Copy Number Variant Analysis of Human Embryonic Stem Cells

¹ Departments of Psychiatry and Biobehavioral Sciences and Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
² Agilent Laboratories, Santa Clara, CA, USA
³ NYU/Courant Bioinformatics Group, Courant Institute of Mathematical Sciences, NYU, New York, USA
⁴ Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
⁵ Molecular Immunology and Medical Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA; Molecular Biology Institute, Jonsson Comprehensive Cancer Center, and Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, USA
⁶ Molecular, Cell and Developmental Biology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA; Molecular Biology Institute, Jonsson Comprehensive Cancer Center, and Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, USA
⁷ Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA; Molecular Biology Institute, Jonsson Comprehensive Cancer Center, and Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, USA
⁸ Departments of Psychiatry and Biobehavioral Sciences and Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA; Molecular Biology Institute, Jonsson Comprehensive Cancer Center, and Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, USA
⁹ Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA; Molecular Biology Institute, Jonsson Comprehensive Cancer Center, and Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, USA

^* To whom correspondence should be addressed. E-mail: mteitell{at}ucla.edu.

	Abstract

Differences between individual DNA sequences provide the basis for human genetic variability. Forms of genetic variation include single nucleotide polymorphisms (SNPs), insertions/duplications, deletions, and inversions/translocations. The genome of human embryonic stem cells (hESCs) has been mainly characterized by karyotyping and comparative genomic hybridization (CGH), techniques whose relatively low resolution at 2 – 10-Mb cannot accurately determine most copy number variability, which is estimated to involve 10 – 20% of the genome. In this brief technical report we examined HSF1 and HSF6 hESCs using array-CGH (aCGH) to determine copy number variants (CNVs) as a higher resolution method for characterizing hESCs. Our approach utilized 5 samples for each hESC line and showed 4 consistent CNVs for HSF1 and 5 consistent CNVs for HSF6. These consistent CNVs included amplifications and deletions that ranged in size from 20-Kb to 1.48-Mb involving 7 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.