This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Strategies to shortlist True LoF mutations

I was curious as to what strategies are applied by everyone to shortlist true LoF(Loss of function) variations post variant annotation.

Some of the ones I could get from literature and tools are:-

  1. Selecting the variations which are stop codon introducing/splice site disrupting/indels disrupting reading frame
  2. Removing the variants present towards the end of transcripts
  3. Removing the one where the LoF allele is same as the ancestral one
  4. Removing variations in introns/exons with non-cannonical splice sites.

Also are there any other tools which can automatically filter and help find true LoF variations

snp next-gen-sequencing loss-of-function
• 2,519 views • link
updated by Ram Ram • written by kautilya kautilya

1 answer

The cBioPortal provides a functional impact score for mutations using mutation assessor (Reva B, Antipin Y, Sander C. Nucleic Acids Research (2011) Predicting the Functional Impact of Protein Mutations: Application to Cancer Genomics).

• 0 views • link
updated by Ram Ram • written by Jean-Karim Heriche Jean-Karim Heriche

Thanks for the answer. The tool is helpful but could not find any annotation/filtering regarding Lof however will use it add some annotations which might be helpful in filtering the Lofs

• 0 views • link
updated by Ram Ram • written by kautilya kautilya

Log in to answer this question.

More posts like this