title: Genetic heterogeneity of induced pluripotent stem cells: results from 24 clones derived from a single C57BL/6 mouse.
abstract: Induced pluripotent stem cells (iPSCs) have tremendous potential as a tool for disease modeling, drug testing, and other applications. Since the generation of iPSCs "captures" the genetic history of the individual cell that was reprogrammed, iPSC clones (even those derived from the same individual) would be expected to demonstrate genetic heterogeneity. To assess the degree of genetic heterogeneity, and to determine whether some cells are more genetically "fit" for reprogramming, we performed exome sequencing on 24 mouse iPSC clones derived from skin fibroblasts obtained from two different sites of the same 8-week-old C57BL/6J male mouse. While no differences in the coding regions were detected in the two parental fibroblast pools, each clone had a unique genetic signature with a wide range of heterogeneity observed among the individual clones: a total of 383 iPSC variants were validated for the 24 clones (mean 16.0/clone, range 0-45). Since these variants were all present in the vast majority of the cells in each clone (variant allele frequencies of 40-60% for heterozygous variants), they most likely preexisted in the individual cells that were reprogrammed, rather than being acquired during reprogramming or cell passaging. We then tested whether this genetic heterogeneity had functional consequences for hematopoietic development by generating hematopoietic progenitors in vitro and enumerating colony forming units (CFUs). While there was a range of hematopoietic potentials among the 24 clones, only one clone failed to differentiate into hematopoietic cells; however, it was able to form a teratoma, proving its pluripotent nature. Further, no specific association was found between the mutational spectrum and the hematopoietic potential of each iPSC clone. These data clearly highlight the genetic heterogeneity present within individual fibroblasts that is captured by iPSC generation, and suggest that most of the changes are random, and functionally benign.
authors: Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America.
authors: Cheng
authors: C
authors: Li
authors: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America.
authors: Jeffery M
authors: JM
authors: Klco
authors: Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America.
authors: Nichole M
authors: NM
authors: Helton
authors: Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America.
authors: Daniel R
authors: DR
authors: George
authors: Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America.
authors: Jacqueline L
authors: JL
authors: Mudd
authors: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America.
authors: Christopher A
authors: CA
authors: Miller
authors: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America.
authors: Charles
authors: C
authors: Lu
authors: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America.
authors: Robert
authors: R
authors: Fulton
authors: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America.
authors: Michelle
authors: M
authors: O'Laughlin
authors: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America.
authors: Catrina
authors: C
authors: Fronick
authors: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America.
authors: Richard K
authors: RK
authors: Wilson
authors: Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America.
authors: Timothy J
authors: TJ
authors: Ley
mesh_terms: D000818:Animals; D002454:Cell Differentiation; D002999:Clone Cells; D005347:Fibroblasts / Q000166:cytology; D015870:Gene Expression; D020869:Gene Expression Profiling; D018740:Genetic Heterogeneity; D006410:Hematopoiesis; D059014:High-Throughput Nucleotide Sequencing; D057026:Induced Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism*; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL