Question: Somatic variant using Ionreporter
gravatar for saurabhyadav15
2.7 years 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

ion proton ionreporter somatic • 1.0k views
ADD COMMENTlink written 2.7 years ago by saurabhyadav150

Do you also have copy number data ?

ADD REPLYlink written 2.7 years ago by poisonAlien2.5k

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 2.7 years ago by saurabhyadav150
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