Dataset Information

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 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.

SUBMITTER: International Stem Cell Initiative

PROVIDER: S-EPMC3454460 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Amps Katherine K Andrews Peter W PW Anyfantis George G Armstrong Lyle L Avery Stuart S Baharvand Hossein H Baker Julie J Baker Duncan D Munoz Maria B MB Beil Stephen S Benvenisty Nissim N Ben-Yosef Dalit D Biancotti Juan-Carlos JC Bosman Alexis A Brena Romulo Martin RM Brison Daniel D Caisander Gunilla G Camarasa María V MV Chen Jieming J Chiao Eric E Choi Young Min YM Choo Andre B H AB Collins Daniel D Colman Alan A Crook Jeremy M JM Daley George Q GQ Dalton Anne A De Sousa Paul A PA Denning Chris C Downie Janet J Dvorak Petr P Montgomery Karen D KD Feki Anis A Ford Angela A Fox Victoria V Fraga Ana M AM Frumkin Tzvia T Ge Lin L Gokhale Paul J PJ Golan-Lev Tamar T Gourabi Hamid H Gropp Michal M Lu Guangxiu G Hampl Ales A Harron Katie K Healy Lyn L Herath Wishva W Holm Frida F Hovatta Outi O Hyllner Johan J Inamdar Maneesha S MS Irwanto Astrid Kresentia AK Ishii Tetsuya T Jaconi Marisa M Jin Ying Y Kimber Susan S Kiselev Sergey S Knowles Barbara B BB Kopper Oded O Kukharenko Valeri V Kuliev Anver A Lagarkova Maria A MA Laird Peter W PW Lako Majlinda M Laslett Andrew L AL Lavon Neta N Lee Dong Ryul DR Lee Jeoung Eun JE Li Chunliang C Lim Linda S LS Ludwig Tenneille E TE Ma Yu Y Maltby Edna E Mateizel Ileana I Mayshar Yoav Y Mileikovsky Maria M Minger Stephen L SL Miyazaki Takamichi T Moon Shin Yong SY Moore Harry H Mummery Christine C Nagy Andras A Nakatsuji Norio N Narwani Kavita K Oh Steve K W SK Oh Sun Kyung SK Olson Cia C Otonkoski Timo T Pan Fei F Park In-Hyun IH Pells Steve S Pera Martin F MF Pereira Lygia V LV Qi Ouyang O Raj Grace Selva GS Reubinoff Benjamin B Robins Alan A Robson Paul P Rossant Janet J Salekdeh Ghasem H GH Schulz Thomas C TC Sermon Karen K Sheik Mohamed Jameelah J Shen Hui H Sherrer Eric E Sidhu Kuldip K Sivarajah Shirani S Skottman Heli H Spits Claudia C Stacey Glyn N GN Strehl Raimund R Strelchenko Nick N Suemori Hirofumi H Sun Bowen B Suuronen Riitta R Takahashi Kazutoshi K Tuuri Timo T Venu Parvathy P Verlinsky Yuri Y Ward-van Oostwaard Dorien D Weisenberger Daniel J DJ Wu Yue Y Yamanaka Shinya S Young Lorraine L Zhou Qi Q

Nature biotechnology 20111127 12

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 prolong ...[more]

PMID: 22119741

Similar Datasets

Project description:OBJECTIVES:Cross-sectional and longitudinal evidence from largely non-Hispanic White cohorts suggests that positive psychosocial factors, particularly self-efficacy and social support, may protect against late-life cognitive decline. Identifying potentially protective factors in racial/ethnic minority elders is of high importance due to their increased risk of Alzheimer's disease. The overall goal of this study was to characterize cross-sectional associations between positive psychosocial factors and cognitive domains among Black, Hispanic, and White older adults. METHODS:A total of 548 older adults (41% Black, 28% Hispanic, 31% White) in the Washington Heights-Inwood Columbia Aging Project completed cognitive and psychosocial measures from the NIH Toolbox and standard neuropsychological tests. Multiple-group regressions were used to compare cross-sectional associations between positive psychosocial factors and cognition across racial/ethnic groups, independent of demographics, depressive symptoms, and physical health. RESULTS:Positive associations between self-efficacy and language did not significantly differ across race/ethnicity, although the bivariate association between self-efficacy and language was not significant among Hispanics. Additional positive associations were observed for Whites and Blacks, but not Hispanics. Negative associations between emotional support and purpose in life and working memory were seen only in Hispanics. CONCLUSIONS:Results confirm and extend the link between self-efficacy and cognition in late life, particularly for White and Black older adults. Previous studies on positive psychosocial factors in cognitive aging may not be generalizable to Hispanics. Longitudinal follow-up is needed to determine whether negative relationships between certain psychosocial factors and cognition in Hispanics reflect reverse causation, threshold effects, and/or negative aspects of having a strong social network. (JINS, 2018, 24, 294-304).

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets