Zombies in TCGA

Abstract

Next-generation sequencing results obtained to detect somatic mutations in human cancers can also be searched for viruses that contribute to cancer. Recently, human papillomavirus 18 RNA was detected in tumor types not typically associated with HPV infection. Analyses reported in this issue of Journal of Virology demonstrate that the apparent presence of HPV18 RNA in these atypical tumors is due in at least some cases to contamination of samples with HeLa cells, which harbor HPV18.

Epstein-Barr Virus-Positive Cancers Show Altered B-Cell Clonality

“…That determination requires fulfilling Koch’s postulates or their modern, genomic-based equivalents ( 2 ). Examples of overinterpreted reports abound, many due to laboratory contaminations ( 3 ), as in the case of simian virus 40 (SV40) ( 4 ), xenotropic murine leukemia virus-related virus ( 5 ), or the finding of HeLa cell-resident human papillomavirus type 18 in non-cervical cancer Cancer Genome Atlas Project (TCGA) mRNA sequencing (mRNA-seq) data ( 6 , 7 ). This led to very stringent criteria, such as requiring at minimum 1,000 bp of combined genome coverage or >1,000 individual reads/sample.…”