Tuesday, Sept 23, 2014
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Allele-Level Sequencing and Phasing of Full-length HLA Class I and II Genes Using PacBio® RS II

Pacific Bioscience SMRT® sequencing technology

The three classes of genes that comprise the MHC gene family are actively involved in determining donor-recipient compatibility for organ transplant, as well as susceptibility to autoimmune diseases via cross-reacting immunization.

Specifically, Class I genes HLA-A, -B, -C, and Class II genes HLA-DR, -DQ and -DP are considered medically important for genetic analysis to determine histocompatibility. They are highly polymorphic and have thousands of alleles implicated in disease resistance and susceptibility.

The importance of full-length HLA gene sequencing for genotyping, detection of null alleles, and phasing is now widely acknowledged. While DNA-sequencing- based HLA genotyping has become routine, only 7% of the HLA genes have been characterized by allele-level sequencing, while 93% are still defined by partial sequences.

The gold-standard Sanger sequencing technology is being quickly replaced by second-generation, high-throughput sequencing methods due to its inability to generate unambiguous phased reads from heterozygous alleles.

However, although these short, high-throughput, clonal sequencing methods are better at heterozygous allele detection, they are inadequate at generating full-length haploid gene sequences. Thus, full-length gene sequencing from an enhancer-promoter region to a 3'UTR that includes phasing information without the need for imputation still remains a technological challenge.

The best way to overcome these challenges is to sequence these genes with a technology that is clonal in nature and has the longest possible read lengths. We have employed Single Molecule Real-Time (SMRT®) sequencing technology from Pacific Biosciences for sequencing full-length HLA class I and II genes.

For more information, please contact us or visit pacificbiosciences.com

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