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Wednesday, January 5, 2022

Computational Advances in Genome and Transcriptome Using HiFi Sequencing

PacBio HiFi sequencing has been used to generate the latest and most complete version of the human genome, characterize population-level structural variations, diplotype pharmacogenetic loci, and elucidate complex alternative splicing at the single-cell level. The two main characteristics of HiFi data – long read length and high accuracy – are critical for applications that either require near-perfect consensus sequencing or long-range phasing information. However, existing computational tools that were designed for short-reads often failed to either utilize the long-range information or employed heuristics that did not apply to HiFi data. Thus, a new generation of alignment, assembly, splicing, and annotation tools had to be…

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Tuesday, November 16, 2021

PacBio HiFiViral SARS-CoV-2 Kit

We created the HiFiViral SARS-CoV-2 Kit for labs working on the front line of the COVID-19 pandemic — tracking and identifying the spread of novel variants in their communities. The kit is an easy-to-use, scalable, and highly accurate solution for sequencing the entire SARS-CoV-2 genome. The differentiated design approach is resilient to novel variants enabling comprehensive detection of all types of mutations.

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Tuesday, November 2, 2021

Integrated Rare Disease using Long-Read Genome Sequencing

Genomic variation beyond single nucleotide variants, including structural variation (SV), copy number variants (CNV), and repeat expansions, plays a significant role in rare disease. However, current technologies require multiple tests to fully access these variants, resulting in complex testing algorithms and the potential for missed diagnoses. Long-read genome sequencing offers the ability to accurately detect SNV, CNV, SV, and expansions with a single test. This presentation will highlight the integrated analyses offered by HiFi sequencing, using case examples demonstrating the potential for a unified test.

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Tuesday, November 2, 2021

Scalable RNA Isoform Sequencing using Intramolecular Multiplexed cDNAs

While RNA-sequencing has dramatically accelerated our understanding of biology, quantitation and discovery of full-length RNA isoforms resulting from alternative splicing remain poorly resolved. Alternative splicing is a core regulatory process that modulates the structure, expression, and localization of expressed proteins through differential exon and/or UTR splicing during transcript maturation. Beyond being an integral component of cellular development and homeostatic maintenance, RNA splicing is implicated in a wide range of pathologies with hallmark isoforms being linked to cardiovascular, neurological, and immunological diseases. Current limitations in isoform quantitation and discovery arise from the inability of existing sequencing platforms to scalably sequence full-length…

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Tuesday, November 2, 2021

Uncovering Neurological Disorders Through an Examination of VNTRs

Many neurological diseases result from expansion of unstable variable nucleotide tandem repeats (VNTRs) that influence gene transcription of neighboring genes. In this talk, Dr. Henne Holstege presents research that investigated VNTRs across several genomes including a 115-year-old cognitively healthy individual. She and her group found that the genes that contained most VNTRs, of which PTPRN2 and DLGAP2 are the most prominent examples, were found to be predominantly expressed in the brain and associated with a wide variety of neurological disorders.

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Tuesday, November 2, 2021

HiFi Sequencing: See What You’ve Been Missing

PacBio Vice President of Segment Marketing, Dr. Jennifer Stone, demonstrates how HiFi sequencing is changing the game in human genetics by sharing some of the exciting milestones and seminal publications our technology has produced this year.

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Thursday, October 28, 2021

HiFiViral: A Novel Method for Surveillance of SARS-CoV-2 that is Robust Across Sample Input Quantities and the Evolution of New Variants

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…

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Thursday, October 28, 2021

Methylation Detection with PacBio HiFi Sequencing

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…

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Thursday, October 28, 2021

Allele-Specific, Isoform-Resolution Single-Cell RNA-Seq Analysis Using Long-Read Sequencing on Concatenated Single-Cell Molecules

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…

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Thursday, October 28, 2021

Using HiFi Reads for Improved and Accurate Haplotyping and Phasing of Pharmacogenomic Alleles

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…

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Thursday, October 28, 2021

A High-Resolution Panel for Uncovering Repeat Expansions that Cause Ataxias

The hereditary ataxias are a group of rare neurological diseases with similar symptoms. Many of these ataxic syndromes are caused by expansions of short tandem repeat (STR) in a number of different genes. Molecular genetic testing to accurately determine the genetic cause of known ataxias is often employed to support clinical diagnoses. We have recently developed an ataxia expansion panel using the PacBio No-Amp targeted sequencing approach to capture and sequence repeat expansion loci associated with fifteen ataxia diseases. The method utilizes CRISPR-Cas9 nuclease and pairs of guide RNAs to excise DNA fragments containing the repeat sequences within ataxia genes.…

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Thursday, October 28, 2021

SFAF NGS Tech Panel

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

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