High-resolution DNA analysis of human embryonic stem cell lines
reveals culture-induced copy number changes and loss of
heterozygosity

J 2010

High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity

NARVA, Elisa; Reija AUTIO; Nelly RAHKONEN; Lingjia KONG; Neil HARRISON et al.

Základní údaje

Originální název

High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity

Autoři

Vydání

Nature Biotechnology, 2010, 1087-0156

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

Genetika a molekulární biologie

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 31.090

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14110/10:00043710

Organizační jednotka

Lékařská fakulta

UT WoS

000276462400026

Klíčová slova anglicky

COMPARATIVE GENOMIC HYBRIDIZATION; ES CELLS; INSTABILITY; EXPRESSION; CANCER; CHROMOSOME-16; CARCINOMA; GENES

Změněno: 18. 1. 2011 14:52, prof. Ing. Petr Dvořák, CSc.

Anotace

V originále

Prolonged culture of human embryonic stem cells (hESCs) can lead to adaptation and the acquisition of chromosomal abnormalities, underscoring the need for rigorous genetic analysis of these cells. Here we report the highest-resolution study of hESCs to date using an Affymetrix SNP 6.0 array containing 906,600 probes for single nucleotide polymorphisms (SNPs) and 946,000 probes for copy number variations (CNVs). Analysis of 17 different hESC lines maintained in different laboratories identified 843 CNVs of 50 kb-3 Mb in size. We identified, on average, 24% of the loss of heterozygosity (LOH) sites and 66% of the CNVs changed in culture between early and late passages of the same lines. Thirty percent of the genes detected within CNV sites had altered expression compared to samples with normal copy number states, of which >44% were functionally linked to cancer. Furthermore, LOH of the q arm of chromosome 16, which has not been observed previously in hESCs, was detected.

Návaznosti

LC06077, projekt VaV

Název: Centrum chemické genetiky

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Centrum chemické genetiky

MSM0021622430, záměr

Název: Funkční a molekulární charakteristiky nádorových a normálních kmenových buněk - identifikace cílů pro nová terapeutika a terapeutické strategie

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Funkční a molekulární charakteristiky nádorových a normálních kmenových buněk - identifikace cílů pro nová terapeutika a terapeutické strategie

Citovat

NARVA, Elisa; Reija AUTIO; Nelly RAHKONEN; Lingjia KONG; Neil HARRISON; Danny KITSBERG; Lodovica BORGHESE; Joseph ITSKOVITZ-ELDOR; Omid RASOOL; Petr DVOŘÁK; Outi HOVATTA; Timo OTONSKI; Timo TUURI; Wei CUI; Oliver BRUSTLE; Duncan BAKER; Edna MALTBY; Harry D. MOORE; Nissim BEVENISTY; Peter W. ANDREWS; Olli YLI-HARJA a Riita LAHESMAA. High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity. Nature Biotechnology. 2010, roč. 28, č. 4, 7 s. ISSN 1087-0156.

@article{879463,
   author = {Narva, Elisa and Autio, Reija and Rahkonen, Nelly and Kong, Lingjia and Harrison, Neil and Kitsberg, Danny and Borghese, Lodovica and ItskovitzandEldor, Joseph and Rasool, Omid and Dvořák, Petr and Hovatta, Outi and Otonski, Timo and Tuuri, Timo and Cui, Wei and Brustle, Oliver and Baker, Duncan and Maltby, Edna and Moore, Harry D. and Bevenisty, Nissim and Andrews, Peter W. and YliandHarja, Olli and Lahesmaa, Riita},
   article_number = {4},
   keywords = {COMPARATIVE GENOMIC HYBRIDIZATION; ES CELLS; INSTABILITY; EXPRESSION; CANCER; CHROMOSOME-16; CARCINOMA; GENES},
   language = {eng},
   issn = {1087-0156},
   journal = {Nature Biotechnology},
   title = {High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity},
   volume = {28},
   year = {2010}
}

TY  - JOUR
ID  - 879463
AU  - Narva, Elisa - Autio, Reija - Rahkonen, Nelly - Kong, Lingjia - Harrison, Neil - Kitsberg, Danny - Borghese, Lodovica - Itskovitz-Eldor, Joseph - Rasool, Omid - Dvořák, Petr - Hovatta, Outi - Otonski, Timo - Tuuri, Timo - Cui, Wei - Brustle, Oliver - Baker, Duncan - Maltby, Edna - Moore, Harry D. - Bevenisty, Nissim - Andrews, Peter W. - Yli-Harja, Olli - Lahesmaa, Riita
PY  - 2010
TI  - High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity
JF  - Nature Biotechnology
VL  - 28
IS  - 4
SN  - 10870156
KW  - COMPARATIVE GENOMIC HYBRIDIZATION
KW  - ES CELLS
KW  - INSTABILITY
KW  - EXPRESSION
KW  - CANCER
KW  - CHROMOSOME-16
KW  - CARCINOMA
KW  - GENES
N2  - Prolonged culture of human embryonic stem cells (hESCs) can lead to adaptation and the acquisition of chromosomal abnormalities, underscoring the need for rigorous genetic analysis of these cells. Here we report the highest-resolution study of hESCs to date using an Affymetrix SNP 6.0 array containing 906,600 probes for single nucleotide polymorphisms (SNPs) and 946,000 probes for copy number variations (CNVs). Analysis of 17 different hESC lines maintained in different laboratories identified 843 CNVs of 50 kb-3 Mb in size. We identified, on average, 24% of the loss of heterozygosity (LOH) sites and 66% of the CNVs changed in culture between early and late passages of the same lines. Thirty percent of the genes detected within CNV sites had altered expression compared to samples with normal copy number states, of which >44% were functionally linked to cancer. Furthermore, LOH of the q arm of chromosome 16, which has not been observed previously in hESCs, was detected.
ER  -

NARVA, Elisa; Reija AUTIO; Nelly RAHKONEN; Lingjia KONG; Neil HARRISON; Danny KITSBERG; Lodovica BORGHESE; Joseph ITSKOVITZ-ELDOR; Omid RASOOL; Petr DVOŘÁK; Outi HOVATTA; Timo OTONSKI; Timo TUURI; Wei CUI; Oliver BRUSTLE; Duncan BAKER; Edna MALTBY; Harry D. MOORE; Nissim BEVENISTY; Peter W. ANDREWS; Olli YLI-HARJA a Riita LAHESMAA. High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity. \textit{Nature Biotechnology}. 2010, roč.~28, č.~4, 7 s. ISSN~1087-0156.

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