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

• Authors: AMPS Katherine; ANDREWS Peter W.; ANYFANTIS George; ARMSTRONG Lyle; AVERY Stuart; BAHARVAND Hossein; BAKER Julie; BAKER Duncan; MUNOZ Maria B.; BEIL Stephen; BENVENISTY Nissim; BEN-YOSEF Dalit; BIANCOTTI Juan-Carlos; BOSMAN Alexis; BRENA Romulo Martin; BRISON Daniel; CAISANDER Gunilla; CAMARASA Maria V.; CHEN Jieming; CHIAO Eric; CHOI Young Min; CHOO Andre B. H.; COLLINS Daniel; COLMAN Alan; CROOK Jeremy M.; DALEY George Q.; DALTON Anne; DE SOUSA Paul A.; DENNING Chris; DOWNIE Janet; DVOŘÁK Petr; MONTGOMERY Karen D.; FEKI Anis; FORD Angela; FOX Victoria; FRAGA Ana M.; FRUMKIN Tzvia; GE Lin; GOKHALE Paul J.; GOLAN-LEV Tamar; GOURABI Hamid; GROPP Michal; LU Guangxiu; HAMPL Aleš; HARRON Katie; HEALY Lyn; HERATH Wishva; HOLM Frida; HOVATTA Outi; HYLLNER Johan; INAMDAR Maneesha S.; IRWANTO Astrid Kresentia; ISHII Tetsuya; JACONI Marisa; JIN Ying; KIMBER Susan; KISELEV Sergey; KNOWLES Barbara B.; KOPPER Oded; KUKHARENKO Valeri; KULIEV Anver; LAGARKOVA Maria A.; LAIRD Peter W.; LAKO Majlinda; LASLETT Andrew L.; LAVON Neta; LEE Dong Ryul; LEE Jeoung Eun; LI Chunliang; LIM Linda S.; LUDWIG Tenneille E.; MA Yu; MALTBY Edna; MATEIZEL Ileana; MAYSHAR Yoav; MILEIKOVSKY Maria; MINGER Stephen L.; MIYAZAKI Takamichi; MOON Shin Yong; MOORE Harry; MUMMERY Christine; NAGY Andras; NAKATSUJI Norio; NARWANI Kavita; OH Steve K. W.; OH Sun Kyung; OLSON Cia; OTONKOSKI Timo; PAN Fei; PARK In-Hyun; PELLS Steve; PERA Martin F.; PEREIRA Lygia V.; QI Ouyang; RAJ Grace Selva; REUBINOFF Benjamin; ROBINS Alan; ROBSON Paul; ROSSANT Janet; SALEKDEH Ghasem H.; SPITS Claudia; SCHULZ Thomas C.; SERMON Karen; MOHAMED Jameelah Sheik; SHEN Hui; SHERRER Eric; SIDHU Kuldip; SIVARAJAH Shirani; SKOTTMAN Heli; STACEY G.; STREHL R.; STRELCHENKO N.; SUEMORI H.; SUN B.; SUURONEN R.; TAKAHASHI K.; TUURI T.; VENU P.; VERLINSKY Y.; WARD-VAN OOSTWAARD D.; WEISENBERGER D.; WU Y.; YAMANAKA S.; YOUNG L.; ZHOU Q.
• Year of publication: 2011
• Type: Article in Periodical
• Magazine / Source: Nature Biotechnology
• MU Faculty or unit: Faculty of Medicine
• Doi: http://dx.doi.org/10.1038/nbt.2051
• Field: Biotechnology
• Keywords: COMPARATIVE GENOMIC HYBRIDIZATION; COPY NUMBER VARIATION; HUMAN ES CELLS; DNA-SEQUENCE; IN-VIVO; CULTURE; LINES; TUMORS; PLURIPOTENCY; GENES
• Description: 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.