Nucleic Acids Research Advance Access originally published online on June 18, 2009
Nucleic Acids Research 2009 37(15):e105; doi:10.1093/nar/gkp526
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Nucleic Acids Research, 2009, Vol. 37, No. 15 e105
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Methods Online |
Identification of small gains and losses in single cells after whole genome amplification on tiling oligo arrays
1Institute of Human Genetics, Medical University of Graz, Harrachgasse 21/8, A-8010 Graz, 2Das Kinderwunsch-Institut Schenk GmbH, Am Sendergrund 11, A-8143 Dobl, 3Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14/V, 8010 Graz, Austria, 4Department of Genetics, Institute for Cancer Research, 5Department of Pathology, Norwegian Radium Hospital, Oslo University Hospital, 0310 Oslo and 6Biomedical Research Group, Department of Informatics, University of Oslo, P.O. Box 1080, Blindern, 0316 Oslo, Norway
*To whom correspondence should be addressed. Tel: +43 316 380 4110; Fax: +43 316 380 9605; Email: michael.speicher{at}medunigraz.at
Received February 13, 2009. Revised June 2, 2009. Accepted June 2, 2009.
Clinical DNA is often available in limited quantities requiring whole-genome amplification for subsequent genome-wide assessment of copy-number variation (CNV) by array-CGH. In pre-implantation diagnosis and analysis of micrometastases, even merely single cells are available for analysis. However, procedures allowing high-resolution analyses of CNVs from single cells well below resolution limits of conventional cytogenetics are lacking. Here, we applied amplification products of single cells and of cell pools (5 or 10 cells) from patients with developmental delay, cancer cell lines and polar bodies to various oligo tiling array platforms with a median probe spacing as high as 65 bp. Our high-resolution analyses reveal that the low amounts of template DNA do not result in a completely unbiased whole genome amplification but that stochastic amplification artifacts, which become more obvious on array platforms with tiling path resolution, cause significant noise. We implemented a new evaluation algorithm specifically for the identification of small gains and losses in such very noisy ratio profiles. Our data suggest that when assessed with sufficiently sensitive methods high-resolution oligo-arrays allow a reliable identification of CNVs as small as 500 kb in cell pools (5 or 10 cells), and of 2.6–3.0 Mb in single cells.