Genomic integrity of human induced pluripotent stem cells across nine studies in the NHLBI NextGen program

Kanika Kanchan, Kruthika Iyer, Lisa R. Yanek, Ivan Carcamo-Orive, Margaret A. Taub, Claire Malley, Kristin Baldwin, Lewis C. Becker, Ulrich Broeckel, Linzhao Cheng, Chad Cowan, Matteo D'Antonio, Kelly A. Frazer, Thomas Quertermous, Gustavo Mostoslavsky, George Murphy, Marlene Rabinovitch, Daniel J. Rader, Martin H. Steinberg, Eric TopolWenli Yang, Joshua W. Knowles, Cashell E. Jaquish, Ingo Ruczinski, Rasika A. Mathias

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


Human induced pluripotent stem cell (hiPSC) lines have previously been generated through the NHLBI sponsored NextGen program at nine individual study sites. Here, we examined the structural integrity of 506 hiPSC lines as determined by copy number variations (CNVs). We observed that 149 hiPSC lines acquired 258 CNVs relative to donor DNA. We identified six recurrent regions of CNVs on chromosomes 1, 2, 3, 16 and 20 that overlapped with cancer associated genes. Furthermore, the genes mapping to regions of acquired CNVs show an enrichment in cancer related biological processes (IL6 production) and signaling cascades (JNK cascade & NFκB cascade). The genomic region of instability on chr20 (chr20q11.2) includes transcriptomic signatures for cancer associated genes such as ID1, BCL2L1, TPX2, PDRG1 and HCK. Of these HCK shows statistically significant differential expression between carrier and non-carrier hiPSC lines. Overall, while a low level of genomic instability was observed in the NextGen generated hiPSC lines, the observation of structural instability in regions with known cancer associated genes substantiates the importance of systematic evaluation of genetic variations in hiPSCs before using them as disease/research models.

Original languageEnglish (US)
Article number101803
JournalStem Cell Research
StatePublished - Jul 2020


  • GWAS, VanillaICE
  • Oncogenes
  • Structural integrity
  • Tumor suppressor genes
  • hiPSCs

ASJC Scopus subject areas

  • Developmental Biology
  • Cell Biology


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