README.rst

REVertant MUTation find & verify (REVMUT)

REVMUT can help to find and verify putative revertant mutations (PRMs) in DNA sequence data. Common workflow is:

1. Find PRMs (deletions of given mutation, indels that restore the reading frame)
2. Annotatote PRMs with Oncotator to get transcript change of putative revertant mutations in HGVS format
3. Verify if one of the transcript change in HGVS format is revertant by looking how the length of the protein changes

There are scripts to do 1 and 3. Steps 2 might be added at a later stage in development.

Installation

pip install revmut

Find

The finding module takes a mutation and finds PRMs that:

• Delete the entire given mutation

• Restore the reading frame in case the given mutation (GM) is an indel. The criterium is:

  length(PRM) +/- length(GM) % 3 == 0
  

Run with:

revmut-find tests/test_data/human_g1k_v37_chr17.fa \
            tests/test_data/germline_mutations/T1_test_mutation.tsv \
            tests/test_data/T1.bam \
            tests/test_data/N1.bam > tests/test_data/output/T1_test.tsv

View input/output files:

• tests/test_data/germline_mutations/T1_test_mutation.tsv
• tests/test_data/output/T1_test.tsv

Annotate

Annotation of the PRMs is currently done semi-manually with Oncotator webserice. Perhaps at a later stage in development this will be done automatically. Missing is a VCF to Oncotator format converter.

Verify

Applies a given mutation in cDNA format to a transcript followed by the cDNA change of the PRM as predicted by Oncotator. Output gives a prediction of how the protein changes.

Run with:

revmut-verify tests/test_data/to_be_reverted_mutations.txt \
              tests/test_data/oncotator.ins.txt \
              tests/test_data/BRCA_transcripts.fa > tests/test_data/oncotator.ins.maf.out.tsv

View input/output files:

• tests/test_data/to_be_reverted_mutations.txt
• tests/test_data/oncotator.ins.txt
• tests/test_data/output/oncotator.ins.maf.out.tsv

For an example that includes only reversion mutations try these BRCA1 mutations from the paper Diverse BRCA1 and BRCA2 Reversion Mutations in Circulating Cell-Free DNA of Therapy-Resistant Breast or Ovarian Cancer.:

revmut-verify tests/test_data/paper/brca1/to_be_reverted_mutations.txt \
              tests/test_data/paper/brca1/oncotator.ins.txt \
              tests/test_data/BRCA_transcripts.fa > tests/test_data/paper/brca1/output/oncotator.ins.maf.out.tsv

View input/output files:

• tests/test_data/paper/brca1/to_be_reverted_mutations.txt
• tests/test_data/paper/brca1/oncotator.ins.txt
• tests/test_data/paper/brca1/output/oncotator.ins.maf.out.tsv

A description of the columns in the output format:

mut = germline mutation
revmut = potential revertant mutation
revmut_pos_adj = the adjusted revertant mutations position after the germline mutation has been applied
transcript = the transcript to apply the cdna change to
normal_protein_length = the length of the protein when you translate the transcript in amino acids
mut_protein_length = how long the protein is after applying the germline mut cdna change and translating
revmut_protein_length = how long the protein is after applying the germline mut cdna change followed by the potential revertant mutation cdna change and translating
mut_p_distance = number of amino acids that differ between original protein and germline mutated protein
revmut_p_distance = number of amino acids that differ between original protein and germline + revertant mutated protein

Developers

Tests

In root dir run:

nosetests