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Tuesday, February 18, 2014

AGBT Day 3 Highlights: Single Contigs, Dazzling Assemblers, Novel Isoforms & Honey Algorithms

Friday morning’s talks were exceptional, and included genomics heavy-hitters Dick McCombie and Gene Myers — both scientists who were truly influential in sequencing the human genome so many years ago. They have kept pushing boundaries, and their talks were fascinating. Cold Spring Harbor Laboratory’s McCombie offered a presentation based on a late-breaking abstract showing the importance of de novo assembly — rather than resequencing, which can miss structural differences — using SMRT® Sequencing. He showed data from genome sequences of two strains of yeast (S. cerevisiae and S. pombe), both of which were generated using P5-C3 chemistry with BluePippin™ size…

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Tuesday, February 11, 2014

AGBT 2014 Preview: Long reads, long flight, long days!

We are flying cross-country to Marco Island, Florida, to attend the fifteenth annual Advances in Genome Biology and Technology conference and, as we have done for years now, we are proud to be sponsoring the event. This year we look forward to connecting with the many researchers who already work with SMRT® Sequencing data, and to meeting others whose scientific efforts could benefit from our technology’s uniquely long reads and base modification information. Here are some of the presentations we’ll be attending: Evan Eichler, University of Washington, “Advances in Sequencing Technology Identify New Mutations, Genes and Pathways Related to Autism” …

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Thursday, January 16, 2014

Looking Ahead: The 2014 PacBio Technology Roadmap

By Jonas Korlach, Chief Scientific Officer 2013 was an eventful and exciting year for PacBio. As I described in the 2013 roadmap post a year ago, we have applied numerous improvements to SMRT® Sequencing, resulting in longer read lengths, greater sequencing throughput, new and improved data-analysis methods, and more efficient workflows. We are very pleased that these advances resulted in so many publications, conference presentations, and social media contributions, with the number of peer-reviewed scientific publications from the scientific community now exceeding 100. On behalf of all of us at Pacific Biosciences, I would like to express my heartfelt gratitude…

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Wednesday, December 4, 2013

In RNA-seq Study, Long PacBio Reads Allow for Detection of Full-Length and Novel Isoforms

A new paper out in PNAS details the usefulness of long reads for isoform sequencing. “Characterization of the human ESC transcriptome by hybrid sequencing” comes from lead author Kin Fai Au and senior author Wing Wong at Stanford University as well as a number of collaborators. The authors detail the problem that they see with current RNA-seq studies: the inability to capture full-length mRNA isoforms (averaging about 2,500 bases) by using reads of just a few hundred base pairs. “We are still far from achieving the original goals of RNA-Seq analysis, namely the de novo discovery of genes, the assembly…

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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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Thursday, October 17, 2013

Stanford Team Finds Novel Transcripts Using Long-Read Isoform Sequencing

An advance online publication in Nature Biotechnology from Michael Snyder’s lab at Stanford University demonstrates the utility of long-read sequencing for assessing transcribed regions across the human genome. Long PacBio reads were able to completely cover full-length RNA molecules, characterizing genetic regions that have not been previously annotated. The paper, entitled “A single-molecule long-read survey of the human transcriptome,” reports the application of Single Molecule, Real-Time (SMRT®) Sequencing to studying RNA, comparing it to results from libraries sequenced with a 454® instrument. The scientists sequenced cDNA synthesized from pooled RNA gathered from 20 human organs and tissues in order to…

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