Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification |
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Authors: | Paez J Guillermo Lin Ming Beroukhim Rameen Lee Jeffrey C Zhao Xiaojun Richter Daniel J Gabriel Stacey Herman Paula Sasaki Hidefumi Altshuler David Li Cheng Meyerson Matthew Sellers William R |
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Institution: | Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA. |
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Abstract: | 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 phi29 polymerase-based genome amplification (phi29MDA) 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 phi29MDA yields high fidelity, near-complete genome representation suitable for high resolution genetic analysis. |
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