Advancing Genomics Research to Improve Global Health
Discover better vaccines, treatments and outcomes with full characterization of pathogens, their mobile elements and communities.
Comprehensive genetic information provided by Single Molecule, Real-Time (SMRT) Sequencing has radically increased our understanding of microbial genomics, pathogenicity, and antimicrobial resistance. The PacBio Systems empower scientists to:
- Elucidate microbial genomes and distinguish mobile elements using whole genome sequencing
- Investigate pathogenicity, virulence and evolution with targeted sequencing
- Characterize complex viral and bacterial populations to further successful design and evaluation of drugs and vaccines
- Explore epigenetic modifications as part of your sequencing reaction
Spotlight: Deciphere genome complexity in pathogens using SMRT sequencing
Scientists were able to successfully work through the well-known AT-bias challenge of the Plasmodium falciparum genome. De novo assembly revealed novel insights for genome architecture and complexity, providing a reference to better understand virulence, drug resistance and disease transmission. Explore this research further:
Vembar, S.S. et al., 2016. Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing. DNA Research, 23(4), pp.339–351.
Spotlight: Single-molecule sequencing to track HIV-1 mutations
The development of novel circular consensus algorithms enabled the tracking of viral evolution of the K103N drug resistant associate mutation in clinical samples. Explore this research further:
Laird Smith, M. et al., 2016. An improved circular consensus algorithm with an application to detect HIV-1 Drug Resistance Associated Mutations (DRAMs). In 2016 ASM Microbe. New Orleans, LA.
Selected Resources
- Douglass, Alexander P et al. (2018) Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii: One species, four names. PLoS Pathogens
- Berná, Luisa et al. (2018) Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi. Microbial Genomics
- Otto, Thomas D et al. (2018) Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres. Wellcome Open Research
- Brese, Robin L et al. (2018) Ultradeep single-molecule real-time sequencing of HIV envelope reveals complete compartmentalization of highly macrophage-tropic R5 proviral variants in brain and CXCR4-using variants in immune and peripheral tissues. Journal of Neurovirology
- Magrini, Vincent et al. (2018) Improving eukaryotic genome annotation using single molecule mRNA sequencing. BMC Genomics
- Haig, Sarah-Jane et al. (2018) A high-throughput approach for identification of nontuberculous mycobacteria in drinking water reveals relationship between water age and Mycobacterium avium. mBio
- Weingarten, Rebecca A et al. (2018) Genomic analysis of hospital plumbing reveals diverse reservoir of bacterial plasmids conferring carbapenem resistance. mBio
- Atack, John M et al. (2018) Phasevarions of bacterial pathogens: Methylomics sheds new light on old enemies. Trends in Microbiology
- Ardui, Simon et al. (2018) Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Research
- Acuña-Amador, Luis et al. (2018) Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains. BMC Genomics
- Li, M et al. (2017) High frequency of mitochondrial DNA mutations in HIV-infected treatment-experienced individuals. HIV Medicine
- Revez, Joana et al. (2017) Survey on the use of whole-genome sequencing for infectious diseases surveillance: Rapid expansion of European national capacities, 2015-2016. Frontiers in Public Health
- Beaulaurier, John et al. (2017) Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nature Biotechnology
- Eren, Kemal et al. (2017) Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons BioRxiv
- Wang, Yuan et al. (2017) Profiling of oral microbiota in early childhood caries using Single-Molecule Real-Time Sequencing Frontiers in Microbiology
- Semler, Matthew R et al. (2017) Novel full-length major histocompatibility complex class I allele discovery and haplotype definition in pig-tailed macaques. Immunogenetics
- Li, Jing et al. (2017) A comparative study on the characterization of hepatitis B virus quasispecies by clone-based sequencing and third-generation sequencing. Emerging Microbes and Infections
- Verhey, Theodore B et al. (2017) Analysis of recombinational switching at the antigenic variation locus of the Lyme spirochete using a novel PacBio sequencing pipeline. Molecular Microbiology
- Whitfield, Zachary J et al. (2017) The diversity, structure, and function of heritable adaptive immunity sequences in the Aedes aegypti genome. Current Biology
- Landais, Elise et al. (2017) HIV envelope glycoform heterogeneity and localized diversity govern the initiation and maturation of a V2 apex broadly neutralizing antibody lineage. Immunity
- Balázs, Zsolt et al. (2017) Long-read sequencing of human cytomegalovirus transcriptome reveals RNA isoforms carrying distinct coding potentials. Scientific Reports
- Nell, Sandra et al. (2017) Genome and methylome variation in Helicobacter pylori with a cag pathogenicity island during early stages of human infection. Gastroenterology
- Young, George R et al. (2017) HIV-1 infection of primary CD4(+) T cells regulates the expression of specific HERV-K (HML-2) elements. Journal of Virology
- Wooddell, Christine I et al. (2017) RNAi-based treatment of chronically infected patients and chimpanzees reveals that integrated hepatitis B virus DNA is a source of HBsAg. Science Translational Medicine
- Patel, Jaymin C et al. (2017) Increased risk of low birth weight in women with placental malaria associated with P. falciparum VAR2CSA clade. Scientific Reports
- Forde, Brian M. et al. (2017) SMRT Sequencing reveals differential patterns of methylation in two O111:H- Shiga toxigenic Escherichia coli isolates from a historic hemolytic uremic syndrome outbreak in Australia BioRxiv
- Teng, Jade LL et al. (2017) PacBio but not Illumina technology can achieve fast, accurate and complete closure of the high GC, complex Burkholderia pseudomallei two-chromosome genome Frontiers in Microbiology
- Dara, Antoine et al. (2017) A new method for sequencing the hypervariable Plasmodium falciparum gene var2csa from clinical samples. Malaria Journal
- Zhao, J et al. (2017) Reduction in fecal microbiota diversity and short-chain fatty acid producers in Methicillin-resistant Staphylococcus aureus infected individuals as revealed by PacBio single molecule, real-time sequencing technology. European Journal of Clinical Microbiology & Infectious Diseases
- Stoesser, N et al. (2017) Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli. Scientific Reports
- Zautner, Andreas E et al. (2017) Monitoring microevolution of OXA-48-producing Klebsiella pneumoniae ST147 in a hospital setting by SMRT Sequencing Journal of Antimicrobial Chemotherapy
- Thomas, Prasad et al. (2017) First report of two complete Clostridium chauvoei genome sequences and detailed in silico genome analysis. Infection, Genetics and Evolution
- 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
- Hazen, Tracy H et al. (2017) Characterization of a large antibiotic resistance plasmid found in enteropathogenic Escherichia coli strain B171 and its relatedness to plasmids of diverse E. coli and Shigella. Antimicrobial Agents and Chemotherapy
- Nakano, Kazuma et al. (2017) Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area. Human Cell
- Poster: Boitano, M. et al. (2018) Full-length cDNA sequencing of prokaryotic transcriptome and metatranscriptome samples
- Poster: Heiner, Cheryl et al. (2018) Multiplexed complete microbial genomes on the Sequel System
- Poster: Lambert, C. et al. (2017) Multiplexing strategies for microbial whole genome sequencing using the Sequel System
- Poster: Kingan, Sarah et al. (2017) A high-quality genome assembly of SMRT sequences reveals long range haplotype structure in the diploid mosquito Aedes aegypti
- Poster: Hall, Richard et al. (2017) Using the PacBio Sequel System to taxonomically and functionally classify metagenomic samples in a trial of patients undergoing fecal microbiota transplantation
- Poster: Kingan, S. et al. (2017) A high-quality genome assembly of SMRT Sequences reveals long-range haplotype structure in the diploid mosquito Aedes aegypti
- 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: Seetin, M. et al. (2016) Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome using long-read sequencing
- Poster: Laird Smith, M. et al. (2016) An improved circular consensus algorithm with an application to detect HIV-1 Drug Resistance Associated Mutations (DRAMs)
- Poster: Oh, S. et al. (2016) Minimization of chimera formation and substitution errors in full-length 16S PCR amplification
- Poster: Heiner, C. et al. (2016) WGS SMRT Sequencing of patient samples from a fecal microbiota transplant trial
- Poster: Hall, R. et al. (2016) Workflow for processing high-throughput, Single Molecule, Real-Time Sequencing data for analyzing the microbiome of patients undergoing fecal microbiota transplantation
- Poster: Hepler, N. Lance et al. (2016) An improved circular consensus algorithm with an application to detection of HIV-1 Drug-Resistance Associated Mutations (DRAMs)
- Poster: Seetin, Matthew et al. (2016) Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- Poster: Hall, Richard et al. (2016) Profiling the microbiome in fecal microbiota transplantation using circular consensus and Single Molecule, Real-Time Sequencing
- Poster: Seetin, Matthew G et al. (2016) Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- (2017) Tutorial: Minor variant analysis [SMRT Link v5.0.0]
- Neafsey, Daniel (2017) AGBT Conference: A community effort using multiple technologies to produce a dramatically improved genome assembly of the Zika virus mosquito vector
- Paulin, Lars (2017) AGBT Virtual Poster: Single-molecule sequencing reveals the presence of distinct JC polyomavirus populations in patients with progressive multifocal leukoencephalopathy
- Matthews, Ben (2017) PAG PacBio Workshop: Genome assembly and molecular genetics of the dengue, yellow fever, and zika vector Aedes aegypti
- Laird Smith, Melissa (2016) ASHG PacBio Workshop: SMRT Sequencing as a translational research tool to investigate germline, somatic and infectious diseases
- Pollard, Martin (2016) ASHG Virtual Poster: The MHC Diversity in Africa Project (MDAP) pilot – 125 African high resolution HLA types from 5 populations
- Korlach, J. and Kingan, S. (2016) i5K Webinar: High-quality de novo insect genome assemblies using PacBio sequencing
- Ameur, Adam (2016) AGBT Roche and PacBio Workshop: Clinical SMRT Sequencing – from single genes to complete genomes
- Murrell, Ben (2016) AGBT Roche and PacBio Workshop: Deeply sequencing entire genes from rapidly evolving viruses
- Paxinos, Ellen (2016) AGBT Virtual Poster: An improved circular consensus algorithm with an application to detect HIV-1 Drug Resistance Associated Mutations (DRAMs)
- Seetin, Matthew (2016) AGBT Virtual Poster: Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- Hall, Richard (2016) AGBT Virtual Poster: Profiling the microbiome in fecal microbiota transplantation using circular consensus and Single Molecule, Real-Time Sequencing
- Application Brief: Microbial whole genome sequencing – Best Practices. (2018)
- SMRT Sequencing Brochure: Revolutionize genomics with SMRT Sequencing. (2018)
- PacBio Certified Service Providers (2018)
- Case Study: SMRT sequencing brings clarity to HIV vaccine and transplant research at the Wisconsin national primate research center. (2017)
- Application Brochure: Microbial communities – Complex microbial populations simplified. (2017)
- Case Study: Scientists advance understanding of microbial genomes, epigenomes and communities with SMRT Sequencing. (2016)
- Epigenetics Application Brochure: Characterize the epigenetic landscape of your genome. (2016)