HLA‐F: A Non‐Classical Gene With Growing Interest

TL;DR

This paper introduces a new method to study the HLA-F gene, revealing new genetic variations and their frequency in a donor cohort.

Contribution

A novel long-range PCR and NGS-based genotyping method for HLA-F, uncovering new alleles and linkage patterns.

Findings

A 3.8 kb LR-PCR amplicon covering the HLA-F gene and UTRs was developed and validated.

New allelic variations and allele frequency patterns were identified in 763 donor samples.

Linkage disequilibrium between HLA-F and neighboring HLA-A and HLA-E loci was assessed.

Abstract

The HLA‐F is a non‐classical HLA class I gene that belongs to the class Ib major histocompatibility complex (MHC) molecules. It is distinguished in the literature from its classical MHC class Ia counterparts by a minor frequency of polymorphisms. The exact function of HLA‐F remains unknown, but recent publications emphasise the essential immunological role of this gene in infectious diseases, cancer research, organ transplantation and autoimmune diseases. The rapidly evolving sequencing techniques within the last years allow the accession of larger genomic regions at reasonable costs. In this regard we developed a long‐range PCR assay, covering the entire HLA‐F gene, including the flanking untranslated regions (UTRs). According to the positions of the 5′ and 3′ amplification primers, the PCR amplicon has a total length of 3.8 kb. After verification of our in‐house developed LR‐PCR with pre‐typed cell‐line derived DNA‐samples from International HLA Reference Standards (IHWG), we analysed a randomly selected cohort of 763 DNA samples from the Stefan Morsch Stiftung stem cell donor registry on a MiSeq next generation sequencing (NGS) platform. This HLA‐F genotyping project revealed so far unpublished data regarding the allele frequency distribution pattern as well as several new allelic variations, not listed yet in the IPD‐IMGT/HLA Database. Prior to submission, all novel alleles were confirmed with Oxford Nanopore sequencing. Linkage disequilibrium between HLA‐F and its neighbouring loci HLA‐A and HLA‐E was also assessed.

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