HLA Typing Workflow Uses Pippin Prep for Size Selection

We’ve written before about the shift toward NGS-based technologies for the HLA typing market. HLA typing is used for everything from understanding autoimmune and infectious diseases to matching organ transplants to recipients.

But the HLA locus really make scientists and clinicians work for their answers. This region of the genome is one of the most polymorphic, with more than 14,000 recognized HLA alleles so far. The rise of affordable, high-throughput NGS platforms is an appealing alternative for labs responsible for typing these genes.

In a paper published in the December 2016 issue of Clinical Chemistry, scientists from The Children’s Hospital of Philadelphia describe an NGS-based HLA typing workflow that uses a kit from Omixon to report relevant class I alleles. We were pleased to see that our Pippin Prep system proved valuable in the pipeline; the team used it to select DNA fragments between 650 bp and 1300 bp prior to sequencing on an Illumina MiSeq.

Generation of Full-Length Class I Human Leukocyte Antigen Gene Consensus Sequences for Novel Allele Characterization” comes from lead author Peter Clark, senior author Dimitri Monos, and collaborators. In it, they describe their evaluation of the Omixon Holotype HLA assay using samples from 50 individuals. “HLA genotyping results and fully phased consensus sequences were successfully generated for all 50 participants using the Omixon Twin algorithm (300 total alleles) and were found to be concordant with SBT/SSP genotyping results,” the authors report.

Interestingly, the team found that 7.7% of samples featured novel alleles and predicted that this discovery rate means “there are likely to be numerous yet undiscovered alleles of unknown significance.” They add that “full-length gene characterization is paramount for unambiguous HLA genotyping and facilitates a deeper understanding of HLA gene polymorphisms and the eventual role they may play in the immune response.”

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