20 months ago by
The mutations are supported by the same reads. It's a bit suspicious to me because this could indicate that the reads are from another part of the genome.
It could also indicate that there are three adjacent mutations, or another sort of mutation. Without additional context, is it difficult to determine whether the reads are true variants. In addition to the properties you have identified, you should consider:
prior somatic mutation: are any of the SNVs in COSMIC?
strand bias: looks fine as there are reads supporting the variant originating from both strands
allele frequency: the variants appear to be have somewhere around 20-40% BAF. Is this consistent with the BAF of upstream and downstream SNV?
sequence context/alignment artifacts: do the reads actually represent three nearby SNV? Have a look at the sequence context of the mutations. Depending on the flanking sequence there may be a more parsimonious explanation. For example, in some sequencing contexts, the 3 SNVs could be explained by 1bp insertion that the aligner prefers to align as 3 SNVs. Are the reads containing the variants soft clipped? Is this aactually a STR repeat expansion/contraction?
normal coverage: is there sufficient coverage in the normal for the variants to be reliably called as somatic? (the SNV caller should calculate this)
kataegis: do these mutations occur in a region of kataegis?
variant quality score: what quality score does the variant caller assign to these variants?
SV: is the tumour highly structurally rearranged? Could these be explained by a single DNA repair event? More generally, any explanation that results in the simultaneous generation of the mutations increases the plausibility of the SNVs as a single event explanation removes your implicit assumption that somatic SNVs should not be clustered so closely.
But as I said before, I think that the fact that they are on the same reads is not a good signal.
It just means they are phased together and all occurred on the same chromatid. It does not necessarily make them less likely - especially if they can be explained by a single event. Events such as chromothripsis result in hundreds of structural rearrangements from the same chromatid.
TLDR: from the limited information available, they look plausible.
modified 20 months ago
20 months ago by
d-cameron • 1.9k