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cancervariants / fusions

A repository for tracking documents, issues, and tools for the VICC / ClinGen gene fusion curation SOP
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inverted templated sequence #14

Open ahwagner opened 2 years ago

ahwagner commented 2 years ago

On today's call, Scott Myrand brought up the notion of inverted sequence fusions. He provided some that with references that we may select from for our use cases:

LTBP1-ALK Aguado 2018 29535536 SFPQ-TFE3 Ishikawa 2019 31153695 c11orf95-LOC105369347-RELA de Sousa 2019 30631904 RUNX1-GRIK2 Abe 2020 32544910 MYB-PDCDILG2 Mitani 2011 26631609 ETV6-CHIC2 Mueller 2021 34587239 FOS-RUNX2 PANAGOPOULOS 2020 32108038 FOS-VIM Makise 2021 33318581 CSF1-NOTCH2 Tsuda 2019 31107544 ESR1-NCOA3 Piscuoglio 2016 26592504 PPP1R10-TFEB Xia 2019a 31764220

ahwagner commented 2 years ago

@dsonkin suggested we may use the HGVS inversion syntax to represent these:

It looks like HGVS nomenclature would work well for fusion inverted templates.

NC_000023.10:g.32361330_32361333inv (inversion of nucleotides g.32361330 to g.32361333, changing ..CATCAGCCT.. to ..CACTGACCT..)

https://varnomen.hgvs.org/recommendations/DNA/variant/inversion/

ahwagner commented 2 years ago

Resolution: no further concepts needed for structural components of gene fusions; examples met (pending review by Scott)