Menu

Scientific posters

ESHG 2025  |  2025

Saliva, a convenient sample type enabling large scale PacBio HiFi sequencing project

Deborah Moine, Sarah Kingan, Shreyasee Chakraborty, Heather Ferrao, Kristina Weber, Christina Dillane*, Mike Tayeb*, Duncan Kilburn *DNA Genotek, Inc. Ottawa, ON, Canada

Saliva samples collected with OrageneTM devices and DNA extracted using Nanobind kits are a good alternative to blood for HiFi sequencing. High-throughput workflow from extraction using Nanobind HT kit through HiFi sequencing on the Revio system is available for saliva and blood samples.
ESHG 2025  |  2025

Sawfish2: Integrating copy number segmentation with structural variant haplotype modeling to improve large-variant calling accuracy

Christopher T. Saunders, James M. Holt, Juniper A. Lake, Jonathan R. Belyeu, Zev Kronenberg, William J. Rowell, Michael A. Eberle, PacBio, 1305 O’Brien Drive, Menlo Park, CA 94025

Sawfish is a general-purpose structural variant (SV) caller for HiFi sequencing data. It has already been shown to provide best-in- class SV accuracy in both single-sample and joint-genotyping contexts1 . Sawfish2 adds depth-based CNV calling as a joint operation integrated with sawfish’s existing breakend-based SV calling methods.
ESHG 2025  |  2025

Streamlined hybridization capture workflow for targeted long- read sequencing

Elizabeth Tseng1, Davy Lee1, Camille Connor1, Katelyn Larkin2, Justin Jacques2, Ashley Dvorak2 1) PacBio, 1305 O’Brien Drive, Menlo Park, CA 94025, USA, 2) IDT, 1710 Commercial Park, Coralville, IA 52241, USA

Here, we combine IDT hybridization capture with PacBio full-length RNA sequencing for deep isoform characterization. We show that the new IDT xGen Hyb and Wash Kit v3 is compatible with the PacBio Kinnex full-length RNA kit and can achieve an on-target rate of 85%, increasing detection of low abundance isoforms by several thousand-fold.
ESHG 2025  |  2025

SVX: Population-scale merging of structural variants with tandem repeat-aware refinement

T. Mokveld1, J. A. Lake1, W. J. Rowell1, E. Dolzhenko1, M. A. Eberle1; 1 PacBio, Menlo Park, CA,

Studies of structural variants (SVs) in large cohorts remain challenging due to high data volumes and imprecise breakpoints in low sequence complexity regions, such as tandem repeats. We developed SVX, a fast, memory-efficient SV merging tool implemented in Rust. SVX is in early development. It currently only works with Sawfish.
ESHG 2025  |  2025

Targeted long-read sequencing of native DNA for genetic disease diagnostic and screening research

Sarah B. Kingan, Guilherme De Sena Brandine, Jeff Zhou, Tom Mokveld, Jocelyne Bruand, Egor Dolzhenko, Michael A. Eberle, Duncan Kilburn PacBio, 1305 O’Brien Drive, Menlo Park, CA 94025

Despite advances in DNA sequencing, the causal mutations of many human diseases remain challenging to characterize with standard methods. The adoption of long-read sequencing can improve and simplify sequencing and analysis of these complex regions. The ability to detect methylation enables simultaneous generation of sequence- level and epigenetic data. We present new panel content for the PureTarget assay, which uses the CRISPR/Cas9 system to generate targeted sequencing libraries of native DNA, sequenced with long and accurate HiFi sequencing.
AACR 2025  |  2025

Comprehensive, multi-omic detection of somatic variants from the GIAB HG008 matched tumor-normal pair

Alex Sockell1, Khi Pin Chua1, Christine Lambert1, Matt Boitano1, Melanie Wescott1, Ian J McLaughlin1, Primo Baybayan1, Jennifer McDaniel2, Justin Zook2, Aaron M Wenger1 1 PacBio, 1305 O’Brien Drive, Menlo Park, CA 94025, 2Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD 20899, USA

Here we apply PacBio HiFi to perform whole-genome sequencing of the newly described HG008 matched tumor- normal pair from the Genome in a Bottle (GIAB) consortium. 1 This reference sample includes an adherent, epithelial-like pancreatic adenocarcinoma (PDAC) cell line as the tumor material, with the matched normal obtained from adjacent duodenal and pancreatic tissue. We perform whole-genome sequencing of the tumor cell line and matched pancreatic normal tissue with PacBio HiFi, resulting in a more robust and comprehensive picture of somatic variation in this reference sample and contributing to the development of this novel benchmark.
AACR 2025  |  2025

Precise characterization of complex repeat regions in cancer genomes

Khi Pin, Chua1,2, Egor Dolzhenko1, Tom Mokveld1, Zev N Kronenberg1, Seiya Imoto2, Seiichi Mori3, Michael A Eberle1 1. Pacific Biosciences of California, Menlo Park, CA, USA 2. Institute of Medical Sciences, University of Tokyo, Japan 3. Japan Foundation for Cancer Research, Japan

The characterization of somatic variation, especially in complex genomic regions, is crucial for understanding the molecular drivers of cancer progression. Accurate PacBio long-read sequencing (HiFi) enables detection of all variant classes, from simple SNVs and INDELs up to complex structural variation, tandem repeats, and changes in epigenetic signatures. Complex and repetitive regions, while fully sequenced by HiFi reads, remain bioinformatically challenging, requiring tailored solutions. Here, we describe new tools to genotype understudied repetitive regions in cancer genomes, a task that has historically posed significant challenges for short-read sequencing.
ACMG 2025  |  2025

Extracting HMW DNA from saliva for HiFi sequencing applications

Sarah Kingan, Deborah Moine, Nina Gonzaludo, Shreyasee Chakraborty, Heather Ferrao, Kristina Weber, Christina Dillane*, Mike Tayeb*, Duncan Kilburn, PacBio, 1305 O’Brien Drive, Menlo Park, CA 94025, *DNA Genotek Inc., Ottawa, ON, Canada

In this proof-of-concept study, we demonstrate that high quality PacBio HiFi sequencing results can be obtained from DNA extracted from saliva collected in DNA Genotek Oragene devices and extracted using the Nanobind PanDNA or CBB kits.
ACMG 2025  |  2025

StarPhase: Leveraging Long-Read Sequencing to Update Pharmacogenomic Benchmarks

J. Matthew Holt, John Harting, Xiao Chen, Daniel Baker, Nina Gonzaludo, Zev Kronenberg, Christopher T. Saunders, Michael A. Eberle PacBio, 1305 O’Brien Drive, Menlo Park, CA 94025

StarPhase is a long-read pharmacogenomic diplotyper that provides highly accurate diplotype results from long-read observations, provides refined PGx diplotypes for GeT-RM benchmark samples, and generates full-length haplotype sequences and visualizations for complex pharmacogenes
ACMG 2025  |  2025

Targeted long-read sequencing of native DNA for genetic disease diagnostic and screening research

Jocelyne Bruand, Sarah B. Kingan, Jeff Zhou, Davy Lee, Heather Ferrao, Ian McLaughlin, Sijie Wei, Richa Pathak, Ravi Dalal, Tom Mokveld, Guilherme De Sena Brandine, Egor Dolzhenko, Nat Echols, Michael A. Eberle, Duncan Kilburn PacBio, 1305 O’Brien Drive, Menlo Park, CA 94025

Short tandem repeats (STRs) are DNA sequences composed of repetitions of 2 – 6 bp motifs. Expansions of STRs are the cause of over 60 monogenic diseases, including Huntington’s disease, fragile X syndrome, and amyotrophic lateral sclerosis1. In addition to their length, the pathogenicity of these STRs can be impacted by sequence composition, methylation status and mosaicism. One such example is the FMR1 repeat whose CGG repeat expansions are typically hypermethylated and where AGG interruption sequences can stabilize the repeat. Detecting all the characteristics associated with pathogenic repeat expansions traditionally required multiple assays, however high-accuracy long-read sequencing of unamplified DNA can resolve all these features in a single assay.
PAG 2025  |  2025

High-resolution microbiome species profiling at scale with the Kinnex kit for full- length 16S rRNA sequencing

Jeremy E Wilkinson1, Jocelyne Bruand1, Khi Pin Chua1, Heather Ferrao1, Davy Lee1, Jeff Zhou1, Kristopher Locken2, Shuiquan Tang2, Ethan Thai2, John Sherman2, Brett Farthing2, Elizabeth Tseng1 1 PacBio, 1305 O’Brien Drive, Menlo Park, CA 94025, USA, 2 Zymo Research Corporation, 17062 Murphy Avenue, Irvine, CA 92614, USA

Targeted 16S sequencing is a cost-effective approach for assessing the bacterial composition of microbial communities. This is especially true for low bacterial biomass samples where amplicon sequencing is the best option. However, the high similarity between the 16S rRNA genes of related bacteria means that sequencing the entirety of the 16S gene (~1.5 kb) with high accuracy is essential for species- or strain-level characterization. Many recent comparative studies have shown that PacBio full-length (FL) 16S sequencing outperforms other sequencing methods for taxonomic resolution and data accuracy
PAG 2025  |  2025

Long-read metagenome assembly produces hundreds of high-quality MAGs from different soil types

Daniel M. Portik1, Luis E. Valentin-Alvarado2,3,, Jillian F. Banfield2, Boyke Bunk4, Jorg Overmann4, and Jeremy E. Wilkinson1, 1. PacBio, 1305 O’Brien Dr, Menlo Park, California 93025 USA;, 2. Innovative Genomics Institute, University of California, Berkeley, California 94720 USA;, 3. Department of Plant and Microbial Ecology, University of California, Berkeley, California USA;, 4. Leibniz Institute, DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany

Metagenome assembly of soil has been historically difficult using short reads. The combination of high species diversity and ultra-low relative abundances poses a challenge and requires a higher sequencing depth to achieve success. Here, we demonstrate that the amount of HiFi data from the high-throughput Revio system is sufficient to assemble high-quality MAGs in complex microbiomes such as wetland soil.
PAG 2025  |  2025

Optimised Workflow for HMW DNA Extraction, Sample Preparation and Sequencing for Marine Vertebrates on the PacBio Revio System

Liam Anstiss1, Adrianne Doran1, Lara Parata1, Emma de Jong1, Deborah Moine2, James Miller3, Paul Gooding4, Shannon Corrigan5 and OceanOmics Centre, (1)University of Western Australia, Perth, Western Australia, Australia, (2)PacBio, Menlo Park, CA, (3)PacBio, Adelaide, SA, Australia, (4)Millennium Science, Adelaide, SA, Australia, (5)Minderoo Foundation, Perth, Western Australia, Australia

Here we describe our ocean genome laboratory workflow developed for processing marine vertebrates for HiFi sequencing on the PacBio Revio System. We outline methods optimised for High Molecular Weight (HMW) DNA extraction using the Nanobind PanDNA kit from various tissue types, our strategy for size selection, and the implementation of automated library preparation method using the Beckman Biomek i7 system.
AMP 2024  |  2024

Targeted long-read sequencing of native DNA for comprehensive characterization of repeat expansions

Sarah B Kingan1, Guilherme De Sena Brandine1, Jocelyne Bruand1, Jeff Zhou1, Valeriya Gaysinskaya1, Janet Aiyedun1, Julian Rocha1, Duncan Kilburn1, Egor Dolzhenko1, Zoi Kontogeorgiou2, Anita Szabo3, Christina Zarouchlioti3, Robert Thaenert4, Pilar Alvarez Jerez5, Kimberley Billingsley5, Sonia Lameiras6, Sylvain Baulande6, Alice Davidson3, Georgios Koutsis7, Georgia Karadima2, Stéphanie Tomé8, Michael A Eberle1 1. Pacific Biosciences (PacBio), Menlo Park, United States, 2. National and Kapodistrian University of Athens, 1st Department of Neurology, Athens, Greece, 3. University College London, Institute of Ophthalmology, United Kingdom, 4. Quest Diagnostics, Marlborough, United States, 5. National Institutes of Health, Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, United States, 6. Institut Curie, PSL Research University, ICGex Next-Generation Sequencing Platform, Paris, France, 7. National and Kapodistrian University of Athens, Neurogenetics Unit, 1st Department of Neurology, Eginition Hospital, School of Medicine, Athens, Greece 8. Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en myologie, Paris, France

Short tandem repeats (STRs) are DNA sequences composed of repetitions of 1 – 6 bp motifs. Expansions of STRs are the cause of over 60 monogenic diseases, including Huntington’s disease, fragile X syndrome, and amyotrophic lateral sclerosis1. In addition to their length, the pathogenicity of these STRs can be impacted by sequence composition, methylation status and mosaicism. One such example is the FMR1 repeat whose CGG repeat expansions are typically hypermethylated and where AGG interruption sequences can stabilize the repeat. Detecting all the characteristics associated with pathogenic repeat expansions traditionally required multiple assays, however long-read sequencing of unamplified DNA holds the promise to resolve all these features in a single assay.
AMP 2024  |  2024

Improved detection of low frequency mutations in ovarian and endometrial cancers by utilizing a highly accurate sequencing platform

Ovarian and endometrial cancers are the 4th highest (combined) cancer killer of Canadian women. In 2020, over 3000 women were diagnosed with an ovarian cancer, of which 75% were in the later stages. The goal of the DOvEEgene (Detecting Ovarian and Endometrial cancer Early using Genomics) project is to detect these cancers as early as the first stage through a low-cost, low invasiveness and widely available test, similar to what the Pap test has done for cervical cancers. In this assay, for each subject, an intra-uterine brush sample is collected along with a saliva sample. The genomic DNA is extracted from both these samples, captured using probes with a total size of 146.46 kb using SureSelect XT HS (see target design), sequenced at 20 million reads to a median DNA fragment depth of at least 80% at 1000x, and deduplicated using UMIs. In parallel, uncaptured libraries are also used for Low-pass whole genome sequencing (LP-WGS). Somatic and copy number variants are called, as well as germline variants for 10 genes, and microsatellite instability (MSI) status is determined for known microsatellite loci within the target region. Separately, clinical MSI testing is performed on each sample using a PCR-based assay. As the ability to detect early stage cancers relies on high sensitivity and specificity, we were interested in testing the PacBio Onso sequencing by binding (SBB) technology which promises much higher sequencing qualities and better performance in homopolymer regions, thus should potentially increase variant detection and MSI calling performance.
Keyword search
Author search

咨询专家

如果您有疑问、需要查看订单状态或想要购买仪器，我们随时乐意提供帮助。

姓名(Required)
这个字段是用于验证目的，应该保持不变。

在本网页上注册，即表示您同意，并同意 PacBio 根据我们的隐私政策收集和使用该信息.