Evaluation of HLA Region-Specific High-Throughput Sequencing FASTQ Reads Combined with Ensemble HLA-Typing Tools for Rapid and High-Confidence HLA Typing.

ABSTRACT:

Background

Accurate human leukocyte antigen (HLA) genotyping is a critical step in the implementation of neoantigen peptide-based cancer immunotherapy. Existing computational tools for HLA genotyping using high-throughput sequencing data often lack sufficient accuracy when used individually. Employing an ensemble of multiple software tools and sequencing sources can potentially address this limitation; however, this approach is hindered by increased processing time.

Methods

We evaluated an ensemble method that utilizes four HLA-genotyping software tools applied to three sequencing sources-tumor exome, normal exome, and tumor RNA-seq-from the same individual to achieve high-confidence HLA genotyping. To reduce processing time, we incorporated an HLA region-specific FASTQ read

SUBMITTER: Padul VG 

PROVIDER: S-EPMC12731231 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature