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Friday, August 26, 2016

Scientists Turn to SMRT Sequencing to Decode Chardonnay Genome

A case study produced by QRIScloud, an Australia-based cloud computing service, offers interesting insight into a recent project that is using SMRT Sequencing to generate a reference-quality de novo genome assembly for the grape used to make Chardonnay wine. The sequencing effort was conducted by collaborating scientists at the Australian Wine Research Institute (AWRI) and the BC Genome Sciences Centre in Canada. This new assembly, which is still undergoing polishing and in-depth analysis, adds to very sparse genome resources for wine grapes. Until recently, the only genome assemblies available were draft-quality ones for the Pinot Noir varietal. With PacBio long-read…

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Thursday, August 25, 2016

Precision Medicine Review Highlights Need for Accuracy & Comprehensiveness in Genome Sequencing

Stanford’s Euan Ashley wrote a terrific review about the clinical use of genome sequencing for Nature Reviews Genetics. “Towards Precision Medicine” is well worth a read, covering topics from the ethnic background of the human reference genome to public interest in precision medicine.  He also covers technical angles such as mapping of sequence reads for variant calling across challenging regions of the genome with known clinical significance. Ashley’s premise is that many of the current standards in genomics — from sequencers to analysis tools and more — were developed for use in basic research, where the consequences of inaccurate information…

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Tuesday, August 2, 2016

SMRT Sequencing Accurately Detects Gene Copy Numbers in Complex Maize Genome

Scientists from Rutgers University and the University of California, Davis, used SMRT Sequencing to study structural variation in maize. They found that this approach delivered more complete information at lower cost than standard methods and generated new findings that could be important for crop breeding. From lead author Jiaqiang Dong, senior author Jo Messing, and collaborators, “Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads” was published in PNAS recently. They chose to evaluate SMRT Sequencing for copy number detection as an alternative to short-read sequencing, which doesn’t span long repeats, and BAC cloning, which…

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Monday, August 1, 2016

Histogenetics Ramps Up HLA Typing with SMRT Sequencing

PacBio customer HistoGenetics was just awarded a major, multi-year contract to perform HLA typing on as many as thousands of samples per week using SMRT Sequencing. The company is a pioneer and global leader in high-resolution sequence-based HLA typing services. As blog readers know, HLA typing involves analysis of highly polymorphic human leukocyte antigen (HLA) genes comprised within the major histocompatibility complex (MHC) on chromosome 6. Accurate HLA typing is essential for research on donor recipient tissue matching during transplantation, autoimmune disease-association studies, drug hypersensitivity research, and several other applications. But the complexity of the region, which contains thousands of…

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