iPSCs and fibroblast subclones from the same fibroblast population contain comparable levels of sequence variations.
Genome integrity of induced pluripotent stem cells (iPSCs) has been extensively studied in recent years, but it is still unclear whether iPSCs contain more genomic variations than cultured somatic cells. One important question is the origin of genomic variations detected in iPSCs-whether iPSC reprogramming induces such variations. Here, we undertook a unique approach by deriving fibroblast subclones and clonal iPSC lines from the same fibroblast population and applied next-generation sequencing to compare genomic variations in these lines. Targeted deep sequencing of parental fibroblasts revealed that most variants detected in clonal iPSCs and fibroblast subclones were rare variants inherited from the parental fibroblasts. Only a small number of variants remained undetectable in the parental fibroblasts, which were thus likely to be de novo. Importantly, the clonal iPSCs and fibroblast subclones contained comparable numbers of de novo variants. Collectively, our data suggest that iPSC reprogramming is not mutagenic.
Oncogenesis and Development Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892.
Erika M
EM
Kwon
Oncogenesis and Development Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892.
John P
JP
Connelly
Comparative Genomics Unit, NIH Intramural Sequencing Center, National Human Genome Research Institute, NIH, Bethesda, MD 20892.
Nancy F
NF
Hansen
Genomics Core, National Human Genome Research Institute, NIH, Bethesda, MD 20892.
Frank X
FX
Donovan
Hematology Branch, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892.
Thomas
T
Winkler
Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892.
Brian W
BW
Davis
Oncogenesis and Development Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892.
Halah
H
Alkadi
Genomics Core, National Human Genome Research Institute, NIH, Bethesda, MD 20892.
Settara C
SC
Chandrasekharappa
Hematology Branch, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892.
Cynthia E
CE
Dunbar
Comparative Genomics Unit, NIH Intramural Sequencing Center, National Human Genome Research Institute, NIH, Bethesda, MD 20892.
James C
JC
Mullikin
Oncogenesis and Development Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892; pliu@mail.nih.gov.
Paul
P
Liu
D002454:Cell Differentiation; D002460:Cell Line; D002469:Cell Separation; D002478:Cells, Cultured; D065150:Cellular Reprogramming / Q000235:genetics*; D056915:DNA Copy Number Variations; D005347:Fibroblasts / Q000502:physiology*; D005434:Flow Cytometry; D005787:Gene Frequency; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000502:physiology*; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D000073359:Exome Sequencing
exome sequencing; fibroblasts; genomic variation; iPSCs; reprogramming