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Published online 18 May 2004

Nucleic Acids Research, 2004, Vol. 32, No. 9 e71
© 2004 Oxford University Press

Genome coverage and sequence fidelity of {phi}29 polymerase-based multiple strand displacement whole genome amplification

J. Guillermo Paez1, Ming Lin2, Rameen Beroukhim1,3, Jeffrey C. Lee1, Xiaojun Zhao1, Daniel J. Richter9, Stacey Gabriel9, Paula Herman1, Hidefumi Sasaki10, David Altshuler4,5,6,9, Cheng Li2,8, Matthew Meyerson1,7 and William R. Sellers*,1,3,6

1 Department of Medical Oncology and 2 Department of Biostatistical Sciences, Dana-Farber Cancer Institute, 3 Department of Medicine, Brigham and Women’s Hospital, 4 Department of Molecular Biology and Diabetes Unit, Massachusetts General Hospital, 5 Department of Genetics, 6 Department of Medicine and 7 Department of Pathology, Harvard Medical School and 8 Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA, 9 Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA and 10 Nagoya City University Medical School, Nagoya, Japan

*To whom correspondence should be addressed at: Dana-Farber Cancer Institute, D720C, 44 Binney Street, Boston, MA 02115, USA. Tel: +1 617 632 4750; Fax: +1 617 632 5417; Email: william_sellers{at}dfci.harvard.edu

Received January 21, 2004; Revised March 29, 2004; Accepted April 21, 2004

Major efforts are underway to systematically define the somatic and germline genetic variations causally associated with disease. Genome-wide genetic analysis of actual clinical samples is, however, limited by the paucity of genomic DNA available. Here we have tested the fidelity and genome representation of {phi}29 polymerase-based genome amplification ({phi}29MDA) using direct sequencing and high density oligonucleotide arrays probing >10 000 SNP alleles. Genome representation was comprehensive and estimated to be 99.82% complete, although six regions encompassing a maximum of 5.62 Mb failed to amplify. There was no degradation in the accuracy of SNP genotyping and, in direct sequencing experiments sampling 500 000 bp, the estimated error rate (9.5 x 10–6) was the same as in paired unamplified samples. The detection of cancer-associated loss of heterozygosity and copy number changes, including homozygous deletion and gene amplification, were similarly robust. These results suggest that {phi}29MDA yields high fidelity, near-complete genome representation suitable for high resolution genetic analysis.


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