inverted templated sequence

[ahwagner]

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]

@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]

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