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Monday, April 30, 2018

An Interview with Baylor’s Fritz Sedlazeck on New Long-Read Algorithms

Fritz Sedlazeck Nature Methods just published “Accurate detection of complex structural variations using single-molecule sequencing,” a publication that presents the NGMLR aligner and Sniffles structural variant caller, both designed for use with long-read sequencing data. We chatted with developer and lead author Fritz Sedlazeck from the Human Genome Sequencing Center at Baylor to learn more. Q: Why was a new alignment tool needed when many scientists already use BWA and other methods? A: When I started my postdoc in Mike Schatz’s lab at Cold Spring Harbor, I had the opportunity to look at the complex SK-BR-3 cell lines. We soon…

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Thursday, April 26, 2018

AACR 2018 Recap: Iso-Seq Method Meets Cancer Research

The PacBio team is just back from Chicago, where we saw outstanding talks and posters at the American Association for Cancer Research (AACR) Annual Meeting and enjoyed that city’s well-deserved reputation for exciting weather. We hope everyone remembered to pack their hats and gloves and enjoyed the late-season snow! This year multiple researchers presented work featuring the use of the Iso-Seq method for full-length transcript sequencing in cancer research. The first was a poster presented by Yeung Ho from University of Minnesota, entitled ‘The role of androgen receptor variant AR-V9 in prostate cancer’. The poster describes their discovery that the…

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Tuesday, April 24, 2018

Nature Webinar and SMRT Grant Winner Explore Structural Variation for Disease Gene Discovery

Structural variants account for most of the base pairs that differ between human genomes, and are known to cause more than 1,000 genetic disorders, including ALS, schizophrenia, and hereditary cancer. Yet they remain overlooked in human genetic research studies due to inherent challenges of short-read sequencing methods to resolve complex variants, which often involve repetitive DNA.   At a recent webinar co-hosted by Nature Research, Professor Alexander Hoischen joined Principal Scientist Aaron Wenger to discuss how advances in long-read sequencing and structural variant calling algorithms have made it possible to affordably detect the more than 20,000 such variants that are…

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Tuesday, April 17, 2018

Scientists Aim to Develop “Genomic Ark” of High-Quality Bat Genomes

Pop quiz: Which animal accounts for around 20% of all living mammals, harbors (yet survives) some of the world’s deadliest diseases, lives proportionately longer than humans given its body size, and helps make tequila possible? Answer: Bats. From the tiniest bumblebee bat (Craseonycteris thonglongyai) to the large (1kg) golden-capped fruitbat (Acerodon jubatus), the diversity and rare adaptations in bats have both fascinated and terrified people for centuries. Now, an international consortium of bat biologists, computational scientists, conservation organizations, and genome technologists has set out to decode the genomes of all 1,300 species of bats using SMRT Sequencing and other technologies.…

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Thursday, April 12, 2018

SMRT Sequencing Enables Characterization of Cavities-Causing Bacteria in Children

We’re told to avoid sugar and refined carbohydrates if we want our teeth to remain strong and cavity-free. But what is the role of microbiota in our oral health? Cavities – or caries – actually occur as the result of bacterial infection that leads to sustained decalcification of tooth enamel and the layer beneath it, the dentin. Left unchecked, it can reach the tooth’s inner layer, with its soft pulp and sensitive nerve fibers, and, in some cases, can cause serious complications such as phylogenetic osteomyelitis and the life-threatening bacterial endocarditis. In addition to diet and host factors, the occurrence…

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Wednesday, April 11, 2018

HudsonAlpha Chooses Sequel System for NIH-Funded Program Focused on Challenging Pediatric Cases

At the HudsonAlpha Institute for Biotechnology, scientists are building on advances in agricultural research to power a clinical pediatric research program. For this work, they’re using the Sequel System to perform whole-genome sequencing on trios of children with developmental disabilities and their parents. HudsonAlpha researchers have been using SMRT Sequencing to resolve challenging plant genomes, deploying a Sequel System and a PacBio RS II for these complex projects. The successfulness of that program led the institute to add a second Sequel System for use in sequencing human genomes. The organization is part of the NIH-funded Clinical Sequencing Exploratory Research Program,…

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Monday, April 9, 2018

Rice Revelations: Nine New Genome Assemblies Uncover Key Traits and Evolutionary Clues

Revered around the world, rice is a staple food for nearly half of the population. But as that population grows, rice breeders are faced with the challenge of producing crops that are high yielding, disease-resistant and nutritious, while at the same time being more sustainable. The International Oryza Map Alignment Project (OMAP) was initiated in 2003 to develop a set of high-quality genomic resources for the wild relatives of rice that could be used as a resource to discover and utilize novel genes, traits and/or genomic regions for crop improvement and basic research. Members of the consortium recently released new…

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Thursday, April 5, 2018

New M. Oryzae Assembly Reveals Importance of Previously Missed Transposable Elements

Rice blast symptoms. Photo by Donald Groth. A publication from the Molecular Plant journal demonstrates the use of SMRT Sequencing to characterize activity of transposable elements in Magnaporthe oryzae, the destructive fungus responsible for rice blast disease. This information will help scientists better understand pathogen biology and potentially find new ways to reduce its impact on an important food source. Lead authors Jiandong Bao, Meilian Chen, Zhenhui Zhong, Wei Tang, senior author Zonghua Wang, and collaborators at Fujian Agriculture and Forestry University and Minjiang University report their findings in “PacBio Sequencing Reveals Transposable Element as a Key Contributor to Genomic…

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Monday, April 2, 2018

Disease-Causing Mobile Element Identified with SMRT Sequencing, Validated with CRISPR

The coast of Panay Island in the Philippines. U.S. Navy photo by Jennifer S. Kimball In an exciting new Cell paper, scientists report identification of an intronic structural variant that causes a neurodegenerative Mendelian disorder that primarily affects people on the island of Panay in the Philippines. The team used a number of approaches, including SMRT Sequencing and the Iso-Seq method, to solve the medical mystery. “Dissecting the Causal Mechanism of X-Linked Dystonia-Parkinsonism by Integrating Genome and Transcriptome Assembly” comes from lead authors Tatsiana Aneichyk, William Hendriks, Rachita Yadav, David Shin, and Dadi Gao; senior authors Cristopher Bragg and Michael Talkowski;…

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