The personalized cancer network explorer (PeCaX) as a visual analytics tool to support molecular tumor boards.

BACKGROUND: Personalized oncology represents a shift in cancer treatment from conventional methods to target specific therapies where the decisions are made based on the patient specific tumor profile. Selection of the optimal therapy relies on a complex interdisciplinary analysis and interpretation of these variants by experts in molecular tumor boards. With up to hundreds of somatic variants identified in a tumor, this process requires visual analytics tools to guide and accelerate the annotation process. RESULTS: The Personal Cancer Network Explorer (PeCaX) is a visual analytics tool supporting the efficient annotation, navigation, and interpretation of somatic genomic variants through functional annotation, drug target annotation, and visual interpretation within the context of biological networks. Starting with somatic variants in a VCF file, PeCaX enables users to explore these variants through a web-based graphical user interface. The most protruding feature of PeCaX is the combination of clinical variant annotation and gene-drug networks with an interactive visualization. This reduces the time and effort the user needs to invest to get to a treatment suggestion and helps to generate new hypotheses. PeCaX is being provided as a platform-independent containerized software package for local or institution-wide deployment. PeCaX is available for download at https://github.com/KohlbacherLab/PeCaX-docker .

ClinVAP: a reporting strategy from variants to therapeutic options.

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.

NOS knockout or inhibition but not disrupting PSD-95-NOS interaction protect against ischemic brain damage.

Promising results have been reported in preclinical stroke target validation for pharmacological principles that disrupt the N-methyl-D-aspartate receptor-post-synaptic density protein-95-neuronal nitric oxide synthase complex. However, post-synaptic density protein-95 is also coupled to potentially neuroprotective mechanisms. As post-synaptic density protein-95 inhibitors may interfere with potentially neuroprotective mechanisms and sufficient validation has often been an issue in translating basic stroke research, we wanted to close that gap by comparing post-synaptic density protein-95 inhibitors with NOS1(-/-) mice and a NOS inhibitor. We confirm the deleterious role of NOS1 in stroke both in vivo and in vitro, but find three pharmacological post-synaptic density protein-95 inhibitors to be therapeutically ineffective.