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Sunday, October 25, 2020

AGBT Virtual Poster: Genome variation in chronic viral infection – SMRT Sequencing for HCV

Ellen Paxinos, a scientist at PacBio, shares her AGBT poster on work done in collaboration with reference lab Monogram Biosciences using Single Molecule, Real-Time (SMRT) sequencing to detect minor species and variants in HCV. Using two genotypes mixed together, the team was able to detect variants down to 1% and to identify both viral haplotypes from the data. Paxinos says the study is a model for looking at genomic variation in chronic viral infection.

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Sunday, October 25, 2020

AGBT Virtual Poster: Single-molecule HIV-1 full genome sequence from linked transmission pairs

PacBio scientist Ellen Paxinos discusses a study presented at AGBT that gnerated single-molecule full genome sequencing of HIV 1 from two pairs of linked transmission from a Zambian cohort. Sequencing was done on full-length amplicons from the virus, and clustering accurately placed the virus from each pair together, distinguishing between the two pairs. Paxinos notes that 50 MB of sequence data was generated in less than four hours.

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Sunday, October 25, 2020

AGBT Conference: High-throughput NGS for screening of microbial pathogens

Ulf Gyllensten from Uppsala University used SMRT Sequencing to study multi-drug-resistant bacteria. Time to results was faster than other NGS platforms and generally resulted in complete genome assemblies, even for an organism with a 70% AT-rich genome. He also applied SMRT Sequencing for the characterization of HPV subtypes, important in cervical cancer.

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Sunday, October 25, 2020

AGBT Virtual Poster: An improved circular consensus algorithm with an application to detect HIV-1 Drug Resistance Associated Mutations (DRAMs)

In this poster presentation, PacBio scientist Ellen Paxinos describes an improved algorithm for circular consensus reads. Using this new algorithm, dubbed CCS2, it is possible to reach arbitrarily high quality across longer insert lengths at a lower cost and higher throughput than Sanger Sequencing. She shows results from the application of CCS2 to the characterization of the HIV-1 K103N drug-resistance associated mutation, which is both important clinically, and represents a challenge due to regional sequence context.

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Sunday, October 25, 2020

AGBT Virtual Poster: Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements

In this AGBT poster, PacBio bioinformatician Matthew Seetin presents a new assembly for Aedes aegypti cell line, the mosquito responsible for spreading viruses like Dengue and Zika. SMRT Sequencing generated a gapless assembly with a contig N50 of 1.4 Mb, compared to 82 kb in the previous assembly. The genome features a number of transposable elements and long tandem repeats.

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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

Tutorial: Circular Consensus Sequence analysis application [SMRT Link v5.0.0]

This tutorial provides an overview of the Circular Consensus Sequence (CCS) analysis application. The CCS algorithm is used in applications that require distinguishing closely related DNA molecules in the same sample. Applications of CCS include profiling microbial communities, resolving viral populations and accurately identifying somatic variations within heterogeneous tumor cells. This tutorial covers features of SMRT Link v5.0.0.

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