Related Experiment Video
Updated: Sep 3, 2025
10:26
RNAscope for In situ Detection of Transcriptionally Active Human Papillomavirus in Head and Neck Squamous Cell Carcinoma
Published on: March 11, 2014
27.5K
Using HPV-meta for human papillomavirus RNA quality detection.
Agustin Ure1, Dhananjay Mukhedkar1,2, Laila Sara Arroyo Mühr3
1Department of Laboratory Medicine, Karolinska Institutet, 141 86, Stockholm, Sweden.
Scientific Reports
|July 29, 2022
Summary
A new open-source pipeline, HPV-meta, accurately detects human papillomavirus (HPV) transcripts in RNA sequencing data. This tool aids in understanding HPV
Area of Science:
- Oncology
- Virology
- Bioinformatics
Background:
- Accurate detection of human papillomavirus (HPV) is crucial for cervical cancer elimination efforts.
- Understanding HPV's role in human cancers requires validated detection methods.
Purpose of the Study:
- To introduce "HPV-meta", an open-source pipeline for detecting HPV transcripts in RNA sequencing data.
- To provide a tool that includes measures to identify potential viral contamination.
Main Methods:
- The HPV-meta pipeline performs quality trimming and human genome filtering.
- It utilizes blastx for HPV detection with specific cut-offs (10 reads, 690 bp coverage).
- The pipeline generates fasta files for HPV-positive samples for further analysis.
Main Results:
- Analysis of 10,908 TCGA RNA sequencing files identified 25 HPV types in 488 specimens.
- The pipeline achieved 99.98% agreement in validation.
- Generated fasta files facilitated the detection of high sequence identity, indicating potential contamination in some samples.
Conclusions:
- HPV-meta is a robust and validated pipeline for detecting HPV in RNA sequencing data.
- The generated fasta files are valuable for investigating contamination in next-generation sequencing data.
