ClinVAP: a reporting strategy from variants to therapeutic options

Abstract

Motivation Next-generation sequencing has become routine in oncology and opens up new avenues of therapies, particularly in personalized oncology setting. An increasing number of cases also implies a need for a more robust, automated and reproducible processing of long lists of variants for cancer diagnosis and therapy. While solutions for the large-scale analysis of somatic variants have been implemented, existing solutions often have issues with reproducibility, scalability and interoperability. Results Clinical Variant Annotation Pipeline (ClinVAP) is an automated pipeline which annotates, filters and prioritizes somatic single nucleotide variants provided in variant call format. It augments the variant information with documented or predicted clinical effect. These annotated variants are prioritized based on driver gene status and druggability. ClinVAP is available as a fully containerized, self-contained pipeline maximizing reproducibility and scalability allowing the analysis of larger scale data. The resulting JSON-based report is suited for automated downstream processing, but ClinVAP can also automatically render the information into a user-defined template to yield a human-readable report. Availability and implementation ClinVAP is available at https://github.com/PersonalizedOncology/ClinVAP. Supplementary information Supplementary data are available at Bioinformatics online.

The Personalized Cancer Network Explorer (PeCaX) as a visual analytics tool to support molecular tumor boards

“…PeCaX relies on VCF files for information on SNVs and TSV files for optional CNV information. It integrates ClinVAP [15] to create a case report by processing variants using functional and clinical annotations of the genomic aberrations observed in a patient. ClinVAP employs Ensemble Variant Effect Predictor (VEP) [10] to obtain functional effects of the observed variants and filters them based on the severity of the predictions.…”

“…We present PeCaX (Personalized Cancer Network Explorer), an integrated application for personalized oncology workflows. PeCaX performs clinical variant annotation by processing SNVs and CNVs and identifying clinically relevant variants and their targeting therapeutics using Clin-VAP [15]. Networks containing the connections between the driver genes and the genes in their neighborhood as well as drugs targeting genes in this network are created through SBML4j [17] and they are visualized with the use of BioGraphVisart [11].…”

A comprehensive personal omics clinical interpreter based on genomic and transcriptomic profiles

“…Several interpretation tools have been developed to address this demand, primarily focusing on somatic alterations [6][7][8][9][10][11]. However, a select few, such as PORI [12], MOAlmanac [13], CCAS [14], and PanDrugs2.0 [7,15], have broadened their interpretative scope to encompass germline variants, RNA outliers, and other relevant factors.…”

Efficient privacy-preserving whole-genome variant queries

“…As genome sequencing technologies become faster and more efficient, genome are increasingly used in a variety of areas including direct-to-consumer services (23andMe, Ancestry, Gene By Gene, MyHeritage) ( Khan and Mittelman, 2018 ), forensic medicine ( Børsting and Morling, 2016 ), personalized medicine ( Amendola et al , 2018 ; Deng and Nakamura, 2017 ; Sürün et al , 2020 ) and, genome-disease association studies ( Consortium et al , 2007 ; Hyde et al , 2016 ). For example, it is now possible for doctors to give the right drug at the right time (for some drugs) by examining the patient’s genome ( Akgün et al , 2015 ; Erlich and Narayanan, 2014 ; Naveed et al , 2015 ).…”