Dataset Information

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

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.

SUBMITTER: Mosaieby E

PROVIDER: S-EPMC9356546 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature

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Publications

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

Mosaieby Elaheh E Martínek Petr P Ondič Ondrej O

Molecular genetics & genomic medicine 20220527 8

<h4>Introduction</h4>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.<h4>Method</h4>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 ...[more]

PMID: 35621010

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Dataset Information

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

Introduction

Method

Results

Conclusion

Publications

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

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