CNAs observed in pluripotent stem cells (PSCs) are known to recur at certain genomic locations11–13. We observed 35 regions where CNAs occurred significantly more often than expected under a uniform genomic distribution, including whole chromosome duplication of the X chromosome (P = 1.5x10-9), 20 sub-chromosomal duplications, 11 deletions and three regions with both duplications and deletions (Fig. 2a, Supplementary Table 2). The three most frequent CNAs (X trisomy, chromosome 17 and 20) have been previously observed in PSCs12,14,15, but others are newly identified, to our knowledge.
