Virus Detection from Exome Sequencing in Oral Leukoplakia.
For detecting the presence of viral sequences in exome sequencing data, we have used VirusFinder 2 (Wang et al. 2015) with default parameters and other required tools, NCBI BLAST (ncbi-blast-2.2.29+), BOWTIE 2 (Version 2.2.2), BWA (version 0.7.11), TRINITY (version r20140717) and SVDetect (version r0.8b). For virus database, virus.fa file containing viruses of all known classes (32,102 classes), which is integrated with the RINS package, was used (Bhaduri et al. 2012). Search for viruses was performed in data of tissue and blood samples separately. Viral association with OL was identified when a virus was found in data generated from a patient’s tissue sample, but not in the blood sample. To validate our findings, we mapped the unmapped reads (each of 100 bp length) obtained after the initial alignment from the exome sequencing data against the virus.fa database (as used in VirusFinder 2) using BLASTN. As a safeguard against false positive inferences, we considered a stringent similarity level (<1 x e-10) of reads with virus sequences.