scHLAcount

scHLAcount quantifies allele-specific expression of HLA class I (HLA-A, HLA-B, HLA-C) and class II (DPA1, DPB1, DRA1, DRB1, DQA1, DQB1) genes from single-cell RNA-seq data to enable cell-type-specific and allelic-resolution studies of immune-related biology.

Key Features:

• Allele-specific HLA expression analysis: Counts molecules specific to HLA alleles in single-cell RNA-seq data for both class I and class II genes.
• Personalized reference genome: Uses an individualized reference genome to improve accuracy of allele-specific quantification.
• HLA typing and quantification: Accepts known HLA types from external methods or calls HLA types directly from the data and quantifies expression against those calls.
• Cell-type-specific detection: Enables identification of cell-type-specific allelic expression patterns across single cells, including comparisons between blood cells and tumor versus normal tissue.
• Disease-focused allelic comparisons: Detects differential allelic expression patterns between tumor and normal cells relevant to immune evasion and HLA loss-of-function analyses.

Scientific Applications:

• Cancer immunology: Characterizes how HLA allelic expression and loss contribute to tumor immune evasion.
• Transplantation medicine: Provides allele-specific expression information relevant to graft rejection and compatibility studies.
• Autoimmune disease research: Supports investigation of HLA allele-specific expression mechanisms underlying autoimmune disorders.

Methodology:

Computes allele-specific molecule counts from single-cell RNA-seq using an individualized reference genome, accepts supplied HLA types or calls HLA types from the data, and quantifies molecules against those allele calls.