Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage

Abstract

The International Stem Cell Initiative analyzed 125 human embryonic stem (ES) cell lines and 11 induced pluripotent stem (iPS) cell lines, from 38 laboratories worldwide, for genetic changes occurring during culture. Most lines were analyzed at an early and late passage. Single-nucleotide polymorphism (SNP) analysis revealed that they included representatives of most major ethnic groups. Most lines remained karyotypically normal, but there was a progressive tendency to acquire changes on prolonged culture, commonly affecting chromosomes 1, 12, 17 and 20. DNA methylation patterns changed haphazardly with no link to time in culture. Structural variants, determined from the SNP arrays, also appeared sporadically. No common variants related to culture were observed on chromosomes 1, 12 and 17, but a minimal amplicon in chromosome 20q11.21, including three genes, ID1, BCL2L1 and HM13, expressed in human ES cells, occurred in >20% of the lines. Of these genes, BCL2L1 is a strong candidate for driving culture adaptation of ES cells.

Alternative Cultures for Human Pluripotent Stem Cell Production, Maintenance, and Genetic Analysis

“…It is important that the starting hPSC colonies or subset of colonies used for NCM culture should be well-characterized in terms of their homogeneity and chromosomal stability at the time for NCM adaptation. Notably, the rate of abnormal karyotypes under NCM conditions is much lower than that reported in a recent cohort analysis, in which the authors reveal 34% abnormal karyotypes under predominant colony-type culture conditions 20 . Hence, our study indicates that we can grow dissociated single-cells and maintain their chromosomal stability under NCM conditions.…”

“…, < 50 kb), as some minor lesions ( e.g. , the 20q11.21 amplicon) at these frequently altered chromosomes cannot be detected by conventional karyotyping and FISH 20–22 . Furthermore, the development of diverse NCM protocols would enable us to identify robust and safe methods for future applications.…”

Developmental insights from early mammalian embryos and core signaling pathways that influence human pluripotent cell growth and differentiation

“…They identified ~20% abnormal lines, of which ~9% of the lines had at least one trisomy (Mayshar et al, 2010). In a second cohort study, Andrews and colleagues reported 34% abnormal karyotypes in 129 hPSC lines, in which 20% of cytogenetically normal lines carried a conserved amplicon at 20q11.12 (Amps et al, 2011). These studies define a putative rate of chromosomal abnormalities, ranging from 20% to 54%.…”

“…These methods have led to time-consuming production of relatively low numbers of cells (Hartung et al, 2010; Kehoe et al, 2010; Serra et al, 2012), heterogeneous cellular and molecular states (Bendall et al, 2007; Chen et al, 2012a; Moogk et al, 2010; Stewart et al, 2006), and frequent reports of chromosomal abnormalities (reviewed in Baker et al, 2007; Lee et al, 2013). Certain chromosomal alterations such as trisomies 12, 17, and 20 have the capacity to confer growth advantages as indicated by comparative genetic analyses (Amps et al, 2011; Catalina et al, 2008; Draper et al, 2004; Lefort et al, 2008). …”

Nucleosome positioning changes during human embryonic stem cell differentiation

“…Middle East -East European ancestry 52 and in a normal (nondiseased) genome of an individual of European ancestry (NA12892) that was sequenced to approximately the same coverage (11.8X). For point/oligo-base changes, we identified about 2.6 million single nucleotide polymorphisms (SNPs) when compared to the human reference genome (Table S5C), with base transitions (C$T and G$A) occurring at a higher frequency (»70%) compared to base transversions (»30%) (Fig.…”