PHLAT: Inference of High-Resolution HLA Types from RNA and Whole Exome Sequencing

Abstract

Inferring HLA types from genome-wide sequencing data has gained growing attention with the development of new cost-efficient sequencing technologies and the increasing need to integrate HLA types with transcriptomic or other genomic information for insights into immune-mediated diseases, vaccination, and cancer immunotherapy. PHLAT is a computational tool designed for high-resolution (4-digit) typing of the major class I and class II HLA genes using RNAseq or exome sequencing data as input. We illustrate here how PHLAT can be installed, configured, and executed. This document also provides guidance for how to read and interpret the output results. Finally, the best practices of using PHLAT are also discussed.

Keywords: Autoimmune; Bayesian inference; Cancer vaccine; HLA matching; Hematopoietic transplant; High-resolution HLA typing; Human leukocyte antigen; Immuno-oncology; Organ transplant; RNAseq; Transcriptome sequencing; Whole exome sequencing.