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
Workflow: from targeted region to simultaneously resolved genotypes and haplotypes
- Library preparation
- SMRT Sequencing with PacBio Systems
- Data analysis with SMRT Analysis or PacBio DevNet
Featured research: Obtain complete, phased-genomic sequences over extended immunogenomic regions associated with type I diabetes
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.
- Trowsdale, J., and Knight, J., (2013) Major histocompatibility complex genomics and human disease. Annual Review Genomics and Human Genetics. 14, 301-323.
- 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.
- Ruan, Rui et al. (2016) Assembly and characterization of the MHC class I region of the Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis). Immunogenetics
- Schwartz, John C et al. (2015) The assembly and characterisation of two structurally distinct cattle MHC class I haplotypes point to the mechanisms driving diversity. Immunogenetics
- Poster: Watson, C. T. et al. (2016) Characterizing haplotype diversity at the immunoglobulin heavy chain locus across human populations using novel long-read sequencing and assembly approaches
- Poster: Ekholm, JM et al. (2016) Resolving KIR genotypes and haplotypes simultaneously using Single Molecule, Real-Time Sequencing
- Poster: Ranade, Swati et al. (2016) Immune regions are no longer incomprehensible with SMRT Sequencing
- Poster: Hall, Richard J. et al. (2015) Assembly of complete KIR haplotypes from a diploid individual by the direct sequencing of full-length fosmids.
- Poster: Pyo, Chul-Woo et al. (2015) Complete resequencing of extended genomic regions using fosmid target capture and single molecule real-time (SMRT) long read sequencing technology.
- Poster: Kujawa, Steve et al. (2015) Targeted SMRT Sequencing and phasing using Roche NimbleGen’s SeqCap EZ enrichment
- Poster: Eng, Kevin et al. (2014) Unique haplotype structure determination in human genome using Single Molecule, Real-Time (SMRT) Sequencing of targeted full-length fosmids.
- Poster: Ashby, Meredith et al. (2015) Highly contiguous de novo human genome assembly and long-range haplotype phasing using SMRT Sequencing
- Cereb, Nezih (2017) AGBT PacBio Workshop: High-throughput HLA class I whole gene and HLA class II long range typing on PacBio RSII and Sequel Platforms
- Ranade, Swati (2016) AGBT Virtual Poster: Immune regions are no longer incomprehensible with SMRT Sequencing
- Hon, Lawrence and Raterman, Denise (2015) Xtalks Webinar: Long genomic DNA fragment capture and SMRT Sequencing enables accurate phasing of cancer and HLA loci
- Geraghty, Dan (2015) AGBT Virtual Poster: Insight into MHC and KIR genomic regions associated with autoimmune disease
- Maiers, Martin (2014) ASHI PacBio Workshop: KIR haplotypes – The long and short of it
- Geraghty, Dan (2014) Mendelspod: Major sequencing projects should be done with long reads
- Geraghty, Dan (2015) Customer Experience: SMRT Sequencing – delivering answers to decades-old problems
- SMRT Sequencing Brochure: Revolutionize genomics with SMRT Sequencing (2017)
- Application Note: Multiplex target enrichment using barcoded multi-kilobase fragments and probe-based capture technologies (2016)
- Immunology Brochure: Invaluable insights into immunology (2015)
- Targeted Sequencing Application Brochure: Capture your regions of interest in high resolution (2015)
- Featured Interview: “We’re Going to Find the Keys” – Dan Geraghty discusses an approach to understanding causal genetic variation. (2014)