Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage
- 27 November 2011
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Biotechnology
- Vol. 29 (12), 1132-1144
- https://doi.org/10.1038/nbt.2051
Abstract
The International Stem Cell Initiative compares 125 ethnically diverse human embryonic stem cell lines at early and late passage. Data on karotype, single-nucleotide polymorphisms and methylation shed light on how the cells adapt to long-term culture. 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 expressed in human ES cells, ID1, BCL2L1 and HM13, occurred in >20% of the lines. Of these genes, BCL2L1 is a strong candidate for driving culture adaptation of ES cells.This publication has 71 references indexed in Scilit:
- Bcl-xL enhances single-cell survival and expansion of human embryonic stem cells without affecting self-renewalStem Cell Research, 2012
- Dynamic Changes in the Copy Number of Pluripotency and Cell Proliferation Genes in Human ESCs and iPSCs during Reprogramming and Time in CultureCell Stem Cell, 2011
- The landscape of somatic copy-number alteration across human cancersNature, 2010
- Jarid2/Jumonji Coordinates Control of PRC2 Enzymatic Activity and Target Gene Occupancy in Pluripotent CellsCell, 2009
- Genes mirror geography within EuropeNature, 2008
- A second generation human haplotype map of over 3.1 million SNPsNature, 2007
- Principal components analysis corrects for stratification in genome-wide association studiesNature Genetics, 2006
- Control of Developmental Regulators by Polycomb in Human Embryonic Stem CellsCell, 2006
- DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineageNature, 2006
- Characterization and culture of human embryonic stem cellsNature Biotechnology, 2005