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Friday, December 27, 2013

Breakpoint Detection in Cancer Structural Variants with PacBio May Yield Patient-Specific Data

A new publication from scientists at the University of California, San Diego, demonstrates the use of Single Molecule, Real-Time (SMRT®) Sequencing to identify structural variation (SV) breakpoints in cancer. “Amplification and thrifty single molecule sequencing of recurrent somatic structural variations” was published in Genome Research and comes from authors Anand Patel, Richard Schwab, Yu-Tsueng Liu, and Vineet Bafna. In the paper, the scientists report development of a new method — Amplification of Breakpoints, or AmBre — to detect important structural variant breakpoints. AmBre relies on a PCR-based approach for amplification of the structural variant, followed by sequencing on the PacBio®…

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Monday, December 9, 2013

New Publication Characterizes the Complex Methylomes of Helicobacter pylori

A new paper in Nucleic Acids Research describes the genome-wide methylation state of two strains of Helicobacter pylori, using Single Molecule, Real-Time (SMRT®) Sequencing. The paper represents the first comprehensive study of the myriad of DNA base modifications present across the genome of this major human pathogen. The collaborative study, entitled “The complex methylome of the human gastric pathogen Helicobacter pylori” was led by the laboratory of Sebastian Suerbaum at the Institute of Medical Microbiology & Hospital Epidemiology and German Center for Infection Research, Hannover, Germany, and includes researchers from New England Biolabs, the DSMZ German Collection of Microorganisms and…

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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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Tuesday, December 3, 2013

PacBio Partners with Sanger Institute and Public Health England to Finish 3,000 Bacterial Genomes

Sanger’s Genome Campus We are pleased to announce a new collaboration with the Wellcome Trust Sanger Institute and Public Health England to complete the sequences of 3,000 bacterial genome strains from PHE’s National Collection of Type Cultures (NCTC). Sequencing will be performed on the PacBio® RS II DNA Sequencing System at the Sanger Institute. The three-year project could double the number of finished microbial genomes in GenBank. The NCTC is one of the world’s premier collections for bacterial strains, but most bacteria in NCTC currently have no genome references. Combining reference genomes with the wealth of historical and biological information…

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