consHLA

consHLA leverages next-generation sequencing data from whole genome sequencing and RNA-seq to perform consensus-based HLA typing, enhancing accuracy and resolution compared to traditional methods.

Key Features:

• Consensus HLA typing: Integrates germline WGS, tumour WGS, and tumour RNA-seq data to generate consensus HLA typing results.
• Class I and II HLA gene analysis: Analyses both Class I and II HLA genes at three-field resolution.
• HLA-HD integration: Employs HLA-HD as the underlying HLA typing package, selected for its ability to use all three dataset types.
• HLA alteration detection: Identifies HLA alterations arising in patient tumours and typing inconsistencies across sequencing inputs.
• Automated reporting: Produces a clinician-friendly HLA-typing report in a clinically relevant timeframe.

Scientific Applications:

• Cancer immunotherapy: Informs cancer immunotherapy by providing accurate HLA typing for cancer patients.
• Transplant tissue matching: Supports transplant tissue matching through high-resolution HLA typing.
• Autoimmune disease characterisation: Characterises autoimmune diseases via accurate Class I and II HLA gene typing.
• Tumour HLA evolution: Identifies clinically relevant HLA type changes in tumours by comparing germline and tumour sequencing data.
• Precision medicine programs: Applied in precision medicine programs such as ZERO Childhood Cancer for high-risk paediatric cancer patients.

Methodology:

consHLA employs HLA-HD to perform HLA typing on matched germline WGS, tumour WGS, and tumour RNA-seq data, then generates consensus typing results across these three sequencing inputs.