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Reveal true HLA allelic diversity

Characterizing polymorphisms in HLA genes outside of the protein binding regions is important for strengthening causality association studies1. High-sequence homology and hyper polymorphisms make it challenging to determine true HLA allelic diversity. Even though sequencing is becoming a more popular tool for HLA typing, diploid ambiguities and a reliance on imputation still persist. This is especially true when the length of homologous sequences between alleles extends beyond the capabilities of most sequencing platforms2.

Access the full spectrum of polymorphism across the entire HLA gene

Gain a deeper understanding of immune-related disease causality, graft-versus-host disease in hematopoietic transplantation, and drug hypersensitivity with Single Molecule, Real-Time (SMRT) Sequencing.

SMRT Sequencing delivers single-molecule observations with 10–15 kb reads capable of spanning the majority of HLA class I and II genes. Generate highly accurate consensus sequences (QV50 demonstrated) from amplicons spanning full-length HLA genes without a reference to obtain directly phased, high-resolution HLA types without imputation2.

Features of this application include the ability to:

  • Flexibly scale project size (e.g., phase through either exons 2, 3 and/or 4, or the entire HLA gene) with cost-effective multiplexing solutions
  • Phase polymorphisms with allele specificity across SNP-poor regions of HLA genes
  • Achieve allele-level segregation without imputation
  • Detect variants in regulatory regions within 5’ UTRs, introns, and 3’ UTRs
  • Fully characterize minor variants in polyclonal samples, such as cancer or transcripts
  • Obtain direct evidence for new HLA alleles through de novo, reference-free consensus generation

spotlight-human-icon

Workflow: from targeted region to accurate variant or haplotype

 

Featured research: Build complete gene references for HLA class II genes

HLA-gene

Immunologists at DKMS generated reference-free consensus sequences of HLA-DPB 1 complete genes. At the time of the study, the IGMT/HLA database contained 12 full-length references out of 550 known HLA-DPB1 alleleles. In a single SMRT Sequencing run, scientists discovered 9 new alleles while generating fully-phased class II HLA genotypes for 48 samples3.

Explore this research further.

To learn more about how SMRT Sequencing powers imputation-free HLA typing, contact us.


References

  1. Hosomichi, K., et al., (2015) The impact of next-generation sequencing technologies on HLA research. Journal of Human Genetics. 60 (11), 665–673.
  1. Nelson, W. C., et al., (2015) An integrated genotyping approach for HLA and other complex genetic systems. Human Immunology. 76 (12), (928-938).
  1. Lang, K. et al. (September, 2015) Phased full-length SMRT Sequencing of HLA DPB1. Poster presented at 41st Annual Meeting of the American Society for Histocompatibility and Immunogenetics. Savannah, GA..

Selected Resources