TGex

TGex performs genome analysis and clinical variant interpretation for Whole Genome Sequencing (WGS) and exome data by integrating GeneCards, GeneHancer, and VarElect to prioritize coding and non-coding variants in clinical genetics.

Key Features:

• Phenotype-Driven Variant Prioritization: Prioritizes genetic variants using patient phenotypic data to rank candidate variants relevant to clinical symptoms.
• Automated ACMG/ClinGen Classification: Implements automated variant classification according to ACMG and ClinGen guidelines.
• Comprehensive Evidence Collection & Reporting: Aggregates over 150 data sources via the GeneCards knowledgebase to provide comprehensive genomic annotations and supports automated case report generation.
• Non-Coding Variant Interpretation: Annotates and interprets non-coding variants using the GeneHancer database of human enhancers and promoters to extend WGS utility.
• VarElect Knowledge-Driven Scoring: Applies VarElect for knowledge-driven variant scoring and evidence-based prioritization using GeneCards-derived annotations.
• Integration with EHR and LIMS via APIs: Supports integration with Electronic Health Records (EHR) and Laboratory Information Management Systems (LIMS) through APIs to enable automated data exchange and customizable reporting.

Scientific Applications:

• Rare Disease Diagnostics: Enables diagnostic variant identification in rare genetic disease cases, with reported diagnostic yields of 42% for single exome analyses and 50% for trio analyses across 1,500 cases.
• Cancer Predisposition and Tumor Analysis: Supports analysis of cancer predisposition and tumor biopsy sequencing for identification of actionable variants.
• Genetic Screening and Clinical Testing Workflows: Facilitates genetic screening and clinical testing workflows, including automated reporting and integration with laboratory systems.

Methodology:

Uses a knowledge-driven variant interpretation approach via VarElect with GeneCards integration, aggregates over 150 data sources, applies automated ACMG/ClinGen classification, and annotates non-coding elements using GeneHancer.