In-Depth Investigation of Archival and Prospectively Collected Samples Reveals No Evidence for XMRV Infection in Prostate Cancer
SNP analysis of deep sequencing reads corresponding to the XMRV genomes of 22Rv1 (A) and LNCaP (B), as well as the mitochondrial genomes of these two cell lines (C) was performed. (A and B) SNP variants within the XMRV genome for 22Rv1 and LNCaP (x-axis) are shown in order of decreasing frequency (y-axis). Shared SNPs in XMRV genomes corresponding to 3 XMRV-positive prostate cancer samples (VP35, VP42, VP62) and LNCaP (z-axis) at a frequency cutoff of 0.5% are plotted on the graph, with key SNPs highlighted in red. SNPs with variant frequencies <0.5% are plotted as zero; missing values (blank squares) refer to SNP positions for which the coverage is <10X. (C) SNP variants within the mitochondrial genome for 22Rv1 and LNCaP are shown (x-axis), with the frequency of each 22Rv-1−/LNCaP-associated SNP in the general human population, as determined by a population-level human mitochondrial database , given in parentheses. For each prostate cancer-associated mitochondrial genome (z-axis), the minority SNP frequency (y-axis) is plotted against the cell line-associated SNP variant (x-axis), using a frequency cutoff of 3%. For each minority SNP identified, the variant frequency and coverage at the corresponding nucleotide position is shown. Minority SNPs with variant frequencies <3% are plotted as zero; missing values (blank squares) refer to SNP positions for which the coverage is <30X. Note that the VP62 sample shares a 146C mitochondrial SNP with LNCaP (asterisks).