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Tuesday, May 30, 2017

At ASM Microbe 2017, SMRT Sequencing Advances Microbial Applications

We can’t wait for ASM Microbe! It’s one of the largest microbiology conferences in the world and is taking place June 1-5 in New Orleans. With more than 10,000 people expected to attend, it’s a key event for connecting with this community, hearing the latest scientific and clinical advances, and introducing microbial experts to the opportunities afforded by long-read SMRT Sequencing. If you’ll be at the conference, please stop by booth #1328 to meet the PacBio team. We will be happy to provide updates on the newest enhancements coming to SMRT Sequencing in the next few months. One of those…

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Wednesday, May 24, 2017

Genome Assembly Advances Featured in Genome Research Special Issue

The May issue of Genome Research is a special edition focusing on advances in sequencing technologies and genome assembly techniques. The research papers selected for this special issue cover reference-grade genome assemblies, structural variant detection, diploid assemblies, and other features enabled by new high-quality sequencing tools. The issue kicks off with a perspective from NHGRI’s Adam Phillippy, who reflects on the history of sequencing and assembly. Dusting off publications from as early as 1979, he illustrates the remarkable pace of advances in this field for the past four decades. Phillippy has worked with just about every kind of sequence data,…

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Thursday, May 18, 2017

TB Study Finds Some Previously Reported Virulence Variants Were Sequencing Errors

A publication in BMC Genomics upends some of the conventional wisdom about variants that may cause virulence in Mycobacterium tuberculosis. Scientists at San Diego State University used SMRT Sequencing to produce a complete assembly of the pathogen, finding that earlier assemblies encountered problems due to GC bias and repetitive DNA. “SMRT genome assembly corrects reference errors, resolving the genetic basis of virulence in Mycobacterium tuberculosis” comes from Afif Elghraoui, Samuel Modlin, and Faramarz Valafar. The team used long-read PacBio sequencing on an attenuated strain of M. tuberculosis, which is often compared to a virulent strain to highlight sources of pathogenicity. The same strain was…

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Tuesday, May 2, 2017

New Iso-Seq Chicken Analysis Finds Missing Genes and Transcript Complexity

Photo by Timophey Tkachik A new publication in BMC Genomics explores the use of RNA normalization and 5’ cap selection to enhance results from Iso-Seq studies using SMRT Sequencing. Scientists from the University of Edinburgh report that these modifications significantly boosted transcriptome coverage in a study of chicken. “Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human” comes from lead author Richard Kuo, senior author David Burt, and collaborators. The team chose this project because existing chicken annotation resources have far fewer genes than expected, with very little evidence of alternative splicing. This situation was believed…

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Monday, May 1, 2017

SMRT Sequencing Enables Accurate Calling of Pathogenic Variants in Medically Relevant Genes

Screening for pathogenic variants associated with polycystic kidney disease is now more accurate and affordable with SMRT Sequencing. A new paper in Human Mutation from scientists at Leiden University Medical Center and other institutes reports the evaluation of long-read PacBio sequencing as a potential replacement for costly, time-consuming Sanger pipelines. “Detecting PKD1 variants in polycystic kidney disease patients by single-molecule long-read sequencing” comes from lead author Daniel Borràs, senior author Seyed Yahya Anvar, and collaborators. The team notes that previous efforts to get away from conventional tools by implementing short-read sequencing were never successful enough for clinical use. “A genetic diagnosis of…

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