|Publication Type||Journal Article|
|Year of Publication||2004|
|Authors||Paez, GJ, Lin, M, Beroukhim, R, Lee, JC, Zhao, X, Richter, DJ, Gabriel, S, Herman, P, Sasaki, H, Altshuler, D, Li, C, Meyerson, M, Sellers, WR|
|Journal||Nucleic Acids Research|
|Pages||e71 - e71|
|Keywords||Alleles, Bacillus Phages, Cancer, Cell Line, Chromosome Deletion, DNA-Directed DNA Polymerase, Gene Dosage, Genome, Genomics, Genotype, Homozygote, Human, Humans, Loss of Heterozygosity, Oligonucleotide Array Sequence Analysis, Polymerase Chain, Tumor|
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.