NovAT tool—Reliable novel HLA alleles identification from next‐generation sequencing data

Abstract

HLA molecules are expressed in almost all nucleated cells of the body. These molecules are extremely variable and responsible for tissue specificity recognition. Precise HLA typing is crucial for tissue and organ transplantation. Usually, HLA‐typing NGS methods are based on the assignment of reads to a certain previously reported HLA allele presented in the IPD‐IMGT/HLA Database. But there is a limited number of tools able to identify novel alleles that have not yet been reported and thus absent in the database. Such alleles carry mismatches distinguishing them from all known alleles in the database. Therefore, manual evaluation of the identified HLA alleles in the genome browser is a compulsory step in the analysis, and one that is labor intensive and time consuming. We present the development and validation of a freely available web‐application for the identification of novel HLA alleles in the most relevant HLA class I and II genes from NGS data. The tool can also be used for automated data quality assessment. The software was validated by analyzing 330 alleles. The results are concordant with orthogonal methods.

Description of two new alleles: HLA‐B*50:79 and HLA‐DRB1*04:332

“…These sequences were analyzed with PARallele HLA software v.1.10.3 (Parseq Lab, Saint Petersburg, Russia). The novel alleles were identified using software NovAT 1 …”

Characterization of seven new HLA alleles, HLA‐A*01:407, ‐A*01:408, ‐A*03:434, ‐B*40:508N, ‐B*40:511N, ‐DRB1*04:336, and ‐DRB1*11:297Q

“…Allele assignment and phasing was performed by the PARallele HLA software v.1.10.3 (Parseq Lab, Saint Petersburg, Russia) using the IPD‐IMGT/HLA Database version 3.44.0 2 . Novel alleles were identified using software NovAT 3 …”

Detection of the HLA‐A*68:99:02 allele in a Russian unrelated hematopoietic cell donor

“…The reads were analyzed using the PARallele HLA software v.1.10.3 (Parseq Lab, Saint Petersburg, Russia). The novel allele was identified using software NovAT 2 …”

“…The novel allele was identified using software NovAT. 2 HLA-A*68:99:02 has one coding change at position 232 in exon 2 from C to T when compared with the closely related HLA-A*68:99:01, this corresponds to a codon 10 change from ACC to ACT, resulting in a silent mutation, threonine is not changed. The novel allele was submitted to GenBank and the IPD-IMGT/HLA Database 1 and the allele name was officially assigned by the World Health Organization (WHO) Nomenclature Committee for Factors of the HLA System in December 2021.…”