Genomic abnormalities observed in mouse and human PSCs
| Aberration type | Mouse PSCs | Human PSCs | Comparison of human and mouse PSCs | Origin | Gene enrichment | Likely mechanism of formation | |
| Chromosomal aberrations | Recurrent aberrations | Gains 8 and 11Deletions 10qB and 14q(a, b, c, d, e, f) | Gains 1, 12, 17, 20 and X (g, h, i, j, k, l, m, n) | Human chromosome 17 is completely syntenic to the distal half of mouse chromosome 11(c) | Most aberrations arise in culture during propagation (culture adaptation) (i, n) | Difficult to analyze, as aberrations contain multiple genes | Defects in chromosomal segregation during cell division |
| Frequency of aberrations | ∼38% in mESCs ∼23% in miPSCs (c) ∼25% of the aberrations involve chromosomes 8 and 11 (c) | ∼32–34% in hESCs (i, n) ∼20% in hiPSCs (n) ∼50% of the aberrations involve chromosomes 1,12,17 or 20 (i) | |||||
| Subchromosomal aberrations and copy number alterations | Recurrent aberrations | Gains within chromosome 8 (o) Multiple deletions (including in 14q) (c, p) | 20q11.21 and 12p13.31(i, m, q, r, s) | Small chromosomal aberrations occur both in mouse and human ESCs, but no syntenic recurrent aberrations have been identified. | Most CNVs arise from selection for rare populations in the parental cells during reprogramming or culturing (u, v, w) The total number of CNVs decreases in culture(t) | Specific genes have been suggested, such as BCL2L1 (i) and NANOG (m>, n) May be associated with pluripotency pseudo-genes, cancer-related genes, and genes within common fragile sites (m, o, t) | Defects in DNA damage response and replication stress |
| Frequency of aberrations | ? | Average of 109 CNVs per hiPSC line and 55 CNVs per hESC line (t) 10–25% of hESCs display the recurrent amplification of 20q11.21 (i, m) 13% of hESCs display the recurrent amplification of 12p13.31 (m) | |||||
| Single nucleotide variations (SNVs) | Recurrent aberrations | Not identified | Not identified | One study identified the same variants in four mouse iPS clones. This has not been observed in human PSCs. (w) | Most SNVs can be traced back to the parental cells | Shared SNVs were not observed between different iPS cell lines derived from the same somatic fibroblasts | Replication defects |
| Frequency of aberrations | ∼11 point mutations in coding regions per clone (w) | ∼6 point mutations in coding regions per clone (v, x, y) | |||||
| Aberration type | Mouse PSCs | Human PSCs | Comparison of human and mouse PSCs | Origin | Gene enrichment | Likely mechanism of formation | |
| Chromosomal aberrations | Recurrent aberrations | Gains 8 and 11Deletions 10qB and 14q(a, b, c, d, e, f) | Gains 1, 12, 17, 20 and X (g, h, i, j, k, l, m, n) | Human chromosome 17 is completely syntenic to the distal half of mouse chromosome 11(c) | Most aberrations arise in culture during propagation (culture adaptation) (i, n) | Difficult to analyze, as aberrations contain multiple genes | Defects in chromosomal segregation during cell division |
| Frequency of aberrations | ∼38% in mESCs ∼23% in miPSCs (c) ∼25% of the aberrations involve chromosomes 8 and 11 (c) | ∼32–34% in hESCs (i, n) ∼20% in hiPSCs (n) ∼50% of the aberrations involve chromosomes 1,12,17 or 20 (i) | |||||
| Subchromosomal aberrations and copy number alterations | Recurrent aberrations | Gains within chromosome 8 (o) Multiple deletions (including in 14q) (c, p) | 20q11.21 and 12p13.31(i, m, q, r, s) | Small chromosomal aberrations occur both in mouse and human ESCs, but no syntenic recurrent aberrations have been identified. | Most CNVs arise from selection for rare populations in the parental cells during reprogramming or culturing (u, v, w) The total number of CNVs decreases in culture(t) | Specific genes have been suggested, such as BCL2L1 (i) and NANOG (m>, n) May be associated with pluripotency pseudo-genes, cancer-related genes, and genes within common fragile sites (m, o, t) | Defects in DNA damage response and replication stress |
| Frequency of aberrations | ? | Average of 109 CNVs per hiPSC line and 55 CNVs per hESC line (t) 10–25% of hESCs display the recurrent amplification of 20q11.21 (i, m) 13% of hESCs display the recurrent amplification of 12p13.31 (m) | |||||
| Single nucleotide variations (SNVs) | Recurrent aberrations | Not identified | Not identified | One study identified the same variants in four mouse iPS clones. This has not been observed in human PSCs. (w) | Most SNVs can be traced back to the parental cells | Shared SNVs were not observed between different iPS cell lines derived from the same somatic fibroblasts | Replication defects |
| Frequency of aberrations | ∼11 point mutations in coding regions per clone (w) | ∼6 point mutations in coding regions per clone (v, x, y) | |||||
Liu et al., 1997; bBrimble et al., 2004; cBen-David and Benvenisty, 2012b; dLiang et al., 2008; eSugawara et al., 2006; fSommer et al., 2010; gBen-David et al., 2011; hTaapken et al., 2011; iAmps et al., 2011; jDraper et al., 2004; kBaker et al., 2007; lMartins-Taylo et al., 2011; mLaurent et al., 2011; nMayshar et al., 2010; oPasi et al., 2011; pArlt et al., 2012; qNärvä et al., 2010; rLefort et al., 2008; sWerbowetski-Ogilvie et al., 2009; tHussein et al., 2011; uAbyzov et al., 2012; vGore et al., 2011; wYoung et al., 2012; xCheng et al., 2012; yRuiz et al., 2013.