Are You Working on Coronavirus?
Explore our COVID-19 sequencing tools and resources
Unlock the hidden complexity of the immune system
From SNVs to structural variants, isoforms and somatic hypermutation, see the full range of variation that impacts the immune response in infectious disease, cancer, or autoimmunity.
The loci encoding the critical components of the vertebrate immune system are at once highly variable from person to person and hard to sequence. Only HiFi sequencing combines single-molecule accuracy with long read lengths, allowing you to:
- Generate fully phased haplotypes of immunologically important NGS dead zones including the KIR and IGH loci
- Determine HLA haplotypes unambiguously and without imputation
- See the full diversity of the adaptive immune response in action with full-length transcripts and isoforms in targeted, bulk or single cell experiments
Use These Applications to Explore the Immune System with Confidence
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Targeted sequencing to generate fully phased HLA haplotypes without imputation with HiFi reads |
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Profile the BCR repertoire without primer or CDR3 length bias to fully capture somatic hypermutation and resolve both isotype and IgG subclass |
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RNA sequencing to characterize the complete landscape of isoform diversity that distinguishes the many cell types involved in the adaptive immune response |
Spotlight: KIR Haplotyping with Target Capture
Using only 18 IDT xGen Lockdown probes, HiFi Sequencing, and free software all diploid human KIR haplotypes were assembled and phased for the first time. Unlike past KIR sequencing methods, it is efficient enough for population-scale studies. The combination of high accuracy and long read lengths were critical to resolving genes that can be up to 98% identical.
Roe, D., et al. (2020) Efficient sequencing, assembly, and annotation of human KIR haplotypes. bioRxiv Preprint.
IGH Haplotyping with Target Capture
Target capture enrichment of DNA for IGH sequences followed by HiFi sequencing and analysis with iGenotyper allows locus-wide haplotyping of all IGH variant types for multiple samples in a single run, laying the groundwork to study population-level variation in the antibody response.
, et al. (2020) A novel framework for characterizing genomic haplotype diversity. bioRxiv Preprint.
Selected Resources
- Watson, Corey T et al. (2019) A comparison of immunoglobulin IGHV, IGHD and IGHJ genes in wild-derived and classical inbred mouse strains. Immunology and cell biology
- Novák, Karel et al. (2019) Potential of TLR-gene diversity in Czech indigenous cattle for resistance breeding as revealed by hybrid sequencing Archives Animal Breeding
- Zhang, Xiujuan et al. (2019) Full-length transcriptome analysis of Litopenaeus vannamei reveals transcript variants involved in the innate immune system. Fish & shellfish immunology
- Mayor, Neema P et al. (2019) Recipients receiving better HLA-matched hematopoietic cell transplantation grafts, uncovered by a novel HLA typing method, have superior survival: A retrospective study Biology of Blood and Marrow Transplantation
- Deiss, Thaddeus C et al. (2019) Immunogenetic factors driving formation of ultralong VH CDR3 in Bos taurus antibodies. Cellular & molecular immunology
- Bruijnesteijn, Jesse et al. (2018) Extensive alternative splicing of KIR transcripts. Frontiers in immunology
- Hosoya, Tomonori et al. (2018) High-Throughput Single-Cell Sequencing of both TCR-ß Alleles. Journal of immunology
- Suzuki, Shingo et al. (2018) Reference grade characterization of polymorphisms in full-length HLA class I and II genes with short-read sequencing on the Ion PGM system and long-reads generated by Single Molecule, Real-time Sequencing on the PacBio platform Frontiers in immunology
- Sutton, Jolene et al. (2018) A high-quality, long-read de novo genome assembly to aid conservation of Hawaii’s last remaining crow species Genes
- Pollard, Martin O et al. (2018) Long reads: their purpose and place. Human molecular genetics
- Breaux, Breanna et al. (2018) The Florida manatee (Trichechus manatus latirostris) T cell receptor loci exhibit V subgroup synteny and chain-specific evolution. Developmental and comparative immunology
- Bultitude, W P et al. (2018) KIR2DL1 allele sequence extensions and discovery of 2DL1*0010102 and 2DL1*0010103 alleles by DNA sequencing. HLA
- Cousin, Margot A et al. (2018) Utility of DNA, RNA, protein, and functional approaches to solve cryptic immunodeficiencies. Journal of clinical immunology
- Han, Seung Yub et al. (2018) Coupling of single molecule, long read sequencing with IMGT/HighV-QUEST analysis expedites identification of SIV gp140-specific antibodies from scFv phage display libraries. Frontiers in immunology
- Bruijnesteijn, Jesse et al. (2018) Human and rhesus macaque KIR haplotypes defined by their transcriptomes. Journal of immunology
- Cheng, Yuanyuan et al. (2018) Characterisation of MHC class I genes in the koala. Immunogenetics
- Ardui, Simon et al. (2018) Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic acids research
- Turner, T R et al. (2018) Single molecule real-time (SMRT®) DNA sequencing of HLA genes at ultra-high resolution from 126 International HLA and Immunogenetics Workshop cell lines. HLA
- Hemadou, Audrey et al. (2017) Pacific Biosciences sequencing and IMGT/HighV-QUEST analysis of full-length single chain fragment variable from an in vivo selected phage-display combinatorial Library. Frontiers in immunology
- Semler, Matthew R et al. (2017) Novel full-length major histocompatibility complex class I allele discovery and haplotype definition in pig-tailed macaques. Immunogenetics
- Pei, Weike et al. (2017) Polylox barcoding reveals haematopoietic stem cell fates realized in vivo. Nature
- Chen, Shi-Yi et al. (2017) A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing. Scientific reports
- Albrecht, V et al. (2017) Dual redundant sequencing strategy: Full-length gene characterisation of 1056 novel and confirmatory HLA alleles. HLA
- Ries, Moritz et al. (2017) KIR3DL01 upregulation on gut natural killer cells in response to SIV infection of KIR- and MHC class I-defined rhesus macaques. PLoS pathogens
- Novák, Karel et al. (2017) Diversity of the TLR4 immunity receptor in Czech native cattle breeds revealed using the Pacific Biosciences sequencing platform. Animal biotechnology
- Giudicelli, Véronique et al. (2017) IG and TR single chain fragment variable (scFv) sequence analysis: a new advanced functionality of IMGT/V-QUEST and IMGT/HighV-QUEST. BMC immunology
- Roe, D. et al. (2017) Revealing complete complex KIR haplotypes phased by long-read sequencing technology Genes and immunity
- Bassano, Irene et al. (2017) Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes. BMC genomics
- Prall, Trent M et al. (2017) Improved full-length killer cell immunoglobulin-like receptor transcript discovery in Mauritian cynomolgus macaques. Immunogenetics
- Karl, Julie A et al. (2017) Major histocompatibility complex haplotyping and long-amplicon allele discovery in cynomolgus macaques from Chinese breeding facilities. Immunogenetics
- Viluma, Agnese et al. (2017) Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology. Scientific reports
- Hans, Jörg B et al. (2017) Gorilla MHC class I gene and sequence variation in a comparative context. Immunogenetics
- van Bergen, Cornelis A M et al. (2017) Selective graft-versus-leukemia depends on magnitude and diversity of the alloreactive T cell response. The Journal of clinical investigation
- Breaux, Breanna et al. (2017) The Florida manatee (Trichechus manatus latirostris) immunoglobulin heavy chain suggests the importance of clan III variable segments in repertoire diversity. Developmental and comparative immunology
- Koenig, Patrick et al. (2017) Mutational landscape of antibody variable domains reveals a switch modulating the interdomain conformational dynamics and antigen binding. Proceedings of the National Academy of Sciences of the United States of America
- Poster: Ranade, S. et al. (2018) High-throughput SMRT Sequencing of clinically relevant targets
- Poster: McLaughlin, I., et al. (2017) Targeted sequencing using a long-read sequencing technology
- Poster: Oh, Steve et al. (2017) T-cell receptor profiling using PacBio sequencing of SMARTer libraries
- 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: Pollard, M. O. et al. (2016) The MHC Diversity in Africa Project (MDAP) pilot – 125 African high resolution HLA types from 5 populations
- Poster: Cereb, N et al. (2016) Whole gene sequencing of KIR-3DL1 with SMRT Sequencing and the distribution of allelic variants in different ethnic groups
- Poster: Jenny Gu, Kevin Eng, Anand Sethuraman, Steve Kujawa et al. (2016) Multiplex target enrichment using barcoded multi-kilobase fragments and probe-based capture technologies
- Poster: Ekholm, JM et al. (2016) Resolving KIR genotypes and haplotypes simultaneously using Single Molecule, Real-Time Sequencing
- Poster: Baybayan, Primo et al. (2016) Application specific barcoding strategies for SMRT Sequencing
- Poster: Ranade, Swati et al. (2016) Immune regions are no longer incomprehensible with SMRT Sequencing
- Wenger, Aaron (2021) Complete and Accurate Human Genomes with HiFi Reads
- Hoischen, Alexander (2021) Long Reads to Identify Hidden Structural Variants in Rare Disease
- Matsumoto, Naomichi (2021) The Utility of HiFi Long-Read WGS in Solving Patients with Rare Diseases
- Rowell, William and LIeras, Roberto (2021) A Bioinformatics Workflow for Comprehensive Detection and Prioritization of Variants with PacBio HiFi Reads
- Pastinen, Tomi (2021) Genomic Answers for Kids
- Ekholm, Jenny (2021) Increasing Solve Rates in Rare and Mendelian Disease Research with Long-Read Sequencing
- Lambert, Christine (2021) Scalable Workflow for Constructing HiFi Libraries
- Wenger, Aaron (2021) The Present and Future of HiFi Whole-Genome Sequencing for Rare Disease
- Tseng, Elizabeth (2021) PacBio SMRT Link SARS-CoV-2 Workflow Overview
- Blethrow, Justin and Smith, Melissa L. and Vinnere Pettersson, Olga (2021) Webinar: Unleashing the Power of HiFi Sequencing – How the Sequel IIe System Removes Barriers and Empowers Life Scientists
- Miller, Dave and Hernandez, Alvaro (2021) Creating Core Demand with HiFi Sequencing
- Wenger, Aaron (2021) Not All Long Reads Are Equal – High Accuracy Sets PacBio Apart
- Miller, David and Smith, Melissa Laird (2021) The Long and Short of Sequencing – Why HiFi Reads are the Future
- Becker, Aaron and Ekholm, Jenny and Harris, Charlotte and Kingham, Brewster and Vinnere Pettersson, Olga (2021) SMRT Sequencing as a Service – How to Bring Long-Read Technology to Your Core Lab
- Korlach, Jonas (2021) AGBT Presentation: Increasing the Solve Rate of Rare and Undiagnosed Genetic Diseases with HiFi Sequencing
- Levandoski, Michael (2020) Webinar: Geographic and Temporal Mapping of the SARS-CoV-2 Pandemic in the United States
- (2020) Introduction to highly accurate long-read sequencing (HiFi Sequencing)
- Korlach, Jonas (2020) ASHG PacBio Workshop: Latest product and application updates
- Tseng, Elizabeth and Wilson, Joan and Hon, Ting and Eng, Kevin and Lambert, Christine and Chakraborty, Shreyasee and Zhu, Lei and Toepfer, Armin and Xiang, Wenwen and Harting, John and Li, Qiang and Underwood, Jason G. and Baybayan, Primo and Ashby, Meredith and Bostick, Maggie and Farmer, Andrew (2020) Video Poster: Long-read sequencing of the SARS-CoV-2 genome and the human immune repertoire
- (2020) Video: HiFi Sequencing – Unlock your next great discovery
- Ameur, Adam (2020) Webinar: SMRT Sequencing applications for human genomics and medicine
- Ashby, Meredith and Laird-Smith, Melissa and Watson, Corey (2020) Webinar: Understanding SARS-CoV-2 and host immune response to COVID-19 with PacBio sequencing
- Gharbi, Karim (2020) Customer Experience: Advancing UK genomics research with the PacBio Sequel II System
- Schmutz, Jeremy and Conesa, Ana and Gharbi, Karim and Kuo, Richard (2020) Customer Experience: HiFi reads help scientists explore genomes and transcriptomes
- Conesa, Ana (2020) Customer Experience: Improving transcriptome research with PacBio HiFi reads
- Schmutz, Jeremy (2020) Customer Experience: PacBio HiFi reads improve genome sequencing at HudsonAlpha
- Ashby, Meredith (2020) Webinar: Opportunities for using PacBio Long-read sequencing for COVID-19 research
- Mars, Kristin and Laird Smith, Melissa and Vinnere Pettersson, Olga and Hardigan, Michael (2020) Webinar: Sequencing 101 – How long-read sequencing improves access to genetic information
- (2020) Video: Introduction to PacBio highly accurate long-read sequencing
- Korlach, Jonas (2018) Webinar: New PacBio solutions for high-resolution microbiology & immunology analysis
- Jacob, Howard (2017) Podcast: Huh? 30 million Americans have a rare disease? Howard Jacob on the state of clinical sequencing
- Korlach, Jonas (2017) ASHG PacBio Workshop: PacBio applications updates & future roadmap
- Ranade, Swati (2017) Webinar: A paradigm shift in HLA sequencing: from exons to high-resolution allele-level HLA yyping
- 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
- Laird Smith, Melissa (2016) ASHG PacBio Workshop: SMRT Sequencing as a translational research tool to investigate germline, somatic and infectious diseases
- SMRT Sequencing Brochure: Delivering highly accurate long reads to drive discovery in life science (2020)
- Application Brief: No-Amp targeted sequencing – Best Practices (2020)
- Product Brochure: Sequel IIe System – Sequencing evolved (2020)
- Informational Guide: Understanding accuracy in DNA sequencing (2020)
- Application Brochure: HiFi reads for highly accurate long-read sequencing (2020)
- Infographic: Mapping the interplay of viral and host genomics with HiFi sequencing (2020)
- PacBio Certified Service Providers (2020)
- Application Brief: Long-read RNA sequencing – Best Practices (2019)
- Infographic: Structural variants and disease (2017)