HLA Typing for the Next Generation

Abstract

Allele-level resolution data at primary HLA typing is the ideal for most histocompatibility testing laboratories. Many high-throughput molecular HLA typing approaches are unable to determine the phase of observed DNA sequence polymorphisms, leading to ambiguous results. The use of higher resolution methods is often restricted due to cost and time limitations. Here we report on the feasibility of using Pacific Biosciences' Single Molecule Real-Time (SMRT) DNA sequencing technology for high-resolution and high-throughput HLA typing. Seven DNA samples were typed for HLA-A, -B and -C. The results showed that SMRT DNA sequencing technology was able to generate sequences that spanned entire HLA Class I genes that allowed for accurate allele calling. Eight novel genomic HLA class I sequences were identified, four were novel alleles, three were confirmed as genomic sequence extensions and one corrected an existing genomic reference sequence. This method has the potential to revolutionize the field of HLA typing. The clinical impact of achieving this level of resolution HLA typing data is likely to considerable, particularly in applications such as organ and blood stem cell transplantation where matching donors and recipients for their HLA is of utmost importance.

Fig 1. Basic stages of the Single Molecule Real-Time (SMRT) DNA sequencing method.

SMRTbell adaptors are ligated onto the ends of a blunt-ended PCR amplicon to facilitate continuous sequencing of both strands of the amplicon. The entire sequence generated may include multiple copies of the sense and anti-sense strands of the PCR amplicon in a single read known as the Continuous Long Read (CLR). The post-sequencing bioinformatic post-processes are able to break down the CLR into shorter sub-reads, which encompass the sequence of one strand of the amplicon. These sub-reads can then be compared and used to create a consensus sequence.