By biallelic mutation (inactivation), I mean several cases:
1) The first mutation is inherited (germline) mutation and the second mutation occurs as somatic at other loci, but within the same gene. Each one of these mutations inactivates one copy of the same gene.
2) The first mutation is inherited (germline) mutation and the second mutation occurs as somatic at the same loci of another allele. Both mutations are inactivating mutations.
For 1), I guess if both observed mutations are truncating or at least predicted as detrimental, we can assume biallelic inactivation of the gene (two inactivating mutations at the same allele would be redundant). But is there any method for more confident detection?
For 2), this would be difficult to detect since both tumor sample and matched normal tissue contain variant allele with different VAF depending on the tumor purity. Can anyone share some insight on how to detect this?
This paper does it analyzing whole exome sequencing.