Method To Identify Viral Integration Site In Human Genome From Ngs Data?

Question

[Obi Griffith]

Hi all,

Conceptually I can imagine how to do this. But, does anyone have a recommendation for a well established pipeline or tool for identifying a viral integration site in the human genome. Suppose I have 50X WGS data for a tumor sample and 30X WGS data for a normal sample and am looking for a specific virus (e.g. HBV) which is known to integrate into the genome for my cancer of interest. I want to be able to answer two simple questions: (1) Is there evidence of viral integration? (2) What is the exact breakpoint/integration site?

Any suggestions will be greatly appreciated.

[PoGibas]

This nice blog post by cureffi might be useful
http://www.cureffi.org/2013/01/25/aligning-unmapped-reads-to-viral-genomes/

[lh3]

Related: Can Tophat Be Used To Find The Virus-Host Junctions ?

[Bioinfosm]

<bump>

Any update on this in 2017 .. what has been the experience and any new ones worth trying? Especially for viral integration detection from DNA capture based NGS data.

thanks!

Answer 1

[lh3]

My suggestion is to put human and the virus in one file, build index and then align reads with bwa-sw, bwa-mem, or bowtie2 --local -k2. You can trivially get your answer.

Answer 2

[Rm]

VirusSeq: Software to identify viruses and their integration sites using nextgeneration sequencing of human cancer tissue

http://odin.mdacc.tmc.edu/~xsu1/VirusSeq.html

The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients

Answer 3

[jluebeck]

ViFi performs the analysis you're asking about and outperforms other existing methods (e.g. VERSE) in speed and sensitivity, particularly if coverage is low or the viral strain is evolved from the reference by any considerable amount.

https://www.ncbi.nlm.nih.gov/pubmed/29579309