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Wednesday, November 20, 2013

New Publication Demonstrates Long-Read Sequences Needed to Thoroughly Resolve Short Tandem Repeats

In a new paper reporting a protocol for using short-read sequence data to locate short tandem repeats (STRs), scientists find that long-read sequence information is necessary to resolve regions with repeat complexity, extreme GC content, and other challenging factors. Their solution is to use short-read data to find STRs, and then to use long-read sequencing to fully characterize those repeat expansions. The Bioinformatics publication is entitled “Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing” and came from scientists Koichiro Doi, Shinichi Morishita, et al. at the University of Tokyo. They focused on resolving STRs across…

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Thursday, November 14, 2013

ASHG Workshop Recordings: Resolving Structural Variation in Human Genomes

We hosted a structural varation workshop at the annual meeting of the American Society of Human Genetics, and were pleased to see that the speakers’ presentations really resonated with attendees – the event was standing-room-only! Jonas Korlach, PacBio CSO, opened the session by sharing a brief update on SMRT® technology, noting that the new P5-C3 chemistry delivers 50% of bases in 10 kb or longer reads. View presentation recording Evan Eichler, Howard Hughes Medical Investigator from the University of Washington discussed his use of the PacBio® system to study difficult-to-sequence regions of the human and chimp genomes. Eichler has identified a…

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Thursday, November 7, 2013

Event Recap: Fall User Group Meeting Presentations & Review

In September we were excited to have 100+ customers gather in Palo Alto, Calif., to discuss their use of Single Molecule, Real-Time (SMRT®) Sequencing and hear about what’s next for the PacBio® RS II. Many thanks to all the scientists who attended and shared their experiences. For anyone who couldn’t make it, we’ve included some highlights from each talk below (and links to full presentations when possible): Chongyuan Luo from the Ecker lab at the Salk Institute for Biological Studies spoke about studying the genome and epigenome of several Arabidopsis thaliana strains using SMRT Sequencing. Luo noted that Arabidopsis is…

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Wednesday, November 6, 2013

At Institute for Genome Sciences, Long Reads Offer New Path to Finished Genomes

The Genomics Resource Center (GRC) at the Institute for Genome Sciences (IGS) has a scientific pedigree and a sample-to-interpretation service commitment that place it in a league of its own. The team operates under a simple mantra: ‘If it can be sequenced, we can do it.’ Both GRC and IGS were founded in 2007 when a high-powered team of investigators formerly at The Institute for Genomic Research (TIGR), led by Claire Fraser, joined the University of Maryland School of Medicine. “The group of faculty and senior staff that came here to start the institute was heavily focused on infectious disease…

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Monday, November 4, 2013

Comparative Transcriptome Analysis: Insights from a Single SMRT Cell

In a new paper published in the journal Gene, scientists from Rutgers University and King’s College London report the use of a single SMRT® Cell to sequence and assemble more than 400 wheat-storage protein transcripts from 10 strains of the crop. In “PacBio sequencing of gene families — A case study with wheat gluten genes,” authors Wei Zhang, Paul Ciclitira, and Joachim Messing note that traditional studies of these cDNA sequences are so costly and labor-intensive that they have not allowed for intensive study of “the variation of each orthologous gene copy among cultivars.” That kind of study for complex…

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