Databases and annotation of translocations

Question

[alons]

Hi all,

I'm currently working on a structural variants calling pipeline on NGS data from cancer patients, specifically the annotation and intersection/joining with different databases.

While the vast majority of the structural variants I find, including indels of all sizes, CNVs, ITDs, duplications & inversions, are successfully joined+intersected and annotated, translocations are yet to be either annotated or successfully found in the databases even if i'm extending the search ranges in their supposed chromosomes.

Has anyone experienced the same difficulty?

I'm using VEP for annotation and the databases are Cosmic, DGV & DbVar.

I will greatly appreciate your suggestions on annotators and databases suitable for translocations, preferably related to cancer but not necessarily.

Thank you, Alon

Answer 1

[natasha.sernova]

Hello!

There are very few articles about translocations.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4062837/

This one just mentions mod-files with all rearrangements

My scientific search failed.

There are few papers about everything but not translocation in particular.

database AND annotation AND translocations AND Database[journal]

http://www.ncbi.nlm.nih.gov/pmc/?term=database+AND+annotation+AND+translocations+AND+Database[journal]

1. Baysal B, Badner J, Corona W, et al. A mannosyltransferase gene at 11q23 is disrupted by a translocation breakpoint that co-segregates with bipolar affective disorder in a small family. Neurogenetics. 2002;4:43–53. [PubMed]

But I’ve looked in Google. There is some information there.

I searched www.google.com for cancer AND translocation databases

I got the following:

https://www.google.ru/?gfe_rd=cr&ei=qAYEV534NYfAtAG-lqPwBg&gws_rd=ssl#newwindow=1&q=cancer+AND+translocation+databases

If I used just “translocation database”, I got this:

https://www.google.ru/?gfe_rd=cr&ei=qAYEV534NYfAtAG-lqPwBg&gws_rd=ssl#newwindow=1&q=translocation+database

It is almost the same.

I ran also this 'cancer AND translocation databases AND structural variants'.

I also received some information.

https://www.google.ru/?gfe_rd=cr&ei=qAYEV534NYfAtAG-lqPwBg&gws_rd=ssl#newwindow=1&q=cancer+AND+translocation+databases+AND+structural+variants

Hopefully it will help you.