Using Exome and Amplicon-Based Sequencing Data for High-Resolution HLA Typing with ATHLATES

Area of Science:

• Genomics
• Immunogenetics
• Bioinformatics

Background:

• Accurate Human Leukocyte Antigen (HLA) typing is crucial for transplantation and disease association studies.
• Existing methods for HLA genotyping can be complex and computationally intensive.

Purpose of the Study:

• To describe the protocol for using ATHLATES (Accurate Typing of Human Leukocyte Antigen through Exome Sequencing) for HLA genotyping.
• To expand the application of ATHLATES to analyze targeted sequencing data from HLA gene amplicons.

Main Methods:

• ATHLATES utilizes whole-exome sequencing (exome-seq) data.
• It involves stringent read mapping to the IMGT/HLA database.
• The process includes read assembly, candidate allele identification, and genotype inference.

Main Results:

• ATHLATES accurately predicts HLA genotypes at 2-field or higher resolution from exome-seq data.
• The protocol has been successfully adapted for targeted sequencing data analysis.

Conclusions:

• ATHLATES provides a robust method for high-resolution HLA genotyping.
• The expanded application enhances its utility for diverse sequencing data types, including targeted amplicon sequencing.