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

J 2011

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

AMPS, Katherine, Peter W. ANDREWS, George ANYFANTIS, Lyle ARMSTRONG, Stuart AVERY et. al.

Basic information

Original name

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

Authors

AMPS, Katherine (826 United Kingdom of Great Britain and Northern Ireland, guarantor), Peter W. ANDREWS (826 United Kingdom of Great Britain and Northern Ireland), George ANYFANTIS (826 United Kingdom of Great Britain and Northern Ireland), Lyle ARMSTRONG (826 United Kingdom of Great Britain and Northern Ireland), Stuart AVERY (702 Singapore), Hossein BAHARVAND (364 Islamic Republic of Iran), Julie BAKER (840 United States of America), Duncan BAKER (826 United Kingdom of Great Britain and Northern Ireland), Maria B. MUNOZ (826 United Kingdom of Great Britain and Northern Ireland), Stephen BEIL (840 United States of America), Nissim BENVENISTY (840 United States of America), Dalit BEN-YOSEF (376 Israel), Juan-Carlos BIANCOTTI (840 United States of America), Alexis BOSMAN (756 Switzerland), Romulo Martin BRENA (840 United States of America), Daniel BRISON (826 United Kingdom of Great Britain and Northern Ireland), Gunilla CAISANDER (752 Sweden), Maria V. CAMARASA (826 United Kingdom of Great Britain and Northern Ireland), Jieming CHEN (702 Singapore), Eric CHIAO (840 United States of America), Young Min CHOI (410 Republic of Korea), Andre B. H. CHOO (702 Singapore), Daniel COLLINS (826 United Kingdom of Great Britain and Northern Ireland), Alan COLMAN (702 Singapore), Jeremy M. CROOK (36 Australia), George Q. DALEY (840 United States of America), Anne DALTON (826 United Kingdom of Great Britain and Northern Ireland), Paul A. DE SOUSA (826 United Kingdom of Great Britain and Northern Ireland), Chris DENNING (826 United Kingdom of Great Britain and Northern Ireland), Janet DOWNIE (826 United Kingdom of Great Britain and Northern Ireland), Petr DVOŘÁK (203 Czech Republic, belonging to the institution), Karen D. MONTGOMERY (840 United States of America), Anis FEKI (756 Switzerland), Angela FORD (826 United Kingdom of Great Britain and Northern Ireland), Victoria FOX (840 United States of America), Ana M. FRAGA (76 Brazil), Tzvia FRUMKIN (376 Israel), Lin GE (156 China), Paul J. GOKHALE (826 United Kingdom of Great Britain and Northern Ireland), Tamar GOLAN-LEV (376 Israel), Hamid GOURABI (364 Islamic Republic of Iran), Michal GROPP (376 Israel), Guangxiu LU (156 China), Aleš HAMPL (203 Czech Republic, belonging to the institution), Katie HARRON (826 United Kingdom of Great Britain and Northern Ireland), Lyn HEALY (826 United Kingdom of Great Britain and Northern Ireland), Wishva HERATH (702 Singapore), Frida HOLM (752 Sweden), Outi HOVATTA (752 Sweden), Johan HYLLNER (752 Sweden), Maneesha S. INAMDAR (356 India), Astrid Kresentia IRWANTO (702 Singapore), Tetsuya ISHII (392 Japan), Marisa JACONI (756 Switzerland), Ying JIN (156 China), Susan KIMBER (826 United Kingdom of Great Britain and Northern Ireland), Sergey KISELEV (643 Russian Federation), Barbara B. KNOWLES (702 Singapore), Oded KOPPER (376 Israel), Valeri KUKHARENKO (840 United States of America), Anver KULIEV (840 United States of America), Maria A. LAGARKOVA (643 Russian Federation), Peter W. LAIRD (840 United States of America), Majlinda LAKO (826 United Kingdom of Great Britain and Northern Ireland), Andrew L. LASLETT (36 Australia), Neta LAVON (840 United States of America), Dong Ryul LEE (410 Republic of Korea), Jeoung Eun LEE (410 Republic of Korea), Chunliang LI (156 China), Linda S. LIM (702 Singapore), Tenneille E. LUDWIG (840 United States of America), Yu MA (156 China), Edna MALTBY (826 United Kingdom of Great Britain and Northern Ireland), Ileana MATEIZEL (56 Belgium), Yoav MAYSHAR (376 Israel), Maria MILEIKOVSKY (124 Canada), Stephen L. MINGER (826 United Kingdom of Great Britain and Northern Ireland), Takamichi MIYAZAKI (392 Japan), Shin Yong MOON (410 Republic of Korea), Harry MOORE (826 United Kingdom of Great Britain and Northern Ireland), Christine MUMMERY (528 Netherlands), Andras NAGY (124 Canada), Norio NAKATSUJI (392 Japan), Kavita NARWANI (840 United States of America), Steve K. W. OH (702 Singapore), Sun Kyung OH (410 Republic of Korea), Cia OLSON (246 Finland), Timo OTONKOSKI (246 Finland), Fei PAN (840 United States of America), In-Hyun PARK (840 United States of America), Steve PELLS (826 United Kingdom of Great Britain and Northern Ireland), Martin F. PERA (826 United Kingdom of Great Britain and Northern Ireland), Lygia V. PEREIRA (76 Brazil), Ouyang QI (156 China), Grace Selva RAJ (702 Singapore), Benjamin REUBINOFF (376 Israel), Alan ROBINS (840 United States of America), Paul ROBSON (702 Singapore), Janet ROSSANT (124 Canada), Ghasem H. SALEKDEH (840 United States of America), Claudia SPITS (56 Belgium), Thomas C. SCHULZ (840 United States of America), Karen SERMON (56 Belgium), Jameelah Sheik MOHAMED (702 Singapore), Hui SHEN (840 United States of America), Eric SHERRER (840 United States of America), Kuldip SIDHU (702 Singapore), Shirani SIVARAJAH (36 Australia), Heli SKOTTMAN (246 Finland), G. STACEY (840 United States of America), R. STREHL (840 United States of America), N. STRELCHENKO (840 United States of America), H. SUEMORI (840 United States of America), B. SUN (840 United States of America), R. SUURONEN (840 United States of America), K. TAKAHASHI (840 United States of America), T. TUURI (840 United States of America), P. VENU (840 United States of America), Y. VERLINSKY (840 United States of America), D. WARD-VAN OOSTWAARD (840 United States of America), D. WEISENBERGER (840 United States of America), Y. WU (840 United States of America), S. YAMANAKA (840 United States of America), L. YOUNG (840 United States of America) and Q. ZHOU (840 United States of America)

Edition

Nature Biotechnology, 2011, 1087-0156

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

Biotechnology and bionics

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

Impact factor

Impact factor: 23.268

RIV identification code

RIV/00216224:14110/11:00055032

Organization unit

Faculty of Medicine

DOI

http://dx.doi.org/10.1038/nbt.2051

UT WoS

000298038700025

Keywords in English

COMPARATIVE GENOMIC HYBRIDIZATION; COPY NUMBER VARIATION; HUMAN ES CELLS; DNA-SEQUENCE; IN-VIVO; CULTURE; LINES; TUMORS; PLURIPOTENCY; GENES

Abstract

V originále

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.

Citovat

AMPS, Katherine, 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, Maria 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 DVOŘÁK, 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, Aleš 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, Claudia SPITS, Thomas C. SCHULZ, Karen SERMON, Jameelah Sheik MOHAMED, Hui SHEN, Eric SHERRER, Kuldip SIDHU, Shirani SIVARAJAH, Heli SKOTTMAN, G. STACEY, R. STREHL, N. STRELCHENKO, H. SUEMORI, B. SUN, R. SUURONEN, K. TAKAHASHI, T. TUURI, P. VENU, Y. VERLINSKY, D. WARD-VAN OOSTWAARD, D. WEISENBERGER, Y. WU, S. YAMANAKA, L. YOUNG and Q. ZHOU. Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. Nature Biotechnology. 2011, vol. 29, No 12, p. 1132-1144. ISSN 1087-0156. Available from: https://dx.doi.org/10.1038/nbt.2051.

@article{967076,
   author = {Amps, Katherine and Andrews, Peter W. and Anyfantis, George and Armstrong, Lyle and Avery, Stuart and Baharvand, Hossein and Baker, Julie and Baker, Duncan and Munoz, Maria B. and Beil, Stephen and Benvenisty, Nissim and BenandYosef, Dalit and Biancotti, JuanandCarlos and Bosman, Alexis and Brena, Romulo Martin and Brison, Daniel and Caisander, Gunilla and Camarasa, Maria V. and Chen, Jieming and Chiao, Eric and Choi, Young Min and Choo, Andre B. H. and Collins, Daniel and Colman, Alan and Crook, Jeremy M. and Daley, George Q. and Dalton, Anne and De Sousa, Paul A. and Denning, Chris and Downie, Janet and Dvořák, Petr and Montgomery, Karen D. and Feki, Anis and Ford, Angela and Fox, Victoria and Fraga, Ana M. and Frumkin, Tzvia and Ge, Lin and Gokhale, Paul J. and GolanandLev, Tamar and Gourabi, Hamid and Gropp, Michal and Lu, Guangxiu and Hampl, Aleš and Harron, Katie and Healy, Lyn and Herath, Wishva and Holm, Frida and Hovatta, Outi and Hyllner, Johan and Inamdar, Maneesha S. and Irwanto, Astrid Kresentia and Ishii, Tetsuya and Jaconi, Marisa and Jin, Ying and Kimber, Susan and Kiselev, Sergey and Knowles, Barbara B. and Kopper, Oded and Kukharenko, Valeri and Kuliev, Anver and Lagarkova, Maria A. and Laird, Peter W. and Lako, Majlinda and Laslett, Andrew L. and Lavon, Neta and Lee, Dong Ryul and Lee, Jeoung Eun and Li, Chunliang and Lim, Linda S. and Ludwig, Tenneille E. and Ma, Yu and Maltby, Edna and Mateizel, Ileana and Mayshar, Yoav and Mileikovsky, Maria and Minger, Stephen L. and Miyazaki, Takamichi and Moon, Shin Yong and Moore, Harry and Mummery, Christine and Nagy, Andras and Nakatsuji, Norio and Narwani, Kavita and Oh, Steve K. W. and Oh, Sun Kyung and Olson, Cia and Otonkoski, Timo and Pan, Fei and Park, InandHyun and Pells, Steve and Pera, Martin F. and Pereira, Lygia V. and Qi, Ouyang and Raj, Grace Selva and Reubinoff, Benjamin and Robins, Alan and Robson, Paul and Rossant, Janet and Salekdeh, Ghasem H. and Spits, Claudia and Schulz, Thomas C. and Sermon, Karen and Mohamed, Jameelah Sheik and Shen, Hui and Sherrer, Eric and Sidhu, Kuldip and Sivarajah, Shirani and Skottman, Heli and Stacey, G. and Strehl, R. and Strelchenko, N. and Suemori, H. and Sun, B. and Suuronen, R. and Takahashi, K. and Tuuri, T. and Venu, P. and Verlinsky, Y. and Wardandvan Oostwaard, D. and Weisenberger, D. and Wu, Y. and Yamanaka, S. and Young, L. and Zhou, Q.},
   article_number = {12},
   doi = {http://dx.doi.org/10.1038/nbt.2051},
   keywords = {COMPARATIVE GENOMIC HYBRIDIZATION; COPY NUMBER VARIATION; HUMAN ES CELLS; DNA-SEQUENCE; IN-VIVO; CULTURE; LINES; TUMORS; PLURIPOTENCY; GENES},
   language = {eng},
   issn = {1087-0156},
   journal = {Nature Biotechnology},
   title = {Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage},
   volume = {29},
   year = {2011}
}

TY  - JOUR
ID  - 967076
AU  - 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.
PY  - 2011
TI  - Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage
JF  - Nature Biotechnology
VL  - 29
IS  - 12
SP  - 1132-1144
EP  - 1132-1144
SN  - 10870156
KW  - COMPARATIVE GENOMIC HYBRIDIZATION
KW  - COPY NUMBER VARIATION
KW  - HUMAN ES CELLS
KW  - DNA-SEQUENCE
KW  - IN-VIVO
KW  - CULTURE
KW  - LINES
KW  - TUMORS
KW  - PLURIPOTENCY
KW  - GENES
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.
ER  -

AMPS, Katherine, 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, Maria 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 DVOŘÁK, 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, Aleš 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, Claudia SPITS, Thomas C. SCHULZ, Karen SERMON, Jameelah Sheik MOHAMED, Hui SHEN, Eric SHERRER, Kuldip SIDHU, Shirani SIVARAJAH, Heli SKOTTMAN, G. STACEY, R. STREHL, N. STRELCHENKO, H. SUEMORI, B. SUN, R. SUURONEN, K. TAKAHASHI, T. TUURI, P. VENU, Y. VERLINSKY, D. WARD-VAN OOSTWAARD, D. WEISENBERGER, Y. WU, S. YAMANAKA, L. YOUNG and Q. ZHOU. Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. \textit{Nature Biotechnology}. 2011, vol.~29, No~12, p.~1132-1144. ISSN~1087-0156. Available from: https://dx.doi.org/10.1038/nbt.2051.

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