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Friday, February 26, 2021

Direct sequencing and identification of damaged DNA bases.

DNA is under constant stress from both endogenous and exogenous sources. DNA base modifications resulting from various types of DNA damage are wide-spread and play important roles in affecting physiological states and disease phenotypes. Examples include oxidative damage (8- oxoguanine, 8-oxoadenine; aging, Alzheimer’s, Parkinson’s), alkylation (1-methyladenine, 6-O- methylguanine; cancer), adduct formation (benzo[a]pyrene diol epoxide (BPDE), pyrimidine dimers; smoking, industrial chemical exposure, chemical UV light exposure, cancer), and ionizing radiation damage (5-hydroxycytosine, 5- hydroxyuracil, 5-hydroxymethyluracil; cancer). Currently, these and other products of DNA damage cannot be sequenced with existing sequencing methods. In contrast, single molecule, real-time (SMRT) DNA sequencing can report…

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Friday, February 26, 2021

Full-length cDNA sequencing of alternatively spliced isoforms provides insight into human diseases.

The majority of human genes are alternatively spliced, making it possible for most genes to generate multiple proteins. The process of alternative splicing is highly regulated in a developmental-stage and tissue-specific manner. Perturbations in the regulation of these events can lead to disease in humans. Alternative splicing has been shown to play a role in human cancer, muscular dystrophy, Alzheimer’s, and many other diseases. Understanding these diseases requires knowing the full complement of mRNA isoforms. Microarrays and high-throughput cDNA sequencing have become highly successful tools for studying transcriptomes, however these technologies only provide small fragments of transcripts and building complete…

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Friday, February 26, 2021

Full-length cDNA sequencing of alternatively spliced isoforms provides insight into human cancer

The majority of human genes are alternatively spliced, making it possible for most genes to generate multiple proteins. The process of alternative splicing is highly regulated in a developmental-stage and tissue-specific manner. Perturbations in the regulation of these events can lead to disease in humans (1). Alternative splicing has been shown to play a role in human cancer, muscular dystrophy, Alzheimer’s, and many other diseases. Understanding these diseases requires knowing the full complement of mRNA isoforms. Microarrays and high-throughput cDNA sequencing have become highly successful tools for studying transcriptomes, however these technologies only provide small fragments of transcripts and building…

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Friday, February 26, 2021

Candidate gene screening using long-read sequencing

We have developed several candidate gene screening applications for both Neuromuscular and Neurological disorders. The power behind these applications comes from the use of long-read sequencing. It allows us to access previously unresolvable and even unsequencable genomic regions. SMRT Sequencing offers uniform coverage, a lack of sequence context bias, and very high accuracy. In addition, it is also possible to directly detect epigenetic signatures and characterize full-length gene transcripts through assembly-free isoform sequencing. In addition to calling the bases, SMRT Sequencing uses the kinetic information from each nucleotide to distinguish between modified and native bases.

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Friday, February 26, 2021

Characterization of the Poly-T variants in the TOMM40 gene using PacBio long reads

Genes associated with several neurological disorders have been shown to be highly polymorphic. Targeted sequencing of these genes using NGS technologies is a powerful way to increase the cost-effectiveness of variant discovery and detection. However, for a comprehensive view of these target genes, it is necessary to have complete and uniform coverage across regions of interest. Unfortunately, short-read sequencing technologies are not ideal for these types of studies as they are prone to mis-mapping and often fail to span repetitive regions. Targeted sequencing with PacBio long reads provides the unique advantage of single-molecule observations of complex genomic regions. PacBio long…

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Friday, February 26, 2021

A method for the identification of variants in Alzheimer’s disease candidate genes and transcripts using hybridization capture combined with long-read sequencing

Alzheimer’s disease (AD) is a devastating neurodegenerative disease that is genetically complex. Although great progress has been made in identifying fully penetrant mutations in genes such as APP, PSEN1 and PSEN2 that cause early-onset AD, these still represent a very small percentage of AD cases. Large-scale, genome-wide association studies (GWAS) have identified at least 20 additional genetic risk loci for the more common form of late-onset AD. However, the identified SNPs are typically not the actual risk variants, but are in linkage disequilibrium with the presumed causative variant (Van Cauwenberghe C, et al., The genetic landscape of Alzheimer disease: clinical…

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Friday, February 26, 2021

A method for the identification of variants in Alzheimer’s disease candidate genes and transcripts using hybridization capture combined with long-read sequencing

Alzheimer’s disease (AD) is a devastating neurodegenerative disease that is genetically complex. Although great progress has been made in identifying fully penetrant mutations in genes such as APP, PSEN1 and PSEN2 that cause early-onset AD, these still represent a very small percentage of AD cases. Large-scale, genome-wide association studies (GWAS) have identified at least 20 additional genetic risk loci for the more common form of late-onset AD. However, the identified SNPs are typically not the actual causal variants, but are in linkage disequilibrium with the presumed causative variant (Van Cauwenberghe C, et al., The genetic landscape of Alzheimer disease: clinical…

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Friday, February 26, 2021

Screening for causative structural variants in neurological disorders using long-read sequencing

Over the past decades neurological disorders have been extensively studied producing a large number of candidate genomic regions and candidate genes. The SNPs identified in these studies rarely represent the true disease-related functional variants. However, more recently a shift in focus from SNPs to larger structural variants has yielded breakthroughs in our understanding of neurological disorders.Here we have developed candidate gene screening methods that combine enrichment of long DNA fragments with long-read sequencing that is optimized for structural variation discovery. We have also developed a novel, amplification-free enrichment technique using the CRISPR/Cas9 system to target genomic regions.We sequenced gDNA and…

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Friday, February 26, 2021

Mitochondrial DNA sequencing using PacBio SMRT technology

Mitochondrial DNA (mtDNA) is a compact, double-stranded circular genome of 16,569 bp with a cytosine-rich light (L) chain and a guanine-rich heavy (H) chain. mtDNA mutations have been increasingly recognized as important contributors to an array of human diseases such as Parkinson’s disease, Alzheimer’s disease, colorectal cancer and Kearns–Sayre syndrome. mtDNA mutations can affect all of the 1000-10,000 copies of the mitochondrial genome present in a cell (homoplasmic mutation) or only a subset of copies (heteroplasmic mutation). The ratio of normal to mutant mtDNAs within cells is a significant factor in whether mutations will result in disease, as well as…

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Friday, February 26, 2021

Full-Length RNA-seq of Alzheimer brain on the PacBio Sequel II System

The PacBio Iso-Seq method produces high-quality, full-length transcripts and can characterize a whole transcriptome with a single SMRT Cell 8M. We sequenced an Alzheimer whole brain sample on a single SMRT Cell 8M on the Sequel II System. Using the Iso-Seq bioinformatics pipeline followed by SQANTI2 analysis, we detected 162,290 transcripts for 17,670 genes up to 14 kb in length. More than 60% of the transcripts are novel isoforms, the vast majority of which have supporting cage peak data and polyadenylation signals, demonstrating the utility of long-read sequencing for human disease research.

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Friday, February 26, 2021

A complete solution for high-quality genome annotation using the PacBio Iso-Seq method

The PacBio Iso-Seq method produces high-quality, full-length transcripts of up to 10 kb and longer and has been used to annotate many important plant and animal genomes. We describe here the full Iso-Seq ecosystem that enables researchers to achieve high-quality genome annotations. The Iso-Seq Express workflow is a 1-day protocol that requires only 60-300 ng of total RNA and supports multiplexing of different tissues. Sequencing on a single SMRT Cell 8M on the Sequel II System produces up to 4 million full-length reads, sufficient to exhaustively characterize a whole transcriptome on the order of 15,000-17,000 genes with 100,000 or more…

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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

AGBT PacBio Workshop: SMRT Sequencing roadmap: better throughput, lower costs

In this AGBT 2017 talk, PacBio CSO Jonas Korlach provided a technology roadmap for the Sequel System, including plans the continue performance and throughput increases through early 2019. Per SMRT Cell throughput of the Sequel System is expected to double this year and again next year. Together with a new higher-capacity SMRT Cell expected to be released by the end of 2018, these improvements result in a ~30-fold increase or ~150 Gb / SMRT Cell allowing a real $1000 real de novo human genome assembly. Also discussed: Additional application protocol improvements, new chemistry and software updates, and a look at…

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Friday, February 5, 2021

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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