Integration of AlphaMissense Pathogenicity Predictions into Genome Nexus and cBioPortal

This project involves the integration of AlphaMissense, an innovative tool for predicting the pathogenicity of missense mutations, into two established platforms: Genome Nexus and cBioPortal. My Objectives and Deliverables are: - Integrate AlphaMissense pathogenicity predictions into Genome Nexus API responses, enriching genetic variant analysis with detailed pathogenicity scores. - Display AlphaMissense predictions within the Genome Nexus variant pages and add dedicated data columns in the cBioPortal mutation tables, complete with functionalities for sorting, filtering, and downloading. -Add AlphaMissense pathogenicity prediction and score into Genome Nexus annotation pipeline as two new columns in the annotation result file The project will be executed in phases, starting with initialization and planning, followed by backend and frontend development to integrate and visualize AlphaMissense data. Subsequent phases will focus on testing, deployment, and documentation, concluding with a final review and official launch. Post-launch, the project will enter a maintenance and support phase to address any arising issues and incorporate user feedback. Backend development will utilize Java and Spring Boot for integrating the AlphaMissense plugin into the Genome Nexus API. Frontend components will be developed using React and TypeScript, ensuring a dynamic and user-friendly interface for displaying genetic predictions.Comprehensive testing phases, including unit, integration, and User Acceptance Testing, will ensure the reliability and accuracy of the integration. This integration represents a significant leap forward in personalized medicine. By making pathogenicity predictions more accessible and interpretable, this project aims to support advancements in genetic research and clinical decision-making, ultimately contributing to improved patient outcomes.