Journal Article

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

Biancotti, Juan-Carlos, Oh, Sun Kyung, Raj, Grace Selva, Lu, Guangxiu, Ludwig, Tenneille E, Avery, Stuart, Andrews, Peter W, Jin, Ying, Denning, Chris, Lee, Jeoung Eun, Kuliev, Anver, Anyfantis, George, Mileikovsky, Maria, Harron, Katie, Qi, Ouyang, Golan-Lev, Tamar, Gokhale, Paul J, Ford, Angela, Nakatsuji, Norio, Beil, Stephen, Jaconi, Marisa, Brison, Daniel, Moon, Shin Yong, Kiselev, Sergey, Irwanto, Astrid Kresentia, Reubinoff, Benjamin, Salekdeh, Ghasem H, Choi, Young Min, Kimber, Susan, Brena, Romulo Martin, Lako, Majlinda, Hyllner, Johan, Oh, Steve K W, Colman, Alan, Mayshar, Yoav, Lee, Dong Ryul, Lagarkova, Maria A, Maltby, Edna, Laslett, Andrew L, Collins, Daniel, Fraga, Ana M, Frumkin, Tzvia, Baker, Julie, Holm, Frida, Baharvand, Hossein, Pera, Martin F, Rossant, Janet, Herath, Wishva, Lim, Linda S, Healy, Lyn, Kukharenko, Valeri, Ge, Lin, Robson, Paul, Mummery, Christine, Inamdar, Maneesha S, Gourabi, Hamid, Kopper, Oded, Daley, George Q, Armstrong, Lyle, Ishii, Tetsuya, Otonkoski, Timo, Montgomery, Karen D, Baker, Duncan, Choo, Andre B H, Caisander, Gunilla, Chiao, Eric, Munoz, Maria B, Ma, Yu, Minger, Step

2011

Overview

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.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 631/208/176 / 631/208/726/649/2157 / 631/61/2320 / Agriculture / bcl-X Protein - genetics / bcl-X Protein - metabolism / Bioinformatics / Biological and medical sciences / Biomedical and Life Sciences / Biomedical Engineering/Biotechnology / Biomedicine / Biotechnology / Cell culture / Cell Differentiation - genetics / Cell Line / Cell separation / Chromosomes / Chromosomes, Human, Pair 20 - genetics / Clonal Evolution - genetics / Deoxyribonucleic acid / Diverse techniques / DNA / DNA Methylation / Embryonic stem cells / Embryonic Stem Cells - cytology / Ethnicity - genetics / Fundamental and applied biological sciences. Psychology / Gene expression / Gene Expression Regulation, Developmental / Genetic aspects / Genetic Variation / Genetics / Genotype / Growth / Growth - genetics / Humans / Induced Pluripotent Stem Cells - cytology / Inhibitor of Differentiation Protein 1 - genetics / Inhibitor of Differentiation Protein 1 - metabolism / Life Sciences / Methods / Minority & ethnic groups / Molecular and cellular biology / Polymorphism / Polymorphism, Single Nucleotide / resource / RNA-Binding Proteins - genetics / RNA-Binding Proteins - metabolism / Selection, Genetic - genetics / Stem cells