Why there is a 50% variant allele frequency in TCGA NSCLC data?
1
1
Entering edit mode
2.6 years ago
sm.hashemin ▴ 90

Hi, I was taking a lot at the variant allele frequencies in TCGA NSCLC data (from the the MAF somatic SNV file). I have seen thet the highest VAF is 50% and it apears that they have a cutoff there. Does it mean that a SNV of 60% vaf can not be a homozygous mutations in 60% of cells (while tumor purity of 60%) or a subclonal snv at higher purities?

As well there is a lot of variants with 0% VAFs! which is also strange.

What I want to learn from this story is: what should I consider when facing a oncoplot? can a variant on oncoplot have only 3% vaf? specially in paired primary vs recurrent tumors, can it be that a variant is simply missing in one because it has a less than cutoff level vaf ?

Best

TCGA VAF Variant alle frequency somatic snv • 1.5k views
ADD COMMENT
1
Entering edit mode
2.2 years ago
sm.hashemin ▴ 90

Answering myself: because mutations are considered to happen in heterozygous state, therefore at 100% purity you will have a 50% VAF. VAF of more than 50% belongs to the LOHs.

ADD COMMENT

Login before adding your answer.

Traffic: 1708 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6