The regions of our genome responsible for encoding the genes that regulate our immune response are some of the most complex and polymorphic known. This complexity encompasses multiple types of genetic variation, from enrichment of single nucleotide variants through large structural differences. In several instances this variation has been shown to contribute to differential, individual susceptibility to disease. Investigating these regions is incredibly difficult using traditional short read approaches, as these reads often do not span entire genes or structural variants. Highly accurate long reads, such as those generated by single-molecule, real time (SMRT) sequencing, provide resolution of full-length immune genes without imputation and assembly of large, complex immune loci in a haplotype-specific manner. This presentation will use two examples, the human leukocyte antigen (HLA) locus, which is critically involved in effective T cell immunity, as well as the immunoglobulin heavy chain (IGH) locus, which encodes antibody responses, to demonstrate the power of SMRT sequencing for unparalleled resolution of these loci. In both cases, end-to-end genotyping pipelines have been developed and are available to leverage the power of long read sequencing to provide HLA and IGH genotyping data for most samples of interest.

Learning Objectives:

1. Identify mechanisms of genomic variation in immune loci that provide the extreme diversity of B and T cell responses

2. Understand the benefits of long read (vs. short read) sequencing approaches for resolving immune loci

3. Design an experiment utilizing HLA and/or IGH genotyping to understand the impact of immune loci variation in your specific disease model