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Unravel complex haplotypes of regions comprising highly polymorphic immune gene

The Major Histocompatibility Complex (MHC) – comprising the HLA genes and the Killer Immune Receptor (KIR) gene clusters – represents some of the key immune haplotypes associated with a variety of disease conditions, including autoimmunity, viral infections, reproductive failure, graft versus host disease, and cancer. Scientists continue to explore the underlying mechanisms of these diseases and the evolution of the immune system. However, enormous linkage disequilibrium, high gene density, copy number variants, large complex repeats, and extreme polymorphisms in these genomic regions make these haplotypes difficult to characterize1.

Access complete extended haplotypes

The long reads produced by Single Molecule, Real-Time (SMRT) Sequencing, along with target-enrichment methods, allow for reference-free de novo assembly of complex haplotypes. PacBio Systems deliver information that is highly accurate, imputation-free, and phased, giving you the ability to:

  • Simultaneously genotype and haplotype complex immune regions without family studies
  • Discover causal variants in complex regions with extended linkage disequilibrium in disease association or population studies
  • Increase the statistical power of your disease association studies using smaller sample size
  • Produce comprehensive views of gene order, copy number variants, and genotypes within the KIR gene complex

spotlight-human-icon

Workflow: from targeted region to simultaneously resolved genotypes and haplotypes

 

Featured research: Obtain complete, phased-genomic sequences over extended immunogenomic regions associated with type I diabetes

aplotype-resolved sequences

Scientists at Fred Hutchinson developed a method utilizing fosmid sequencing and the long reads of SMRT Sequencing to generate complete, haplotype-resolved sequences of the extended genomic subregions of MHC and KIR2. They discovered novel sequence regions unique to individuals with type I diabetes. They now have established cost-effective methods to more comprehensively identify casual variants associated with immunological diseases.

Explore this research further.

To learn more about how SMRT Sequencing helps you characterize your haplotypes, contact us.


References

  1. Trowsdale, J., and Knight, J., (2013) Major histocompatibility complex genomics and human disease. Annual Review Genomics and Human Genetics. 14, 301-323.
  1. Geraghty, D., et al. (February, 2015) Complete resequencing of extended genomic regions using fosmid target capture and Single Molecule Real-Time (SMRT) long read sequencing technology. Poster presented at Advances in Genome Biology & Technology Conference. Marco Island, FL.

Selected Resources