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JhuangLab / BioInstaller

A comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform
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Share variant analysis tools #13

Open Miachol opened 5 years ago

Miachol commented 5 years ago

Configuration file: github.toml Description: VariantTools, software tool for the manipulation, annotation, selection, simulation, and analysis of variants in the context of next-gen sequencing analysis.

[varianttools]
github_url = "https://github.com/vatlab/VariantTools"
install = "pip install ."
Miachol commented 5 years ago

Configuration file: github.toml Description: trimal, A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 1.4 http://trimal.cgenomics.org

[trimal]
github_url = "https://github.com/scapella/trimal"
Miachol commented 5 years ago

Done in commit fc7f22d58.

Miachol commented 5 years ago

configuration file: github.toml

title: From somatic variants towards precision oncology: Evidence-driven reporting of treatment options in molecular tumor boards.

description: BACKGROUND: A comprehensive understanding of cancer has been furthered with technological improvements and decreasing costs of next-generation sequencing (NGS). However, the complexity of interpreting genomic data is hindering the implementation of high-throughput technologies in the clinical context: increasing evidence on gene-drug interactions complicates the task of assigning clinical significance to genomic variants.

METHODS: Here we present a method that automatically matches patient-specific genomic alterations to treatment options. The method relies entirely on public knowledge of somatic variants with predictive evidence on drug response. The output report is aimed at supporting clinicians in the task of finding the clinical meaning of genomic variants. We applied the method to 1) The Cancer Genome Atlas (TCGA) and Genomics Evidence Neoplasia Information Exchange (GENIE) cohorts and 2) 11 patients from the NCT MASTER trial whose treatment discussions included information on their genomic profiles.

RESULTS: Our reporting strategy showed a substantial number of patients with actionable variants in the analyses of TCGA and GENIE samples. Notably, it was able to reproduce experts' treatment suggestions in a retrospective study of 11 patients from the NCT MASTER trial. Our results establish a proof of concept for comprehensive, evidence-based reports as a supporting tool for discussing treatment options in tumor boards.

CONCLUSIONS: We believe that a standardized method to report actionable somatic variants will smooth the incorporation of NGS in the clinical context. We anticipate that tools like the one we present here will become essential in summarizing for clinicians the growing evidence in the field of precision medicine. The R code of the presented method is provided in Additional file 6 and available at https://github.com/jperera-bel/MTB-Report ..

publication: From somatic variants towards precision oncology: Evidence-driven reporting of treatment options in molecular tumor boards. Genome Med. 2018 Mar 15;10(1):18. doi: 10.1186/s13073-018-0529-2.

[mtb_report]
github_url = "jperera-bel/MTB-Report"