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Thursday, November 7, 2019

Customer Experience: At CSHL, new achievements with long-read sequencing

Michael Schatz from Cold Spring Harbor Laboratory talks about using SMRT Sequencing to generate the world’s best crop genome assembly, discovering thousands of gene elements that had never been seen before. He also reports on how long reads made it possible to interrogate a highly complex breast cancer cell line that was too challenging to sequence with previous platforms.

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Thursday, November 7, 2019

Podcast: Going beyond the $1,000 genome with Mark Gerstein

Mark Gerstein is the co-director of the Yale Computational Biology and Bioinformatics program where he focuses on better annotation of the human genome and better ways to mine big genomics data. He has played a big role in some of the large genomics initiatives since the first human genome project, including ENCODE and the 1,000 Genomes Project. “I’m very enthusiastic, of course, about the thousand dollar genome, but I don’t think that a true human genome has arrived for a thousand dollars,” Mark says at the outset of this Mendelspod interview. “The great excitement of next generation sequencing—which is deserved—has…

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Thursday, November 7, 2019

Podcast: Marc Salit discusses creating the foundation of genomics

Marc Salit is the leader of the Genome Scale Measurement Group at the National Institute of Standards and Technology or NIST. In this Mendelspod podcast, he explains how NIST played a pivotal, foundational role in enabling the ‘Century of Physics.’ Now Marc and NIST are looking for the right set of standards to enable the already-upon-us “Century of Biology.” The human reference genome is an example of a standard that Marc and his team are developing. Currently they are piloting what they call “Genome in a Bottle,” a physical reference standard to which all other human genomes can be measured.…

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Thursday, November 7, 2019

Xtalks Webinar: Long genomic DNA fragment capture and SMRT Sequencing enables accurate phasing of cancer and HLA loci

In this webinar, the presenters describe a targeted sequencing workflow that combines Roche NimbleGen’s SeqCap EZ enrichment technology with PacBio’ SMRT Sequencing to provide a more comprehensive view of variants and haplotype information over multi-kilobase, contiguous regions. They demonstrate that 6 kb fragments can also be utilized to enrich for long fragments that extend beyond the targeted capture site and well into (and often across) the adjacent intronic regions. When combined with SMRT Sequencing, multi-kilobase genomic regions can be phased and variants, including complex structural variants, can be detected in exons, introns and intergenic regions.

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Thursday, November 7, 2019

ASHG Conference: Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using PacBio long read sequencing

During this presentation from ASHG 2015, Maria Nattestad of Cold Spring Harbor Laboratory described the study of a Her2-amplified breast cancer cell line using long-read sequencing from PacBio. With reads as long as 71 kb, she was able to characterize extensive and complex rearrangements and found more than 11,000 structural variants. She also used the Iso-Seq method to find gene fusions, including some novel ones.

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Thursday, November 7, 2019

ASHG Virtual Poster: De novo assembly of a diploid Asian genome

Yunfei Guo, from the University of Southern California, presents his ASHG 2015 poster on a de novo assembly of a diploid Asian genome. The uniform coverage of long-read sequencing helped access regions previously unresolvable due to high GC bias or long repeats. The assembly allowed scientists to fill some 400 gaps in the latest human reference genome, including some as long as 50 kb.

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Thursday, November 7, 2019

ASHG PacBio Workshop: Of reference genomes and precious metals

Rick Wilson, Director of the McDonnell Genome Institute at Washington University in St. Louis titled his talk “Of reference genomes and precious metals” and walked the audience through definitions and standards for the various quality levels for de novo assembled human genomes, e.g., platinum, gold, and silver. He noted that this was a good topic for this session because of the important role PacBio has played in the community’s work to create reference-grade genomes. For example, PacBio technology has enabled them to sequence additional genomes (CHM1, CHM13) to a very high quality level. Although these sequences were essential for further…

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Thursday, November 7, 2019

Customer Experience: Benefits of long reads

Yunfei Guo, a grad student at the University of Southern California, discusses the benefits of SMRT Sequencing: very long reads that make it possible to resolve long repetitive regions and discover structural variants, and a random error mode that allows for extremely high accuracy.

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Thursday, November 7, 2019

ASHG PacBio Workshop: Medical diagnostic challenges and structural variation detection using the PacBio Platform

Richard Gibbs, Director of Baylor College of Medicine’s Human Genome Sequencing Center, talked about the transition to genomic medicine. This hasn’t been as simple as people would like due to such issues as the incomplete reference genome, the difficulty in characterizing some variation, and the lack of knowledge about the function of some genes. At Baylor, most of the human genome sequencing is done for children with Mendelian disorders. He said that among 7,000 samples processed using short-read exome sequencing, only about 25% of these cases are solved. The relatively low diagnosis rate is likely due to structural variation and…

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Thursday, November 7, 2019

ASHG PacBio Workshop: Going beyond the $1,000 genome? – the future of high quality de novo human genomes, epigenomes and transcriptomes?

Jonas Korlach, Chief Scientific Officer at PacBio, discussed the technology waves that have followed the initial human genome sequencing project, where we are today, and where we are going. Today, we are in what Korlach calls the 4th wave, where more comprehensive whole-genome re-sequencing is occurring, and we are nearing the 5th, when we will actually be able to free ourselves from reference genomes and sequence everything de novo.

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Thursday, November 7, 2019

PAG Conference: Diploid genome assembly and comprehensive haplotype sequence reconstruction

Jason Chin, senior director of bioinformatics at PacBio, talks about using long-read sequence data to generate diploid genome assemblies to produce comprehensive haplotype sequence reconstructions. In the presentation, Chin describes the FALCON Unzip process that combines SNP phasing with the assembly process and allows for determination of the haplotype sequences and identification of structural variants. He presents an example of diploid assembly from inbred Arabidopsis strains.

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