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A New Approach for HLA Typing: SMRT Sequencing

Tuesday, May 13, 2014

Two recent news announcements demonstrate the utility of our Single Molecule, Real-Time (SMRT®) Sequencing technology in the challenging realm of HLA typing.  HLA typing — or analysis of genes in the human leukocyte antigen region of the human genome — is of critical importance for research in tissue transplantation matching, autoimmune disease-association studies, drug hypersensitivity research, and other applications.

But analyzing those genes, which are highly polymorphic and contain thousands of alleles that code for proteins important in recognizing foreign antigens, has proven difficult with most technologies. Use of Sanger or short-read sequencing technologies has required other methods for confirmation of results, adding to the expense of HLA typing.

The long reads provided by SMRT Sequencing are ideally suited for accurate allele-level genotyping of the HLA region since unambiguous allele phasing is critical for high-resolution allele assignment. Now, two leading HLA typing organizations have announced their selection of the PacBio® platform to enhance their ability to comprehensively analyze the HLA region.

HistoGenetics, a global leader in HLA sequence-based typing, has selected SMRT Sequencing for its unique ability to sequence full-length HLA genes and to provide fully phased HLA alleles. The company has purchased two PacBio RS II DNA Sequencing systems, which will be used for HLA typing and will be evaluated as potential replacements for Sanger sequencing.

Anthony Nolan, the UK blood cancer charity that created the world’s first bone marrow registry 40 years ago, has also purchased two PacBio RS II DNA Sequencing systems to incorporate into its HLA typing pipeline, enabling it to conduct allele-level typing as standard. Professor Steven Marsh, Anthony Nolan’s Director of Bioinformatics, maintains the IMGT/HLA Database, a searchable repository of highly curated HLA sequences available to the global HLA community.

We are excited to see the PacBio platform adopted by leaders in the field such as Anthony Nolan and HistoGenetics as they seek novel insights regarding the HLA region and other genes relevant to immunology, such as KIR, that will be immensely useful to the biomedical research community. For more on using our sequencing platform for HLA research, don’t miss our booth at the European Immunogenetics and Histocompatibility Conference (EFI) taking place June 25-28 in Stockholm.

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