Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: The International Stem Cell Initiative analyzed 127 human embryonic stem cell lines and 11 induced pluripotent cell lines, from 39 laboratories worldwide for genetic changes occurring during culture. Most cell lines were analyzed at an early and late passage. Population structure analysis from SNP detection revealed that the cell lines included representatives of all 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 but haphazardly with no link to time in culture. Structural variants (SVs), below the level of standard chromosome banding, determined from the SNP arrays, also appeared sporadically but no common variants related to culture were observed on chromosomes 1, 12 and 17. However, overlapping SV gains acquired in the chromosome 20q11.21 region during extended culture were identified in over 20% of the cell lines. Three genes within the minimal shared region, ID1, BCL2L1, and HM13, are expressed in human ES cells, with BCL2L1 a strong candidate for driving this culture adaptation of ES cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE33522 | GEO | 2011/11/12

SECONDARY ACCESSION(S): PRJNA148805

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Screening a large, ethnically diverse population of human embryonic stem cells identifies a chromosome 20 minimal amplicon that confers a growth advantage

Project description:The International Stem Cell Initiative analyzed 127 human embryonic stem cell lines and 11 induced pluripotent cell lines, from 39 laboratories worldwide for genetic changes occurring during culture. Most cell lines were analyzed at an early and late passage. Population structure analysis from SNP detection revealed that the cell lines included representatives of all 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 but haphazardly with no link to time in culture. Structural variants (SVs), below the level of standard chromosome banding, determined from the SNP arrays, also appeared sporadically but no common variants related to culture were observed on chromosomes 1, 12 and 17. However, overlapping SV gains acquired in the chromosome 20q11.21 region during extended culture were identified in over 20% of the cell lines. Three genes within the minimal shared region, ID1, BCL2L1, and HM13, are expressed in human ES cells, with BCL2L1 a strong candidate for driving this culture adaptation of ES cells. In order to provide better insight into the frequency and types of genetic changes affecting human ES cells on prolonged passage, the ISCI has undertaken a survey by karyology and high resolution SNP array of one hundred twenty seven independent human ES cell lines, provided by thirty nine laboratories in twenty countries around the world, particularly to identify the common genetic changes that occur during prolonged culture. Here we append data from the SNP genotyping of the genomic DNA samples extracted from the human embryonic stem cells. A group of eleven human iPS cells from three laboratories was also included to provide a pilot comparison of these pluripotent cells derived by reprogramming.

2011-11-12 | E-GEOD-33522 | biostudies-arrayexpress

Human ES cells reveal recurrent genomic instability at 20q11.21

Project description:By analyzing five human embryonic stem (hES) cell lines over long-term culture, we detected a recurrent genomic instability in the human genome. An amplification of 2.5â4.6 Mb at 20q11.21, encompassing about 23 genes in common, appeared in four cell lines of different origins. This amplification, which has been associated with oncogenic transformation, may provide a selective advantage to hES cells in culture Array-based comparative genomic hybridization, was performed on genomic DNA samples from different human embryonic stem cell lines, all cultured in our laboratory under the same conditions. VUB05-HD is an hES cell line carrying the Huntingtin mutant gene H1, H9, SA01, and VUB01 are various hES cell lines GSM341552 and GSM341553: SNP analysis GSM341589 to GSM341669: CGH analysis

2010-05-16 | E-GEOD-13565 | biostudies-arrayexpress

Array-based comparative genomic hybridization study of human embryonic stem cell lines

Project description:G-banding of human embryonic stem cells (hESC) has proved their predisposition to aneuploidy of chromosomes 12, 17 and X. Now, using array-based comparative genomic hybridization, we find that hESC also accumulate other recurrent chromosomal abnormalities, such as duplications of stemness genes, submicroscopic instability of 20q11.21 and the appearance of a derivative chromosome 18. Keywords: comparative genomic hybridization, genomic integrity of human embryonic stem cells Array-based comparative genomic hybridization was performed on 48 DNA samples from 17 human embryonic stem cell lines, all cultured in our laboratory under the same conditions. All lines were hybridized against DNA obtained from peripheral blood from donors with a known normal karyotype. No replicates were done from the same DNA sample, but, whenever possible the same stem cell line was analysed at later passages. All detected abnormalities were confirmed by FISH and/or G-banding.

2010-05-17 | E-GEOD-13422 | biostudies-arrayexpress

Human ES cells reveal recurrent genomic instability at 20q11.21

2008-11-19 | GSE13565 | GEO

Array-based comparative genomic hybridization study of human embryonic stem cell lines

2008-11-04 | GSE13422 | GEO

An analysis of genomic structural alteration in three human ES cell lines.

Project description:To elucidate frequencies of genomic structural alterations, we performed an analysis using a SNP genotyping array (Illumina HumanCytoSNP-12 v2.1 DNA Analysis BeadChip Kit) for three human ES cell lines, namely, SEES-1, SEES-2, and SEES-3. Samples were collected after 4 to 60 passages to detect structural mutations occurred during the cell cultivation processes. Our results suggested a higher genomic stability of the ES cells compared to some well-known normal cell lines. Several samples were collected after 4 to 60 passages and subjected to the SNP genotyping array. We searched for structural mutations occurred during the culture of the ES cells.

2015-05-20 | E-GEOD-54576 | biostudies-arrayexpress

Homo sapiens

Project description:Affymetrix SNP array data for various human ES cell lines

| PRJNA231990 | ENA

An analysis of genomic structural alteration in three human ES cell lines.

2015-05-20 | GSE54576 | GEO

Gain of 20q11.21 in human pluripotent stem cells impairs TGFβ-dependent ectodermal commitment

Project description:Altered TGFb signaling in lines with a 20q11.21 amplification has a dramatic negative effect on ectodermal differentiation

2019-06-12 | GSE116372 | GEO

Homo sapiens

Project description:Human ES cells reveal recurrent genomic instability at 20q11.21

| PRJNA110665 | ENA