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Tuesday, October 27, 2020

ASHG CoLab: PacBio HiFi reads for comprehensive characterization of genomes and single-cell isoform expression

In this ASHG 2020 CoLab presentation hear Principal Scientists, Aaron Wenger and Elizabeth Tseng share how highly accurate long reads (HiFi reads) provide comprehensive variant detection for both genomes and transcriptomes. Aaron Wenger describes how new improvements in protocols and analysis methods have increased scalability and accuracy of variant calling. As demonstrated in the precisionFDA Truth Challenge V2, HiFi reads (>99% accurate, 15 kb – 20 kb) now outperform short reads for single nucleotide and structural variant calling and match for small indels. This includes calling >30,000 small variants and >10,000 structural variants missed by short reads, many in medically…

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Tuesday, October 27, 2020

ASHG PacBio Workshop: Latest product and application updates

In this ASHG 2020 PacBio Workshop Jonas Korlach, CSO, shares how the new PacBio Sequel IIe System makes highly accurate long-read sequencing easy and affordable so?all scientists can gain comprehensive views of human genomes and transcriptomes. He goes on to provide updates on the applications including human WGS for variant detection, de novo genome assembly, single-cell full-length RNA sequencing, and targeted sequencing using PCR and No-Amp methods.

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Sunday, October 25, 2020

Video Poster: Capture long-read isoform sequencing (Iso-Seq) for uncovering human isoform diversity in the brain and characterizing SARS-CoV2 viral RNAs

Most genes in eukaryotic organisms produce alternative isoforms, broadening the diversity of proteins and non-coding RNAs encoded by the genome. In contrast to other RNA sequencing platforms that rely on short-read sequencing, long accurate reads from PacBio Single Molecule, Real-Time (SMRT) Sequencing can characterize full-length transcripts without the need for assembly and inference. The PacBio isoform sequencing (Iso-Seq) method generates full-length sequences for transcripts up to 10 kb in length, with scalable throughput using barcoding approaches. The Iso-Seq application can be employed for a wide variety of studies, including improvement of gene annotation, identification of novel isoforms and fusion transcripts,…

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Sunday, October 25, 2020

Movie: The new biology

This documentary film features the wave of cutting-edge technologies that now provide the opportunity to create predictive models of living systems, and gain wisdom about the fundamental nature of life itself. The potential impact for humanity is immense: from fighting complex diseases such as cancer, enabling proactive surveillance of virulent pathogens, and increasing food crop production.

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Sunday, October 25, 2020

Labroots Webinar: More comprehensive views of human genetic variation

In this BioConference Live webinar, PacBio CSO Jonas Korlach highlights how multi-kilobase reads from SMRT Sequencing can resolve many of the previously considered ‘difficult-to-sequence’ genomic regions. The long reads also allow phasing of the sequence information along the maternal and paternal alleles, demonstrated by full-length, fully phased HLA class I & II gene sequencing. In addition, characterizing the complex landscape of alternative gene products is currently very difficult with short-read sequencing technologies, and he describes how long-read, full-length mRNA sequencing can be used to describe the diversity of transcript isoforms, with no assembly required. Lastly, in the exciting area of…

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Sunday, October 25, 2020

ASHG Virtual Poster: Alternative splicing in FMR1 premutations carriers

In this ASHG 2016 virtual poster, Flora Tassone from UC Davis describes her study of the molecular mechanisms linked to fragile X syndrome and associated disorders, such as FXTAS. She is using SMRT Sequencing to resolve the FMR1 gene in premutation carriers because it’s the only technology that can generate full-length transcripts with the causative CGG repeat expansion. Plus: direct confirmation of predicted isoform configurations.

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Sunday, October 25, 2020

AGBT Virtual Poster: Single-molecule sequencing reveals the presence of distinct JC polyomavirus populations in patients with progressive multifocal leukoencephalopathy

At AGBT 2017, Lars Paulin from the University of Helsinki presented this poster on whole genome sequencing of the virus responsible for progressive multifocal leukoencephalopathy, a rare and dangerous brain infection. His team used long amplicon analysis to resolve the whole virus genome from three patient samples, pooled them for SMRT Sequencing, and identified variants and rearrangements. This work represents the first time the viral genome was sequenced from patients.

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Sunday, October 25, 2020

Webinar: PacBio targeted sequencing of long amplicons using PCR or hybrid capture

Targeted sequencing experiments commonly rely on either PCR or hybrid capture to enrich for targets of interest. When using short read sequencing platforms, these amplicons or fragments are frequently targeted to a few hundred base pairs to accommodate the read lengths of the platform. Given PacBio’s long readlength, it is straightforward to sequence amplicons or captured fragments that are multiple kilobases in length. These long sequences are useful for easily visualizing variants that include SNPs, CNVs and other structural variants, often without assembly. We will review methods for the sequencing of long amplicons and provide examples using amplicons that range…

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Sunday, October 25, 2020

Webinar: SMRT Sequencing applications in plant and animal sciences: an overview

In this webinar, Emily Hatas of PacBio shares information about the applications and benefits of SMRT Sequencing in plant and animal biology, agriculture, and industrial research fields. This session contains an overview of several applications: whole-genome sequencing for de novo assembly; transcript isoform sequencing (Iso-Seq) method for genome annotation; targeted sequencing solutions; and metagenomics and microbial interactions. High-level workflows and best practices are discussed for key applications.

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Sunday, October 25, 2020

Webinar: Using Iso-Seq analysis to build a better annotation

Long-read sequencing technologies like Iso-Seq analysis present researchers with a powerful tool for probing the transcriptomes of many species. The ability to sequence transcripts from end-to-end has revealed transcription complexity on a scale that was previously impossible. This sequence rich information has also improved our ability to predict transcript functions and biotypes. Researchers can now use Iso-Seq analysis to discover transcript models in almost any species with an accuracy on par with human and mouse annotations. In this webinar, Richard Kuo discusses the core concepts behind Iso-Seq analysis and how to use it to improve or build a new transcriptome…

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Sunday, October 25, 2020

ASHG PacBio Workshop: Characterization of a large, human-specific tandem repeat array associated with bipolar disorder and schizophrenia

In this ASHG workshop presentation, Janet Song of Stanford School of Medicine shared research on resolving a tandem repeat array implicated in bipolar disorder and schizophrenia. These psychiatric diseases share a number of genomic risk variants, she noted, but scientists continue to search for a specific causal variant in the CACNA1C gene suggested by previous genome-wide association studies. SMRT Sequencing of this region in 16 individuals identified a series of 30-mer repeats, containing a total of about 50 variants. Analysis showed that 10 variants were linked to protective or risk haplotypes. Song aims to study the function of these variants…

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Sunday, October 25, 2020

Webinar: Complete genomes within reach – Closing bacterial genomes from the lakes of Minnesota to NYC hospitals

In this webinar, Ben Auch, Research Scientist, Innovation Lab, University of Minnesota Genomics Center, Cody Sheik, Assistant Professor of Biology, University of Minnesota Duluth, and Harm van Bakel, Assistant Professor of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai provide details of the newly updated microbial whole genome sequencing pipeline, which leverages the multiplexing capabilities of the Sequel System, share new insights into the ecophysiology of Minnesota microbes using long-read sequencing, and show of how whole genome sequencing is used in pathogen surveillance programs at hospitals.

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Sunday, October 25, 2020

AGBT Presentation: The Sequel II System – The next evolution of SMRT Sequencing

In this AGBT presentation, Marty Badgett shares a look at the latest results from circular consensus sequencing (CCS) mode for highly accurate reads and data from our soon-to-be-released Sequel II System. As he demonstrates, CCS reads cover the same molecule many times, delivering high consensus accuracy despite noisy raw reads; on average, reaching 10 passes achieves Q30 accuracy. Badgett offers several examples where this is useful, such as pharmacogenomic gene analysis and resolving metagenomic communities. He also provides an update on the Iso-Seq method, which can now segregate transcripts into haplotype-specific alleles using a new tool called Iso-Phase.

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