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Tuesday, June 1, 2021

Amplification-free protocol for targeted enrichment of repeat expansion genomic regions and SMRT Sequencing

Many genetic disorders are associated with repeat sequence expansions. Obtaining accurate DNA sequence information from these regions will facilitate researchers to further establish the relationship between these genetic disorders and underlying disease mechanisms. Moreover, repeat interruptions have also been shown to act as phenotypic modifiers in some disorders. Targeted sequencing is an economical way to obtain sequence information from one or more defined regions in a genome. However, most targeted enrichment and sequencing methods require some form of DNA amplification. Amplifying large regions with extreme GC content as seen in repeat expansion disorders is challenging and prone to introducing sequence…

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Tuesday, June 1, 2021

Comprehensive variant detection in a human genome with highly accurate long reads

Introduction: Long-read sequencing has revealed more than 20,000 structural variants spanning over 12 Mb in a healthy human genome. Short-read sequencing fails to detect most structural variants but has remained the more effective approach for small variants, due to 10-15% error rates in long reads, and copy-number variants (CNVs), due to lack of effective long-read variant callers. The development of PacBio highly accurate long reads (HiFi reads) with read lengths of 10-25 kb and quality >99% presents the opportunity to capture all classes of variation with one approach.Methods: We sequence the Genome in a Bottle benchmark sample HG002 and an…

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Tuesday, June 1, 2021

Amplification-free targeted enrichment powered by CRISPR-Cas9 and long-read Single Molecule Real-Time (SMRT) Sequencing can efficiently and accurately sequence challenging repeat expansion disorders

Genomic regions with extreme base composition bias and repetitive sequences have long proven challenging for targeted enrichment methods, as they rely upon some form of amplification. Similarly, most DNA sequencing technologies struggle to faithfully sequence regions of low complexity. This has been especially trying for repeat expansion disorders such as Fragile-X disease, Huntington disease and various Ataxias, where the repetitive elements range from several hundreds of bases to tens of kilobases. We have developed a robust, amplification-free targeted enrichment technique, called No-Amp Targeted Sequencing, that employs the CRISPR-Cas9 system. In conjunction with SMRT Sequencing, which delivers long reads spanning the…

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Friday, February 5, 2021

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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Friday, February 5, 2021

ASHG Virtual Poster: Enrichment of unamplified DNA and long-read SMRT Sequencing to unlock repeat expansion disorders

PacBio’s Jenny Ekholm presents this ASHG 2016 poster on a new method being developed that enriches for unamplified DNA and uses SMRT Sequencing to characterize repeat expansion disorders. Incorporating the CRISPR/Cas9 system to target specific genes allows for amplification-free enrichment to preserve epigenetic information and avoid PCR bias. Internal studies have shown that the approach can successfully be used to target and sequence the CAG repeat responsible for Huntington’s disease, the repeat associated with ALS, and more. The approach allows for pooling many samples and sequencing with a single SMRT Cell.

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Friday, February 5, 2021

ASHG PacBio Workshop: Towards precision medicine

Euan Ashley from Stanford University started with the premise that while current efforts in the field of genomics medicine address 30% of patient cases, there’s a need for new approaches to make sense of the remaining 70%. Toward that end, he said that accurately calling structural variants is a major need. In one translational research example, Ashley said that SMRT Sequencing with the Sequel System allowed his team to identify six potentially causative genes in an individual with complex and varied symptoms; one gene was associated with Carney syndrome, which was a match for the person’s physiology and was later…

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Friday, February 5, 2021

ASHG PacBio Workshop: Identification and characterization of informative genetic structural variants for neurodegenerative diseases

Michael Lutz, from the Duke University Medical Center, discussed a recently published software tool that can now be used in a pipeline with SMRT Sequencing data to find structural variant biomarkers for neurodegenerative diseases with a focus on Alzheimer’s disease, ALS, and Lewy body dementia. His team is particularly interested in short sequence repeats and short tandem repeats, which have already been implicated in neurodegenerative disease.

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Friday, February 5, 2021

Nature Webinar: Large interrupted pentanucleotide repeats of SCA10

Tetsuo Ashizawa, Director of the Neuroscience Research Program at Houston Methodist Research Institute, presents a novel amplification-free targeted enrichment method using CRISPR-Cas9 for the disease-causing repeat expansion in SCA10. Using long-read sequencing, he has been able to span multi-kilobase repetitive regions and identify interruption sequence motifs that correlate with alternative clinical phenotypes in individuals from varying ethnic backgrounds. Webinar registration required.

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Friday, February 5, 2021

AGBT Virtual Poster: Targeted SMRT Sequencing of difficult regions of the genome using a Cas9, non-amplification based method

Targeted sequencing has proven to be an economical means of obtaining sequence information for one or more defined regions of a larger genome. However, most target enrichment methods are reliant upon some form of amplification. Amplification removes the epigenetic marks present in native DNA, and some genomic regions, such as those with extreme GC content and repetitive sequences, are recalcitrant to faithful amplification. Yet, a large number of genetic disorders are caused by expansions of repeat sequences. Furthermore, for some disorders, methylation status has been shown to be a key factor in the mechanism of disease. We have developed a…

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Friday, February 5, 2021

AGBT Virtual Poster: Analysis method for amplification-free SMRT sequencing and assessment on repeat expansions in Huntington’s disease

Adam Ameur from the National Genomics Infrastructure at SciLifeLab presented this poster at AGBT 2017. In it, he details a validation study for the use of CRISPR/Cas9 to capture genomic targets without the use of amplification. Results from 12 Huntington’s patients indicate that this approach paired with SMRT Sequencing generates accurate repeat counts in the HTT gene.

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Friday, February 5, 2021

Webinar: Addressing “NGS Dead Zones” with third generation PacBio sequencing

SMRT Sequencing is a DNA sequencing technology characterized by long read lengths and high consensus accuracy, regardless of the sequence complexity or GC content of the DNA sample. These characteristics can be harnessed to address medically relevant genes, mRNA transcripts, and other genomic features that are otherwise difficult or impossible to resolve. I will describe examples for such new clinical research in diverse areas, including full-length gene sequencing with allelic haplotype phasing, gene/pseudogene discrimination, sequencing extreme DNA contexts, high-resolution pharmacogenomics, biomarker discovery, structural variant resolution, full-length mRNA isoform cataloging, and direct methylation detection.

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Friday, February 5, 2021

Podcast: Exploring the exome and the future of genomics with Jay Shendure

Jay Shendure, a Professor in the Department of Genome Sciences at the University of Washington School of Medicine explores the role of exome sequencing in clinical genomics. In this Podcast he discusses his views on the current and future roles of sequencing in diagnosing Mendelian disorders and investigation of complex regions of the genome.

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Friday, February 5, 2021

Webinar: Beyond Gene Editing: How CRISPR/Cas9 enables sequencing of difficult regions of the genome

In this webinar, Jenny Ekholm and Paul Kotturi provide an overview of the PacBio No-Amp targeted sequencing application and its uses for targeting hard-to-amplify genes. This approach couples CRISPR-Cas9 with Single Molecule, Real Time (SMRT) Sequencing to enrich targets, without the need for PCR amplification, and generate complete sequence information with base-level resolution.

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Friday, February 5, 2021

ASHG PacBio Workshop: Long-read sequencing for disease genome analysis: Our experiences

In this presentation, Naomichi Matsumoto from Yokohama City University speaks about the use of SMRT Sequencing to solve Mendelian diseases, including the story of how his lab discovered a 12.4 kb structural variant that’s responsible for progressive myoclonic epilepsy in two siblings. He also reports progress in understanding repeat expansion disorders by pairing SMRT Sequencing with new analysis tools designed to highlight repetitive areas.

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