Next-Generation Sequencing Based HLA Typing: Deciphering Immunogenetic Aspects of Sarcoidosis

Abstract

Unraveling of the HLA-related immunogenetic basis of several immune disorders is complex due to the extensive HLA polymorphism and strong linkage-disequilibrium between HLA loci. A lack of in phase sequence information, a relative deficiency of high resolution genotyping including non-coding regions and ambiguous haplotype assignment make it difficult to compare findings across association studies and to attribute a causal role to specific HLA alleles/haplotypes in disease susceptibility and modification of disease phenotypes. Earlier, historical antibody and DNA-based methods of HLA typing, primarily of low resolution at antigen/alellic group levels, yielded “indicative” findings which were partially improved by high-resolution DNA-based typing. Only recently, next-generation sequencing (NGS) approaches based on deep-sequencing of the complete HLA genes combined with bioinformatics tools began to provide the access to complete information at an allelic level. Analyzing HLA with NGS approaches, therefore, promises to provide further insight in the etiopathogenesis of several immune disorders in which HLA associations have been implicated. These range from coeliac disease and rheumatological conditions to even more complex disorders, such as type-1 diabetes, systemic lupus erythematosus and sarcoidosis. A systemic disease of unknown etiology, sarcoidosis has previously been associated with numerous HLA variants and also other gene polymorphisms, often in linkage with the HLA region. To date, the biological significance of these associations has only partially been defined. Therefore, more precise assignments of HLA alleles/haplotypes using NGS approaches could help to elucidate the exact role of HLA variation in the multifaceted etiopathogenesis of sarcoidosis, including epigenetic mechanisms. NGS-based HLA analyses may be also relevant for defining variable clinical phenotypes and for predicting the disease course or the response to current/plausible novel therapies.

Classical Examples of the Concept of the ASIA Syndrome

“…The pathophysiology has not yet been fully elucidated but there is likely involvement of CD8 + T cell response to T1DM antigen and type 1 diabetes-specific autoantibodies (GAD65) [ 127 ]. See also Table S1 [ 127 , 128 , 129 , 130 , 131 , 132 , 133 , 134 ].…”

HLA-A, -B, -C, -DRB1, -DQA1, and -DQB1 allele and haplotype frequencies defined by next generation sequencing in a population of East Croatia blood donors

“…The implementation of NGS technologies in HLA research and routine clinical work, enables however, elucidation of full-length HLA gene sequences, permitting an in-depth characterisation of population HLA diversity. In this context NGS can overcome limitations of traditional typing techniques, thereby sustaining optimal HLA matching of donor-recipient pairs for organ and particularly, haematopoietic stem cell transplantation (HSCT) 11 , improved estimates of population structure and HLA associated disease risk [12][13][14] , and better understanding of demographic history and geographic origin of a given population 15 .…”

The Polymorphism of HLA-A,-B,-C,-DRB1,-DQB1,-DRB3/4/5 loci in Zhejiang Han Population,China Using NGS Technology

“…Now common HLA genotyping methods were includedpolymerase chain reaction sequencebased typing (PCR-SBT), PCRsequence-speci c primer, PCR sequence-speci c oligonucleotide,next-generation sequencing (NGS) and so on. NGS method for HLAgenotyping has characteristic of economical, rapid andhigh-throughput, which can be improved allelic resolution and fewertyping ambiguities [6][7][8][9][10][11][12]. As the rapidly evolution of precise HLAgenotyping technology, 26,214 HLA alleles have been identi edaccording to the IPD-IMGT/HLA database (IPD-IMGT/HLA release3.39.0; January 2020).…”