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

International Stem Cell Initiative; Katherine Amps; Peter W Andrews; George Anyfantis; Lyle Armstrong; Stuart Avery; Hossein Baharvand; Julie Baker; Duncan Baker; Maria B Munoz; Stephen Beil; Nissim Benvenisty; Dalit Ben-Yosef; Juan-Carlos Biancotti; Alexis Bosman; Romulo Martin Brena; Daniel Brison; Gunilla Caisander; María V Camarasa; Jieming Chen; Eric Chiao; Young Min Choi; Andre B H Choo; Daniel Collins; Alan Colman; Jeremy M Crook; George Q Daley; Anne Dalton; Paul A De Sousa; Chris Denning; Janet Downie; Petr Dvorak; Karen D Montgomery; Anis Feki; Angela Ford; Victoria Fox; Ana M Fraga; Tzvia Frumkin; Lin Ge; Paul J Gokhale; Tamar Golan-Lev; Hamid Gourabi; Michal Gropp; Guangxiu Lu; Ales Hampl; Katie Harron; Lyn Healy; Wishva Herath; Frida Holm; Outi Hovatta; Steve Pells

doi:10.1038/nbt.2051

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

International Stem Cell Initiative, Katherine Amps, Peter W Andrews, George Anyfantis, Lyle Armstrong, Stuart Avery, Hossein Baharvand, Julie Baker, Duncan Baker, Maria B Munoz, Stephen Beil, Nissim Benvenisty, Dalit Ben-Yosef, Juan-Carlos Biancotti, Alexis Bosman, Romulo Martin Brena, Daniel Brison, Gunilla Caisander, María V Camarasa, Jieming ChenEric Chiao, Young Min Choi, Andre B H Choo, Daniel Collins, Alan Colman, Jeremy M Crook, George Q Daley, Anne Dalton, Paul A De Sousa, Chris Denning, Janet Downie, Petr Dvorak, Karen D Montgomery, Anis Feki, Angela Ford, Victoria Fox, Ana M Fraga, Tzvia Frumkin, Lin Ge, Paul J Gokhale, Tamar Golan-Lev, Hamid Gourabi, Michal Gropp, Guangxiu Lu, Ales Hampl, Katie Harron, Lyn Healy, Wishva Herath, Frida Holm, Outi Hovatta, Steve Pells

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	1132-1144
Number of pages	13
Journal	Nature Biotechnology
Volume	29
Issue number	12
DOIs	https://doi.org/10.1038/nbt.2051
Publication status	Published - Dec 2011

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Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantageAccepted author manuscript, 3.97 MB

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International Stem Cell Initiative, Amps, K., Andrews, P. W., Anyfantis, G., Armstrong, L., Avery, S., Baharvand, H., Baker, J., Baker, D., Munoz, M. B., Beil, S., Benvenisty, N., Ben-Yosef, D., Biancotti, J.-C., Bosman, A., Brena, R. M., Brison, D., Caisander, G., Camarasa, M. V., ... Pells, S. (2011). Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. Nature Biotechnology, 29(12), 1132-1144. https://doi.org/10.1038/nbt.2051

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title = "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.",

author = "\{International Stem Cell Initiative\} and Katherine Amps and Andrews, \{Peter W\} and George Anyfantis and Lyle Armstrong and Stuart Avery and Hossein Baharvand and Julie Baker and Duncan Baker and Munoz, \{Maria B\} and Stephen Beil and Nissim Benvenisty and Dalit Ben-Yosef and Juan-Carlos Biancotti and Alexis Bosman and Brena, \{Romulo Martin\} and Daniel Brison and Gunilla Caisander and Camarasa, \{Mar{\'i}a V\} and Jieming Chen and Eric Chiao and Choi, \{Young Min\} and Choo, \{Andre B H\} and Daniel Collins and Alan Colman and Crook, \{Jeremy M\} and Daley, \{George Q\} and Anne Dalton and \{De Sousa\}, \{Paul A\} and Chris Denning and Janet Downie and Petr Dvorak and Montgomery, \{Karen D\} and Anis Feki and Angela Ford and Victoria Fox and Fraga, \{Ana M\} and Tzvia Frumkin and Lin Ge and Gokhale, \{Paul J\} and Tamar Golan-Lev and Hamid Gourabi and Michal Gropp and Guangxiu Lu and Ales Hampl and Katie Harron and Lyn Healy and Wishva Herath and Frida Holm and Outi Hovatta and Steve Pells",

year = "2011",

month = dec,

doi = "10.1038/nbt.2051",

language = "English",

volume = "29",

pages = "1132--1144",

journal = "Nature Biotechnology",

issn = "1087-0156",

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International Stem Cell Initiative, Amps, K, Andrews, PW, Anyfantis, G, Armstrong, L, Avery, S, Baharvand, H, Baker, J, Baker, D, Munoz, MB, Beil, S, Benvenisty, N, Ben-Yosef, D, Biancotti, J-C, Bosman, A, Brena, RM, Brison, D, Caisander, G, Camarasa, MV, Chen, J, Chiao, E, Choi, YM, Choo, ABH, Collins, D, Colman, A, Crook, JM, Daley, GQ, Dalton, A, De Sousa, PA, Denning, C, Downie, J, Dvorak, P, Montgomery, KD, Feki, A, Ford, A, Fox, V, Fraga, AM, Frumkin, T, Ge, L, Gokhale, PJ, Golan-Lev, T, Gourabi, H, Gropp, M, Lu, G, Hampl, A, Harron, K, Healy, L, Herath, W, Holm, F, Hovatta, O & Pells, S 2011, 'Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage', Nature Biotechnology, vol. 29, no. 12, pp. 1132-1144. https://doi.org/10.1038/nbt.2051

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T1 - Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage

AU - International Stem Cell Initiative

AU - Amps, Katherine

AU - Andrews, Peter W

AU - Anyfantis, George

AU - Armstrong, Lyle

AU - Avery, Stuart

AU - Baharvand, Hossein

AU - Baker, Julie

AU - Baker, Duncan

AU - Munoz, Maria B

AU - Beil, Stephen

AU - Benvenisty, Nissim

AU - Ben-Yosef, Dalit

AU - Biancotti, Juan-Carlos

AU - Bosman, Alexis

AU - Brena, Romulo Martin

AU - Brison, Daniel

AU - Caisander, Gunilla

AU - Camarasa, María V

AU - Chen, Jieming

AU - Chiao, Eric

AU - Choi, Young Min

AU - Choo, Andre B H

AU - Collins, Daniel

AU - Colman, Alan

AU - Crook, Jeremy M

AU - Daley, George Q

AU - Dalton, Anne

AU - De Sousa, Paul A

AU - Denning, Chris

AU - Downie, Janet

AU - Dvorak, Petr

AU - Montgomery, Karen D

AU - Feki, Anis

AU - Ford, Angela

AU - Fox, Victoria

AU - Fraga, Ana M

AU - Frumkin, Tzvia

AU - Ge, Lin

AU - Gokhale, Paul J

AU - Golan-Lev, Tamar

AU - Gourabi, Hamid

AU - Gropp, Michal

AU - Lu, Guangxiu

AU - Hampl, Ales

AU - Harron, Katie

AU - Healy, Lyn

AU - Herath, Wishva

AU - Holm, Frida

AU - Hovatta, Outi

AU - Pells, Steve

PY - 2011/12

Y1 - 2011/12

N2 - 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.

AB - 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.

U2 - 10.1038/nbt.2051

DO - 10.1038/nbt.2051

M3 - Article

C2 - 22119741

SN - 1087-0156

VL - 29

SP - 1132

EP - 1144

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 12

ER -

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

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