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

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; Marãa 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; Lu Guangxiu; Ales Hampl; Katie Harron; Lyn Healy; Wishva Herath; Frida Holm; Outi Hovatta; Johan Hyllner; Maneesha S. Inamdar; Astrid Kresentia Irwanto; Tetsuya Ishii; Marisa Jaconi; Ying Jin; Susan Kimber; Sergey Kiselev; Barbara B. Knowles; Oded Kopper; Valeri Kukharenko; Anver Kuliev; Maria A. Lagarkova; Peter W. Laird; Majlinda Lako; Andrew L. Laslett; Neta Lavon; Dong Ryul Lee; Jeoung Eun Lee; Chunliang Li; Linda S. Lim; Tenneille E. Ludwig; Yu Ma; Edna Maltby; Ileana Mateizel; Yoav Mayshar; Maria Mileikovsky; Stephen L. Minger; Takamichi Miyazaki; Shin Yong Moon; Harry Moore; Christine Mummery; Andras Nagy; Norio Nakatsuji; Kavita Narwani; Steve K W Oh; Sun Kyung Oh; Cia Olson; Timo Otonkoski; Fei Pan; In Hyun Park; Steve Pells; Martin F. Pera; Lygia V. Pereira; Ouyang Qi; Grace Selva Raj; Benjamin Reubinoff; Alan Robins; Paul Robson; Janet Rossant; Ghasem H. Salekdeh; Thomas C. Schulz; Karen Sermon; Jameelah Sheik Mohamed; Hui Shen; Eric Sherrer; Kuldip Sidhu; Shirani Sivarajah; Heli Skottman; Claudia Spits; Glyn N. Stacey; Raimund Strehl; Nick Strelchenko; Hirofumi Suemori; Bowen Sun; Riitta Suuronen; Kazutoshi Takahashi; Timo Tuuri; Parvathy Venu; Yuri Verlinsky; Dorien Ward Van Oostwaard; Daniel J. Weisenberger; Yue Wu; Shinya Yamanaka; Lorraine Young; Qi Zhou

doi:10.1038/nbt.2051

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

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, Marãa V. Camarasa, Jieming Chen, Eric ChiaoYoung 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, Lu Guangxiu, Ales Hampl, Katie Harron, Lyn Healy, Wishva Herath, Frida Holm, Outi Hovatta, Johan Hyllner, Maneesha S. Inamdar, Astrid Kresentia Irwanto, Tetsuya Ishii, Marisa Jaconi, Ying Jin, Susan Kimber, Sergey Kiselev, Barbara B. Knowles, Oded Kopper, Valeri Kukharenko, Anver Kuliev, Maria A. Lagarkova, Peter W. Laird, Majlinda Lako, Andrew L. Laslett, Neta Lavon, Dong Ryul Lee, Jeoung Eun Lee, Chunliang Li, Linda S. Lim, Tenneille E. Ludwig, Yu Ma, Edna Maltby, Ileana Mateizel, Yoav Mayshar, Maria Mileikovsky, Stephen L. Minger, Takamichi Miyazaki, Shin Yong Moon, Harry Moore, Christine Mummery, Andras Nagy, Norio Nakatsuji, Kavita Narwani, Steve K W Oh, Sun Kyung Oh, Cia Olson, Timo Otonkoski, Fei Pan, In Hyun Park, Steve Pells, Martin F. Pera, Lygia V. Pereira, Ouyang Qi, Grace Selva Raj, Benjamin Reubinoff, Alan Robins, Paul Robson, Janet Rossant, Ghasem H. Salekdeh, Thomas C. Schulz, Karen Sermon, Jameelah Sheik Mohamed, Hui Shen, Eric Sherrer, Kuldip Sidhu, Shirani Sivarajah, Heli Skottman, Claudia Spits, Glyn N. Stacey, Raimund Strehl, Nick Strelchenko, Hirofumi Suemori, Bowen Sun, Riitta Suuronen, Kazutoshi Takahashi, Timo Tuuri, Parvathy Venu, Yuri Verlinsky, Dorien Ward Van Oostwaard, Daniel J. Weisenberger, Yue Wu, Shinya Yamanaka, Lorraine Young, Qi Zhou

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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. © 2011 Nature America, Inc. All rights reserved.

Original language	English
Pages (from-to)	1132-1144
Number of pages	12
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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10.1038/nbt.2051

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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., Chen, J., ... Zhou, Q. (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

@article{10142e40dc9246649d4e3ca7de20809b,

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. {\textcopyright} 2011 Nature America, Inc. All rights reserved.",

author = "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 Biancotti, {Juan Carlos} and Alexis Bosman and Brena, {Romulo Martin} and Daniel Brison and Gunilla Caisander and Camarasa, {Mar{\~a}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 Lu Guangxiu and Ales Hampl and Katie Harron and Lyn Healy and Wishva Herath and Frida Holm and Outi Hovatta and Johan Hyllner and Inamdar, {Maneesha S.} and Irwanto, {Astrid Kresentia} and Tetsuya Ishii and Marisa Jaconi and Ying Jin and Susan Kimber and Sergey Kiselev and Knowles, {Barbara B.} and Oded Kopper and Valeri Kukharenko and Anver Kuliev and Lagarkova, {Maria A.} and Laird, {Peter W.} and Majlinda Lako and Laslett, {Andrew L.} and Neta Lavon and Lee, {Dong Ryul} and Lee, {Jeoung Eun} and Chunliang Li and Lim, {Linda S.} and Ludwig, {Tenneille E.} and Yu Ma and Edna Maltby and Ileana Mateizel and Yoav Mayshar and Maria Mileikovsky and Minger, {Stephen L.} and Takamichi Miyazaki and Moon, {Shin Yong} and Harry Moore and Christine Mummery and Andras Nagy and Norio Nakatsuji and Kavita Narwani and Oh, {Steve K W} and Oh, {Sun Kyung} and Cia Olson and Timo Otonkoski and Fei Pan and Park, {In Hyun} and Steve Pells and Pera, {Martin F.} and Pereira, {Lygia V.} and Ouyang Qi and Raj, {Grace Selva} and Benjamin Reubinoff and Alan Robins and Paul Robson and Janet Rossant and Salekdeh, {Ghasem H.} and Schulz, {Thomas C.} and Karen Sermon and Mohamed, {Jameelah Sheik} and Hui Shen and Eric Sherrer and Kuldip Sidhu and Shirani Sivarajah and Heli Skottman and Claudia Spits and Stacey, {Glyn N.} and Raimund Strehl and Nick Strelchenko and Hirofumi Suemori and Bowen Sun and Riitta Suuronen and Kazutoshi Takahashi and Timo Tuuri and Parvathy Venu and Yuri Verlinsky and Oostwaard, {Dorien Ward Van} and Weisenberger, {Daniel J.} and Yue Wu and Shinya Yamanaka and Lorraine Young and Qi Zhou",

year = "2011",

month = dec,

doi = "10.1038/nbt.2051",

language = "English",

volume = "29",

pages = "1132--1144",

journal = "Nature biotechnology",

issn = "1546-1696",

publisher = "Springer Nature",

number = "12",

}

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, JC, 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, Guangxiu, L, Hampl, A, Harron, K, Healy, L, Herath, W, Holm, F, Hovatta, O, Hyllner, J, Inamdar, MS, Irwanto, AK, Ishii, T, Jaconi, M, Jin, Y, Kimber, S, Kiselev, S, Knowles, BB, Kopper, O, Kukharenko, V, Kuliev, A, Lagarkova, MA, Laird, PW, Lako, M, Laslett, AL, Lavon, N, Lee, DR, Lee, JE, Li, C, Lim, LS, Ludwig, TE, Ma, Y, Maltby, E, Mateizel, I, Mayshar, Y, Mileikovsky, M, Minger, SL, Miyazaki, T, Moon, SY, Moore, H, Mummery, C, Nagy, A, Nakatsuji, N, Narwani, K, Oh, SKW, Oh, SK, Olson, C, Otonkoski, T, Pan, F, Park, IH, Pells, S, Pera, MF, Pereira, LV, Qi, O, Raj, GS, Reubinoff, B, Robins, A, Robson, P, Rossant, J, Salekdeh, GH, Schulz, TC, Sermon, K, Mohamed, JS, Shen, H, Sherrer, E, Sidhu, K, Sivarajah, S, Skottman, H, Spits, C, Stacey, GN, Strehl, R, Strelchenko, N, Suemori, H, Sun, B, Suuronen, R, Takahashi, K, Tuuri, T, Venu, P, Verlinsky, Y, Oostwaard, DWV, Weisenberger, DJ, Wu, Y, Yamanaka, S, Young, L & Zhou, Q 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

TY - JOUR

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

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, Marãa 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 - Guangxiu, Lu

AU - Hampl, Ales

AU - Harron, Katie

AU - Healy, Lyn

AU - Herath, Wishva

AU - Holm, Frida

AU - Hovatta, Outi

AU - Hyllner, Johan

AU - Inamdar, Maneesha S.

AU - Irwanto, Astrid Kresentia

AU - Ishii, Tetsuya

AU - Jaconi, Marisa

AU - Jin, Ying

AU - Kimber, Susan

AU - Kiselev, Sergey

AU - Knowles, Barbara B.

AU - Kopper, Oded

AU - Kukharenko, Valeri

AU - Kuliev, Anver

AU - Lagarkova, Maria A.

AU - Laird, Peter W.

AU - Lako, Majlinda

AU - Laslett, Andrew L.

AU - Lavon, Neta

AU - Lee, Dong Ryul

AU - Lee, Jeoung Eun

AU - Li, Chunliang

AU - Lim, Linda S.

AU - Ludwig, Tenneille E.

AU - Ma, Yu

AU - Maltby, Edna

AU - Mateizel, Ileana

AU - Mayshar, Yoav

AU - Mileikovsky, Maria

AU - Minger, Stephen L.

AU - Miyazaki, Takamichi

AU - Moon, Shin Yong

AU - Moore, Harry

AU - Mummery, Christine

AU - Nagy, Andras

AU - Nakatsuji, Norio

AU - Narwani, Kavita

AU - Oh, Steve K W

AU - Oh, Sun Kyung

AU - Olson, Cia

AU - Otonkoski, Timo

AU - Pan, Fei

AU - Park, In Hyun

AU - Pells, Steve

AU - Pera, Martin F.

AU - Pereira, Lygia V.

AU - Qi, Ouyang

AU - Raj, Grace Selva

AU - Reubinoff, Benjamin

AU - Robins, Alan

AU - Robson, Paul

AU - Rossant, Janet

AU - Salekdeh, Ghasem H.

AU - Schulz, Thomas C.

AU - Sermon, Karen

AU - Mohamed, Jameelah Sheik

AU - Shen, Hui

AU - Sherrer, Eric

AU - Sidhu, Kuldip

AU - Sivarajah, Shirani

AU - Skottman, Heli

AU - Spits, Claudia

AU - Stacey, Glyn N.

AU - Strehl, Raimund

AU - Strelchenko, Nick

AU - Suemori, Hirofumi

AU - Sun, Bowen

AU - Suuronen, Riitta

AU - Takahashi, Kazutoshi

AU - Tuuri, Timo

AU - Venu, Parvathy

AU - Verlinsky, Yuri

AU - Oostwaard, Dorien Ward Van

AU - Weisenberger, Daniel J.

AU - Wu, Yue

AU - Yamanaka, Shinya

AU - Young, Lorraine

AU - Zhou, Qi

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. © 2011 Nature America, Inc. All rights reserved.

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. © 2011 Nature America, Inc. All rights reserved.

U2 - 10.1038/nbt.2051

DO - 10.1038/nbt.2051

M3 - Article

SN - 1546-1696

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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