Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Sort of a noob here: looking for somatic mutation in tumors (NGS sequencing) lethalfang Bioinformatics 8 10-07-2013 12:08 AM
NGS software for somatic de novo mutation carolW Bioinformatics 1 05-27-2013 01:42 AM
Identifying Somatic mutation candidates question Phantom123 Bioinformatics 0 03-26-2012 07:47 AM
Paired-sample (tumor/normal) somatic mutation detection software alexischr Bioinformatics 1 04-14-2011 05:56 AM

Thread Tools
Old 09-02-2013, 07:49 PM   #1
Junior Member
Location: Taiwan

Join Date: Jun 2013
Posts: 3
Default Somatic mutation analysis

Dear all

I have a project to analysis somatic mutation from clinical sample, maybe serum.

I will choose some gene and design PCR primer to amplify target exon region.

These amplicon will sequenced over 500X by using Illuminar Miseq 150PE.

My question is, how to analysis or define "somatic mutation".

Because the sequence depth is really high, I think the sequence data will has some sequence error to interfere somatic mutation calling, how can I filter out this possible bias? Reads trimming using QV 30 instead of QV20?

Thanks for any help,

WaitingNail is offline   Reply With Quote
Old 09-02-2013, 08:40 PM   #2
Senior Member
Location: Hong Kong

Join Date: Mar 2010
Posts: 498

I think the standard approach is that you also sequence germline DNA. Then you can use it to filter out the germline mutations from the mutations you find. The remaining ones should be somatic mutations
ymc is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 03:07 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO