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EMBRYONIC STEM CELLS

Copy Number Variant Analysis of Human Embryonic Stem Cells

Departments of ^aPsychiatry and Biobehavioral Sciences,
^bMolecular and Medical Pharmacology,
^ePathology and Laboratory Medicine,
^fMolecular Immunology and Medical Genetics,
^jMolecular, Cell and Developmental Biology, and
^kHuman Genetics, David Geffen School of Medicine,
^gMolecular Biology Institute,
^hJonsson Comprehensive Cancer Center, and
ⁱBroad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California, USA;
^cAgilent Laboratories, Santa Clara, California, USA;
^dNew York University/Courant Bioinformatics Group, Courant Institute of Mathematical Sciences, New York University, New York, New York, USA

Key Words. Embryonic stem cells • Oligonucleotide array sequence analysis • Genome stability • Multipoint statistics • Algorithmic biology

Correspondence: Correspondence: Michael A. Teitell, M.D., Ph.D., Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, 675 Charles Young Drive South, 4-762 MRL, Los Angeles, California 90095-1732, USA. Telephone: 310-206-6754; Fax: 310-267-0382; e-mail: mteitell{at}ucla.edu

Received on November 26, 2007; accepted for publication on March 18, 2008.

First published online in STEM CELLS EXPRESS  March 27, 2008.


Differences between individual DNA sequences provide the basis for human genetic variability. Forms of genetic variation include single-nucleotide polymorphisms, insertions/duplications, deletions, and inversions/translocations. The genome of human embryonic stem cells (hESCs) has been characterized mainly by karyotyping and comparative genomic hybridization (CGH), techniques whose relatively low resolution at 2–10 megabases (Mb) cannot accurately determine most copy number variability, which is estimated to involve 10%–20% of the genome. In this brief technical study, we examined HSF1 and HSF6 hESCs using array-comparative genomic hybridization (aCGH) to determine copy number variants (CNVs) as a higher-resolution method for characterizing hESCs. Our approach used five samples for each hESC line and showed four consistent CNVs for HSF1 and five consistent CNVs for HSF6. These consistent CNVs included amplifications and deletions that ranged in size from 20 kilobases to 1.48 megabases, involved seven different chromosomes, were both shared and unique between hESCs, and were maintained during neuronal stem/progenitor cell differentiation or drug selection. Thirty HSF1 and 40 HSF6 less consistently scored but still highly significant candidate CNVs were also identified. Overall, aCGH provides a promising approach for uniquely identifying hESCs and their derivatives and highlights a potential genomic source for distinct differentiation and functional potentials that lower-resolution karyotype and CGH techniques could miss.

Disclosure of potential conflicts of interest is found at the end of this article.

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