Seq2HLA

Seq2HLA determines HLA types from short RNA-Seq reads for high-resolution genotyping of HLA class I and II alleles.

Key Features:

• Input data: Accepts short RNA-Seq reads in FASTQ format.
• Reference: Uses a Bowtie index encompassing known HLA alleles for allele-level comparison.
• Outputs: Reports the most probable HLA class I and II types with associated p-values and expression levels for each class.
• Resolution: Provides high-resolution genotype calls, achieving four- or six-digit resolution for class I alleles in validation experiments.
• Class II focus: Provides high-confidence DRB locus calls and supports class II genotyping efforts.
• Compatibility with amplicon data: Operates with cDNA amplicon-based sequencing datasets that capture HLA class I open-reading frames and DRB loci.
• Throughput and accuracy: Demonstrated high concordance and throughput in multiplexed amplicon validation experiments.
• Workflow integration: Available within a Galaxy server-based analysis workflow.

Scientific Applications:

• Clinical and diagnostic HLA typing: Enables high-resolution HLA genotyping from RNA-Seq for diagnostic and clinical research purposes.
• Research genotyping: Supports large-cohort HLA typing and population-scale studies requiring allele-level resolution.
• Allele discovery and validation: Facilitates allele discovery and validation using high-throughput amplicon or RNA-Seq data.
• HLA expression analysis: Provides expression level estimates for HLA class I and II loci for studies linking genotype and transcript abundance.

Methodology:

Maps short RNA-Seq FASTQ reads against a Bowtie index of known HLA alleles and reports probable HLA class I and II types with p-values and expression levels; provided as a Galaxy workflow.