The COVID-19 pandemic has brought new focus and resources to pathogen surveillance of all kinds. HiFi sequencing, which combines high accuracy, long read lengths, and single-molecule sequencing, is unique in its ability to provide comprehensive, high-resolution views of pathogens — either as isolates or as part of complex systems. Join Meredith Ashby (PacBio) and Haley Fiske (Illumina) as they discuss pathogen sequencing in the COVID era. Meredith Ashby (PacBio) – HiFi Sequencing for the COVID Era: High-Resolution Pathogen Surveillance Haley Fiske (Illumina) – Unlocking the Power of Genomics for Pathogen Detection and Surveillance
The COVID-19 pandemic continues to be a major global epidemiological challenge with the ongoing emergence of new strain lineages that are more contagious, more virulent, drug-resistant, and in some cases evade vaccine-induced immunity. In response, the HiFiViral SARS-CoV-2 kit was developed as a scalable solution for the Sequel II and Sequel IIe Systems. Unlike amplicon sequencing, the HiFiViral SARS-CoV-2 kit uses tiled probes, resulting in robust genome coverage across varying viral input quantities despite the presence of new variants. The use of highly accurate long reads, or HiFi reads, enables comprehensive variant detection, including single nucleotide variants, indels, and structural…
In this talk, Dr. Aaron Wenger, describes how PacBio HiFi reads (15 kb – 25 kb, >99.9% accuracy) provide the most complete view of human genetic variation, including small variants in difficult-to-map regions and structural variants genome-wide. Further, PacBio sequencing simultaneously detects epigenetic modifications without requiring a specialized library preparation step like bisulfite conversion. This ability is commonly used to characterize epigenetic marks in bacterial genomes. Recent improvements in read length and data analysis have extended the ability to include the 5mC methylation that is present at CpG sites in human genomes. Using a deep learning model that integrates sequencing…
In this talk, Dr. Elizabeth Tseng demonstrates a throughput increase for the scIso-Seq method by concatenating single-cell molecules, increasing yield a minimum of 6-fold per SMRT Cell 8M. She explains the bioinformatics workflow for analyzing concatenated scIso-Seq data, which begins with de-concatenation, followed by tagging of UMI and barcode information that can be processed by the isoseq3 pipeline for deduplication. Reads are then aligned against the reference genome, followed by SQANTI3 for transcript classification against a reference annotation (ex: GENCODE) which produces an isoform-level sparse matrix to be analyzed with single-cell tools such as Seurat. She also shows how to…
Pharmacogenomics (PGx) utilizes genomic information to assess an individual’s response to certain medications and can be used to predict adverse drug reactions or decreased efficacy. While numerous assays and genetic tests have been developed to interrogate pharmacogenes, several limitations exist, including lack of phasing information, and poor detection in complex regions with structural variants, pseudogenes, or gene conversions. In this talk, Dr. Nina Gonzaludo, describes amplicon and targeted enrichment capture SMRT Sequencing workflows that generate HiFi reads for high resolution of PGx alleles. To fully resolve CYP2D6, a highly polymorphic gene in a region with extensive homology, she discusses an…
With the September 2021 closing of PacBio’s acquisition of Omniome, PacBio intends to become the first company to offer both long-read and short-read sequencing platforms. What does this mean for customers? How is PacBio leadership thinking about delivering a differentiated set of products and applications into high-growth clinical markets? In this intimate conversation with genomics leaders, Christian Henry, and Richard Shen, they share their vision for the future as a combined company.
In this SMRT Science Journal Club talk, Mikhail Kolmogorov from the University of California Santa Cruz discusses his computational approach to the generation of lineage-resolved complete MAGs by precision phasing.
In this SMRT Science Journal Club talk, John Lovell from HudsonAlpha Institute for Biotechnology discusses his work constructing and analyzing de novo pecan genome assemblies and annotations to help accelerate tree breeding programs.
Understanding genome sequences and how they evolved is critical for harnessing that evolutionary process for agricultural improvement. Whether asking questions about the gain/loss of genes, the role of structural variation on phenotypic diversity, or identifying favorable alleles in exotic and wild species, DNA and RNA sequencing have proven to be extremely valuable tools for breeding programs all over the world. This panel-style webinar brings together three plant biologists to talk about their journeys into sequencing plant genomes and how these efforts have helped push plant breeding forward.
In this ESHG 2021 Workshop, PacBio Chief Scientific Officer Jonas Korlach, Ph.D., describes why HiFi sequencing improves the ability to detect pathogenic variants that previously went undetected with other technologies. He then turns the microphone over to Susan Hiatt, Ph.D. from HudsonAlpha Institute for Biotechnology. Dr. Hiatt discusses how she and her team used HiFi sequencing in their rare disease research to discover genomic variation missed by whole-exome or genome sequencing studies using short reads, allowing her team to uncover medical mysteries that had previously gone unexplained.
The highly polymorphic CYP2D6 gene impacts the metabolism of 25% of the mostly prescribed drugs. Thus, accurate identification of variant CYP2D6 alleles in individuals is necessary for personalized medicine. PacBio HiFi sequencing produces long and accurate reads to identify variant regions. Here, we describe an end-to-end workflow for the characterization of full-length CYP2D6 by HiFi sequencing.
There are many clinically important genes in “dark” regions of the human genome. These regions are characterized as dark due to a paucity of NGS coverage as a result of short-read sequencing or mapping difficulties. Low NGS sequencing yield can arise in these regions due to the presence of various repeat elements or biased base composition while inaccurate mapping can result from segmental duplications. Long-read sequencing coupled with an optimized, robust enrichment method has the potential to illuminate these dark regions.
Many genetic diseases are mapped to structurally complex loci. These regions contain highly similar paralogous alleles (>99% identity) that span kilobases within the human genome. Comprehensive screening for pathogenic variants is incomplete and labor intensive using short-reads or optical mapping. In contrast, long-range amplification and PacBio HiFi sequencing fully and directly resolve and phase a wide range of pathogenic variants without inference. To capitalize on the accuracy of HiFi data we designed a new amplicon analysis tool, pbAA. pbAA can rapidly deconvolve a mixture of haplotypes, enabling precise diplotyping, and disease allele classification.
In this talk, speakers will describe the importance of high accuracy and long read length for generating closed bacterial assemblies. Speakers will also share examples of how hard-to-assemble domains and plasmids impact important biological traits including, pathogen virulence and anti-microbial resistance. Finally, they will provide an overview of the advantages of highly accurate long-read sequencing for outbreak tracking.
In this talk, speakers provide an understanding of how highly accurate long-read sequencing of extended 16S amplicons enables the identification of metagenome community members at higher taxonomic resolution than short-read methods. You’ll also hear examples of how metagenome functions that impact human health can be driven by specific species or strains within a community and learn how the gut microbiome can impact drug efficacy.