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Mol. Hum. Reprod. Advance Access originally published online on August 11, 2009
Molecular Human Reproduction 2009 15(11):739-747; doi:10.1093/molehr/gap066
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© The Author 2009. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Evaluation of genome coverage and fidelity of multiple displacement amplification from single cells by SNP array

Jiawei Ling1,2, Guanglun Zhuang2, Barbara Tazon-Vega1, Chenhui Zhang1, Baoqiang Cao3, Zev Rosenwaks1 and Kangpu Xu1,4

1Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine and Infertility, Weill Cornell Medical College of Cornell University, 1305 York Avenue, New York, NY 10021, USA 2Center for Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou 510080, People's Republic of China 3The Institute for Computational Engineering and Sciences, the University of Texas at Austin, Austin TX 78712, USA

4 Correspondence address. Laboratory of Preimplantation Genetics, Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine and Infertility, Weill Cornell Medical College of Cornell University, Box 30, 1300 York Avenue, New York, NY 10065, USA. E-mail: kpxu{at}med.cornell.edu

The scarce amount of DNA contained in a singe cell is a limiting factor for clinical application of preimplantation genetic diagnosis mainly due to the risk of misdiagnosis caused by allele dropout and the difficulty in obtaining copy number variations in all 23 pairs of chromosomes. Multiple displacement amplification (MDA) has been reported to generate large quantity of products from small amount of templates. Here, we evaluated the fidelity of whole-genome amplification MDA from single or a few cells and determined the accuracy of chromosome copy number assessment on these MDA products using an Affymetrix 10K 2.0 SNP Mapping Array. An average coverage rate (86.2%) from single cells was obtained and the rates increased significantly when five or more cells were used as templates. Higher concordance for chromosome copy number from single cells could be achieved when the MDA amplified product was used as reference (93.1%) than when gDNA used as reference (82.8%). The present study indicates that satisfactory genome coverage can be obtained from single-cell MDA which may be used for studies where only a minute amount of genetic materials is available. Clinically, MDA coupled with SNP mapping array may provide a reliable and accurate method for chromosome copy number analysis and most likely for the detection of single-gene disorders as well.

Key words: chromosomal abnormality/genome coverage/multiple displacement amplification/PGD/SNP array

Submitted on April 3, 2009; resubmitted on July 30, 2009; accepted on August 5, 2009.


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