ALPHLARD-NT: Bayesian Method for Human Leukocyte Antigen Genotyping and Mutation Calling through Simultaneous Analysis of Normal and Tumor Whole-Genome Sequence Data

Abstract

Human leukocyte antigen (HLA) genes provide useful information on the relationship between cancer and the immune system. Despite the ease of obtaining these data through nextgeneration sequencing methods, interpretation of these relationships remains challenging owing to the complexity of HLA genes. To resolve this issue, we developed a Bayesian method, ALPHLARD-NT, to identify HLA germline and somatic mutations as well as HLA genotypes from whole-exome sequencing (WES) and whole-genome sequencing (WGS) data. ALPHLARD-NT showed 99.2% accuracy for WGS-based HLA genotyping and detected five HLA somatic mutations in 25 colon cancer cases. In addition, ALPHLARD-NT identified 88 HLA somatic mutations, including recurrent mutations and a novel HLA-B type, from WES data of 343 colon adenocarcinoma cases. These results demonstrate the potential of ALPHLARD-NT for conducting an accurate analysis of HLA genes even from lowcoverage data sets. This method can become an essential tool for comprehensive analyses of HLA genes from WES and WGS data, helping to advance understanding of immune regulation in cancer as well as providing guidance for novel immunotherapy strategies.

Personalized HLA typing leads to the discovery of novel HLA alleles and tumor‐specific HLA variants

“…For the identification of highly dissimilar novel HLA alleles (as those presenting structural variants such as large insertions or deletions) from NGS data, a de novo alignment approach may be more optimal. 45 Additionally, the personalized germline HLA variant calling steps in this study were restricted to the consensus of three state-of-the-art variant callers. As numerous NGSbased germline variant callers have been developed in recent years, 73 with solutions to variant detection in complex genome regions like HLA continuously emerging 74,75 ; it may be beneficial to investigate ensemble approaches to variant calling, 53 taking input from numerous germline variant callers in order to optimize the accuracy of germline variant detection in the HLA region.…”

“…[41][42][43] Currently a limited number of methods exist that allow the detection of somatic mutations in HLA. 44,45 Unfortunately, these current strategies are unable to discover novel alleles, have a limited variant calling approach, do not assess the expression of HLA in a tumor, and finally, use an outdated version of the IPD-IMGT/HLA Database.…”

HLA Class I Allele Expression and Clinical Outcome in De Novo Metastatic Prostate Cancer

“…In addition, HLA-A2 mutations leading to the allele expression loss have been sporadically reported in the past in melanoma and cervical carcinoma cell lines by standard PCR and sequencing techniques [ 38 , 39 , 40 ]. The detection of somatic mutations in HLA genes using whole-exome sequencing by high-throughput techniques and the interpretation of these remains challenging due to the high polymorphism of the HLA loci [ 41 , 42 ]. This might explain why such mutations have not been detectable and reported so far in large genomic analyses in PCa.…”