Overview of Immunogenetics and NGS

The Human Leucocyte Antigen (HLA) and Killer-cell Immunoglobulin-like Receptor (KIR) genes encode cell-surface proteins that are key elements of the immune system. HLA proteins bind and present endogenous- and exogenously-derived peptide fragments, forming antigens that are inspected by T-cell receptors as part of self/non-self discrimination by the adaptive immune system. As such, HLA polymorphism is central to the elimination of infectious pathogens and development of long term immunity. Class I HLA proteins also serve as ligands for KIRs, stimulatory and inhibitory receptors that participate in the modulation of the NK response in the innate immune system. In this capacity, HLA and KIR polymorphisms are central for rapid immune responses to viral infections and tumor development. In addition, the HLA genes are the primary determinants of histocompatibility – the ability of an individual to serve as an organ donor for a patient in need of a transplant.

HLA and KIR genotyping therefore provide direct insight into the functions of the innate and adaptive immune systems, susceptibility and resistance to infectious, autoimmune and environmental disease, adverse pharmacological responses and cancer, and are key for effective solid-organ, bone-marrow and stem-cell transplantation.

The HLA genes are the most polymorphic loci in the human genome; over 12,000 genetic variants (alleles) have been identified at 19 HLA genes, with some individual genes displaying several thousand alleles. Though they display less allelic polymorphism, the 17 KIR genes are highly homologous and display extensive structural polymorphism. The allelic and structural variation that characterizes these genes pose extreme challenges for routine genotyping of these genetic loci; this variation cannot be characterized by a few SNPs, and the high level of polymorphism confounds de novo sequence assembly efforts.

Until recently, HLA genotyping has been accomplished using a variety of PCR-based approaches involving sequence-specific oligonucleotide probe (SSOP) hybridization and/or Sanger sequencing of 400-600 base pair-long amplicons. These methods do not readily allow the establishment of chromosomal-phase between assessed sequence features, which results in considerable ambiguity regarding an HLA genotype. KIR genotyping has proven more difficult than HLA typing using SSOP- and Sanger-based methods, and has largely been restricted to identifying the presence or absence of a particular KIR gene.

Next generation sequencing (NGS) methods are now being applied for HLA and KIR genotyping with great success. These methods apply a variety of single-molecule sequencing approaches to accomplish extensive phasing across genes, minimizing genotyping ambiguity, and accelerating polymorphism discovery and the understanding of allelic diversity. The inherent high-throughput nature of NGS has a broad potential for therapeutic and diagnostic applications. However, a wide variety of NGS methodologies are used, and their relative strengths and shortcomings for Histocompatibility and Immunogenetics (H&I) research applications remain unexplored.

The goal of the 17th International HLA and Immunogenetics Workshop is to advance the fields of H&I research through the application NGS technologies, and to advance the development of NGS technologies tailored to meet the needs of the H&I community.

Components

Overview of Immunogenetics and NGS

Components

Genetic & Genomic Studies

Functional Studies

Core Workshop Functions