chicago, United States
Constance H Huang
Department of Human Genetics, University of Chicago, Chicago, United States
Amy Mitrano
Department of Human Genetics, University of Chicago, Chicago, United States
Claudia I Chavarria
Department of Human Genetics, University of Chicago, Chicago, United States
Inbar Friedrich Ben-Nun
Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
Yingchun Li
Department of Pathology, University of California San Diego, San Diego, United States; Sanford Consortium for Regenerative Medicine, La Jolla, United States
Karen Sabatini
Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States; Sanford Consortium for Regenerative Medicine, La Jolla, United States; Department of Reproductive Medicine, University of California San Diego, San Diego, United States
Trevor R Leonardo
Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States; Sanford Consortium for Regenerative Medicine, La Jolla, United States; Department of Reproductive Medicine, University of California San Diego, San Diego, United States
Mana Parast
Department of Pathology, University of California San Diego, San Diego, United States; Sanford Consortium for Regenerative Medicine, La Jolla, United States
Tomas Marques-Bonet
Institut de Biologia Evolutiva (CSIC/UPF), Barcelona, Spain; Centro Nacional de Análisis Genómico (CNAG-CRG), Barcelona, Spain
Louise C Laurent
Sanford Consortium for Regenerative Medicine, La Jolla, United States; Department of Reproductive Medicine, University of California San Diego, San Diego, United States
Jeanne F Loring
Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
Yoav Gilad
Department of Human Genetics, University of Chicago, Chicago, United States
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.
