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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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Wednesday, October 9, 2013

Resolving Complex Regions in the Human Genome: SMRT Sequencing Fills Major Mucin Gap

Scientists from University of North Carolina at Chapel Hill, Duke University, and other institutions have teamed up to sequence an important region of the human genome that has until now proven impenetrable. In a paper entitled “Genome Reference and Sequence Variation in the Large Repetitive Central Exon of Human MUC5AC,” published in the American Journal of Respiratory Cell and Molecular Biology, corresponding authors Wanda O’Neal and Judith Voynow along with their collaborators describe the use of Single Molecule, Real-Time (SMRT®) Sequencing to characterize a complex mucin exon. MUC5AC, located on the P arm of chromosome 11, encodes one of the…

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Monday, August 19, 2013

Scientists Assess Error Modes in Sequencing Platforms and Find SMRT Sequencing ‘Least Biased’

A paper from scientists at the Broad Institute reports a rigorous study of bias across all major sequencing platforms. In “Characterizing and measuring bias in sequence data,” published in Genome Biology, lead author Michael Ross and his colleagues report that SMRT® Sequencing on the PacBio® sequencer is the “least biased” in coverage of all the technologies studied. The authors assessed sequences for coverage bias, or uniformity of read distribution, and error bias, or incorrect call at a given position. For coverage bias, they report that PacBio performed best in extreme GC content (both GC-rich and GC-poor) and suggest this may…

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Tuesday, July 30, 2013

Single-Molecule Sequencing Technology Q&A with Nobel Laureate Rich Roberts

BioMed Central has published an interesting Q&A session on its Biome blog with Nobel Laureate Richard Roberts about why he believes in SMRT Sequencing and thinks non-users should take another look at it, too. He also discusses the critical need for funding to support the functional annotation of the genomes being sequenced, including for new bioinformatics tools. “We should be greatly increasing our efforts to gain functional insights into the millions of genes we are discovering by sequencing and for which we either have no idea of what they do, or many of our predictions are simply wrong,” he says.…

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Tuesday, May 14, 2013

Nature Methods Paper Demonstrates a Cost-Effective Process for Finishing Genomes

A paper recently published in Nature Methods offers a deep dive into the use of our HGAP and Quiver tools to generate a high-quality genome assembly with an automated, simplified workflow. (“Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data,” Chin et al., advance online publication.) The publication, which includes lead author Chen-Shan Chin and others at Pacific Biosciences as well as collaborators at the Joint Genome Institute and the Eichler lab at the University of Washington, uses Single Molecule, Real-Time (SMRT®) Sequencing on three microorganisms and one human BAC to compare PacBio-only sequencing to existing high-quality reference genomes.…

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Monday, April 29, 2013

PNAS: Copy Number Analysis in Maize Sheds Light on Tolerance for Acidic Soil

A new study of maize sheds light on the importance of copy-number variation in genes related to stress tolerance with implications to boost crop yield in suboptimal soil environments. A paper published in PNAS, “Aluminum tolerance in maize is associated with higher MATE1 gene copy number,” was published by senior author Leon Kochian and a team of scientists at the US Department of Agriculture, Cold Spring Harbor Laboratory, University of Arizona, and several other institutions. The authors report on the discovery of aluminum stress-tolerance modulation through changing copy-number variation of a rare allele found in maize that has survived in…

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Tuesday, April 23, 2013

Current Opinion in Microbiology: Bacterial Methylomes in Review – ‘An Exciting Era’

A new review paper from Brigid Davis, Michael Chao, and Matthew Waldor at Harvard Medical School considers a number of recent studies and findings that have used single molecule, real-time (SMRT®) sequencing to generate epigenomic information. “Entering the era of bacterial epigenomics with single molecule real time DNA sequencing” was recently published in Current Opinion in Microbiology. In the review, the authors note the importance of fully understanding and analyzing genome-wide methylation data, but say that technologies to date have not made it feasible to generate this information. “The advent of new sequencing platforms in the last decade has allowed…

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Monday, February 11, 2013

SMRT Sequencing Offers First Look at Fragile X Syndrome Repeat Expansion Disorder Sequence

Scientists at the University of California, Davis, School of Medicine have used the PacBio® RS to sequence a previously “unsequenceable” region of highly repetitive DNA on the X chromosome, providing a critical leap forward in understanding the genetic complexity of repeat expansion disorders such as Fragile X Syndrome. Paul Hagerman, a professor of biochemistry and molecular medicine at the University of California, Davis, has spent the better part of the last 30 years trying to parse the molecular biology of Fragile X Syndrome. The FMR1 genetic mutation responsible for the syndrome is a leading cause of heritable cognitive impairment and…

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Thursday, January 31, 2013

SMRT Sequencing for Industrial Biotech Applications

A feature article in the December 2012 issue of Industrial Biotechnology reports on various case studies where scientists have used the unique capabilities of SMRT® Sequencing to make discoveries in applied biotechnology areas. The long read lengths, high consensus accuracy, lack of sequence bias, and sensitivity to chemical base modifications make SMRT sequencing a good fit for a range of industrial applications, including applied microbiology, agricultural biotechnology, enzyme research and design, pathogen research and detection, biofuels development, and many others.  In an example highlighting the return to the gold standard of high-quality, finished genomes, scientists from the Korea Polar Research…

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Monday, January 14, 2013

Baylor Team Uses PacBio’s SMRT® Sequencing to Upgrade and Finish Draft Genomes

Scientists at the Human Genome Sequencing Center at Baylor College of Medicine recently published a paper demonstrating the utility of PacBio’s long reads for upgrading and finishing draft genomes. “Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology,” published in PLoS One late last year from lead author Adam English and senior author Richard Gibbs, details a method for improving draft genomes, many of which have been assembled from short-read sequence data. In addition, the Baylor team has developed its own algorithm called PBJelly to automate the finishing process, optimized for long-read sequence data. According to the…

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