Question: Somatic variant using Ionreporter
0
gravatar for saurabhyadav15
20 months ago by
United States
saurabhyadav150 wrote:

I am doing tumour-normal Ampliseq comprehensive cancer panel analysis on Ionreporter. I am looking for deleterious somatic mutations. For this purpose, I have designed following filter in Ionreporter-

 

(Variant Type in INDEL, LONGDEL, SNV, MNV

 

Variant Effect in stoploss, nonsense, missense, frameshiftInsertion, frameshiftDeletion, frameshiftBlockSubstitution

 

0.0 <= PValue <= 0.05

 

10 <= Allele Read-Count <= 100000

 

0.0 <= SIFT <= 0.05 OR 0.95 <= PolyPhen <= 1.0)

 

Using this filter, I am getting 10 mutations in one tumor-normal pair, in other 3 pairs I am getting fewer mutations (2-3 only in each pair) because of lesser coverage and coverage uniformity in pairs. Mutant allele frequency (allele ratio) ranges from 0.03 to 0.44

Please suggest me how I can find mutations with confidence? And how may I have an idea about sample purity?

Thanks in advance

ADD COMMENTlink written 20 months ago by saurabhyadav150

Do you also have copy number data ?

ADD REPLYlink written 20 months ago by poisonAlien2.2k

Yes, I have. But I think copy number data by Ion Torrent platforms is not trustworthy. So I am focusing on SNVs only.

ADD REPLYlink written 19 months ago by saurabhyadav150
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 496 users visited in the last hour