Nonhuman sequence search identification (“blast hits”) from pretreatment bone marrow. (A) Results of deep-sequencing RNA pools (73 ALLs in 4 pools and 28 AMLs in 2 pools) after ribosomal RNA depletion (RiboZERO). Raw Illumina reads were aggressively quality filtered, then aligned to hg19 using BowTie2; nonaligning reads were categorized using an E value less than or equal to 1 × E⁻¹⁰ with blastn and the nt database. Cytomegalovirus hits were normalized by sequencing effort per pool (blast hits/quality reads × 1.0 × E⁸ ). Odds ratios were calculated by comparing presence/absence of virus in ALL versus AML pools; P values were computed by using Fisher’s exact test (for additional details, see the supplemental Methods section). (B) Results of particle isolation and 454 sequencing from an independent study of 36 ALL and 10 AML patients. Virus was isolated using centrifugation and Millipore filter, and then viral nucleic acids were extracted and sequenced using Roche 454 (for additional details, see the supplemental Methods section). Recovered sequences were assembled into contigs in which alignments to hg19 were removed using Bowtie2. Contigs were then categorized with a cutoff of E value less than or equal to 1.0 × E⁻¹⁰ using blastn and the refseq viral database. Cytomegalovirus contigs were normalized by recovered contigs per patient (blast hits/contigs assembled × 1 × E³ ); odds ratios were calculated comparing presence/absence of virus in ALL versus AML patients; P values were computed using Fisher’s exact test (for additional details, see the supplemental Methods section). CMV was found to be the only virus that showed statistically significant variation between ALL and AML in the Illumina and 454 groups. CI, confidence interval; NA, not applicable; OR, odds ratio.