Somatic mutation analysis

WaitingNail · 09-02-2013, 07:49 PM

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,

WT

ymc · 09-02-2013, 08:40 PM

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

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09-02-2013, 07:49 PM	#1
WaitingNail Junior Member Location: Taiwan Join Date: Jun 2013 Posts: 3	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, WT

09-02-2013, 08:40 PM	#2
ymc 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