The significance of the fusion partner gene genomic neighborhood analysis in translocation‐defined tumors

Abstract

Abstract Introduction This study presents a novel molecular parameter potentially co‐defining tumor biology—the total tumor suppressor gene (TSG) count at chromosomal loci harboring genes rearranged in fusion‐defined tumors. It belongs to the family of molecular parameters created using a black‐box approach. Method It is based on a public curated Texas TSG database. Its data are regrouped based on individual genes loci using another public database (Genecards). The total TSG count for NTRK (NTRK1; OMIM: 191315; NTRK2; OMIM: 600456; NTRK3; OMIM: 191316), NRG1 (OMIM: 142445), and RET (OMIM: 164761) rearranged tumors in patients treated with a theranostic approach is calculated using the results of recently published studies. Results Altogether 138 loci containing at least three TSGs are identified. These include 21 “extremely hot” spots, with 10 to 28 TSGs mapping to a given locus. However, the study falls short of finding a correlation between tumor regression or patient survival and the TSG count owing to a low number of cases meeting the study criteria. Conclusion The total TSG count alone cannot predict the biology of translocation‐defined tumors. The addition of other parameters, including microsatellite instability (MSI), tumor mutation burden (TMB), homologous recombination repair deficiency (HRD), and copy number heterogeneity (CNH), might be helpful. Thus a multi‐modal data integration is advocated. We believe that large scale studies should evaluate the significance and value of the total TSG count.

Keywords

• artificial intelligence
• cancer
• chromosomal instability
• chromothripsis
• copy number heterogeneity
• gene