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Tuesday, October 27, 2020

ASHG PacBio Workshop: Applications of third generation sequencing in unsolved disease

In this ASHG 2020 PacBio Workshop Emily Farrow of Children’s Mercy Kansas City shares how the incorporation of long-read sequencing into the Genomic Answers for Kids research study is increasing diagnostic yields through the identification of novel genetic variation. Emily highlights several cases in which PacBio HiFi sequencing was able to provide insights where short-read sequencing alone was inconclusive, due to limitations stemming from repetitive regions and large structural variants.

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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 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

ASHG PacBio Workshop: Highlighting unexplored genomic regions with SMRT Sequencing – informatics for structural event detection in PacBio

Ali Bashir from the Icahn Institute for Genomics and Multiscale Biology at Mount Sinai describes a tool to detect tandem repeats (PACMonSTR), which he believes are dramatically underrepresented in the human genome reference but that can be discovered with PacBio sequencing. In a collaboration with Cold Spring Harbor Laboratory and Cornell, Bashir and his team generated shotgun, whole-genome sequence data from human genomic DNA using PacBio sequencing. Their goal was to find structural variation features that are not present in the existing reference. He shows numerous examples wherein the long PacBio reads were able to resolve inversions in the sample,…

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Sunday, October 25, 2020

Podcast: Major sequencing projects should be done with long reads

Dan Geraghty explains that while there have been decades’ worth of studies associating the genetics of the major histocompatibility complex (MHC), and the highly polymorphic HLA class 1 and 2 genes, we still haven’t found the key mutations for a variety of different autoimmune diseases such as type 1 diabetes, rheumatoid arthritis, multiple sclerosis, and others. Enormous amounts of linkage disequilibrium in these regions are one factor, as is getting information in phase, so larger stretches of sequence are needed. Recently Geraghty has begun using SMRT Technology with hopes of drilling down to the causal genetics. 

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Sunday, October 25, 2020

AGBT Virtual Poster: Clinical sequencing using Pacific Biosciences RS II for HLA typing and monitoring of drug resistance in chronic myeloid leukemia (CML)

Ulf Gyllensten from Uppsala University describes his AGBT poster showing the use of SMRT Sequencing for HLA allele typing. He says long reads are essential for sequencing the HLA genes because they link exons in a single read and do not introduce bias, as short-read sequencers can. Looking at fusion transcripts from CML patients generated information that couldn’t be achieved with any other technology, he adds.

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Sunday, October 25, 2020

Podcast: Frontiers of sequencing – Putting long reads and graph assemblies to work

The Mike Schatz lab at Cold Spring Harbor is well know for de novo genome assemblies and their work on structural variation in cancer genomes. In this Mendelspod podcast, lab leader, Mike Schatz, and doctorate student, Maria Nattestad tell of two new projects that include the de novo assembly of a very difficult but important flatworm genome and, secondly, making better variant calls for oncogenes such as HER2.

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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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