High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity.
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.
Närvä
Elisa
E
Turku Centre for Biotechnology, University of Turku and Abo Akademi University, Turku, Finland. elisa.narva@btk.fi
Autio
Reija
R
Rahkonen
Nelly
N
Kong
Lingjia
L
Harrison
Neil
N
Kitsberg
Danny
D
Borghese
Lodovica
L
Itskovitz-Eldor
Joseph
J
Rasool
Omid
O
Dvorak
Petr
P
Hovatta
Outi
O
Otonkoski
Timo
T
Tuuri
Timo
T
Cui
Wei
W
Brüstle
Oliver
O
Baker
Duncan
D
Maltby
Edna
E
Moore
Harry D
HD
Benvenisty
Nissim
N
Andrews
Peter W
PW
Yli-Harja
Olli
O
Lahesmaa
Riitta
R
D001483:Base Sequence; D018929:Cell Culture Techniques / Q000379:methods; D004247:DNA / Q000235:genetics*; D056915:DNA Copy Number Variations / Q000235:genetics*; D004252:DNA Mutational Analysis / Q000379:methods*; D053595:Embryonic Stem Cells / Q000145:classification* / Q000502:physiology*; D014644:Genetic Variation / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods*
D004247:DNA