HeLa nucleic acid contamination in the cancer genome atlas leads to the misidentification of human papillomavirus 18.

ABSTRACT:

Unlabelled

We searched The Cancer Genome Atlas (TCGA) database for viruses by comparing non-human reads present in transcriptome sequencing (RNA-Seq) and whole-exome sequencing (WXS) data to viral sequence databases. Human papillomavirus 18 (HPV18) is an etiologic agent of cervical cancer, and as expected, we found robust expression of HPV18 genes in cervical cancer samples. In agreement with previous studies, we also found HPV18 transcripts in non-cervical cancer samples, including those from the colon, rectum, and normal kidney. However, in each of these cases, HPV18 gene expression was low, and single-nucleotide variants and positions of genomic alignments matched the integrated portion of HPV18 present in HeLa cells. Chimeric reads that match a known virus-cell junction of HPV1

SUBMITTER: Cantalupo PG 

PROVIDER: S-EPMC4442357 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature