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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: Long-read sequencing of the SARS-CoV-2 genome and the human immune repertoire

COVID-19 is caused by the infection of SARS-CoV-2, a member of the coronavirus family. Complete and accurate sequencing of the SARS-CoV-2 genome enables discovery and epidemiological tracing of mutations that may be important for antiviral and vaccine research. A complementary approach, sequencing the patients’ immune repertoire, allows for detection of neutralizing antibodies and understanding variation in the adaptive immune response. PacBio’s SMRT Sequencing uses circular consensus sequencing that can generate long, highly accurate (HiFi) reads. We find that a tiled multiplex PCR amplicon approach of ~1-2 kb fragments achieves a balanced tradeoff between ease of library preparation and robustness to…

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Sunday, October 25, 2020

PAG PacBio Workshop: Sequencing the Potentilla micrantha genome to study the evolution of fruiting in strawberry

Judson Ward, principal scientists at Driscoll’s Strawberries in California, introduces a genome assembly for Potentilla micrantha, which is closely related to strawberry but lacks fleshy ‘fruits’ or berries. Comparative genomics between P. micrantha and strawberry will yield significant information regarding the genetic mechanisms controlling fruit development. Using SMRT Sequencing Driscoll’s sequenced the 240 Mb P. micaranthagenome and produced a draft genome assembly, spanning the majority of the predicted sequence length. A comparison of sequence data produced using the Illumina HiSeq2000 and the PacBio RS platform demonstrated that PacBio sequencing produced a significantly longer N50 contig size and permitted a more complete genome…

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Sunday, October 25, 2020

AGBT Virtual Poster: Evaluating the potential of new sequencing technologies for genotyping and variation discovery in human data

Computational biologist Mauricio Carneiro, PhD, describes a Broad Institute technology comparison to determine how PacBio, Ion Torrent, and Illumina MiSeq perform in discovering and validating human SNPs. Noted PacBio advantages: no bias in GC regions, no systematic errors, and no sequence degradation over increased read length. In a study using samples from the 1,000 Genomes project, PacBio outperformed MiSeq and Ion Torrent in sensitivity and specificity.

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Sunday, October 25, 2020

Stanford Symposium: Dynamic chromosome methylation controls cell cycle progression

Stanford University developmental biologist Lucy Shapiro discusses a collaborative research effort with PacBio sequencing that revealed previously unknown aspects of how chromosome methylation regulates cell cycle progression in Caulobacter. The ability to detect DNA modifications through SMRT Sequencing proved critical in determining methylation states throughout the cell cycle.

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Sunday, October 25, 2020

AGBT Virtual Poster: Direct-Seq – towards library-prep free PacBio sequencing

Paul Coupland and his team at the Wellcome Trust Sanger Institute have developed a sequencing method on the PacBio System for small DNA molecules that avoids the need for a standard library preparation. To date this approach has been applied toward sequencing single-stranded and double-stranded viral genomes, bacterial plasmids, plasmid vector models for DNA-modification analysis, and linear DNA fragments covering an entire bacterial genome. Using direct sequencing it is possible to generate sequence data from as little as 1 ng of DNA, offering a significant advantage over current protocols which typically require 400–500 ng of sheared DNA for the library…

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Sunday, October 25, 2020

AGBT Conference: Automated de novo genome assemblies and bacterial epigenomes using PacBio sequencing

In this AGBT plenary talk, Jonas Korlach presented a number of collaborative studies between PacBio and other institutions to make use of highly accurate, long-read sequence data, which has led to a revival of finished genomes. Examples from the infectious disease or pathogen realm included Pertussis, Salmonella, and Listeria, all of which now have closed genomes from PacBio-generated data. Korlach also reported on epigenomic information in Salmonella and Listeria, indicating potential new forms of DNA modifications.

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Sunday, October 25, 2020

AGBT Conference: Whole human genome SMRT Sequencing reveals uncharacterized structural variations providing a path to more informed diagnostic testing

In this AGBT talk, Mount Sinai’s Eric Schadt uses PacBio sequencing on human genomes and reports finding uncharacterized structural variation that could have diagnostic utility. Schadt says that SMRT sequencing is advantageous for long-range genetic information, extreme GC content, and highly repetitive regions. He presents sequence data for a CEPH individual studied for repeat expansions, showing that long reads can resolve the majority of these regions.

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