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Wednesday, October 29, 2014

‘Revolutionizing HLA Typing’: Uppsala’s Ulf Gyllensten on How Long Reads Give Access to New Areas of the Human Genome

In a recent interview with Theral Timpson — part of Mendelspod’s series on long-read sequencing — Ulf Gyllensten, a scientist at Uppsala University, spoke about using PacBio® technology for HLA typing, human genome studies, transcriptomics, and more. Based in the medical genetics and genomics department, Gyllensten focuses on two areas: using systems biology to study biological variation in human physiology and studying the epidemiology of human papilloma virus and its genetic link to cervical cancer. He also works with the National Genomics Infrastructure, a national core facility in Sweden for genotyping and DNA sequencing, where he has access to all…

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Tuesday, October 21, 2014

Data Release: Whole Human Transcriptome from Brain, Heart, and Liver

In higher eukaryotic organisms, like humans, RNA transcripts from the vast majority of genes are alternatively spliced. Alternative splicing dramatically increases the protein-coding potential of eukaryotic genomes and its regulation is often specific to a given tissue or developmental stage. Using our updated Iso-Seq™ sample preparation protocol, we have generated a dataset containing the full-length whole transcriptome from three diverse human tissues (brain, heart, and liver). The updated version of the Iso-Seq method incorporates the use of a new PCR polymerase that improves the representation of larger transcripts, enabling sequencing of cDNAs of nearly 10 kb in length. The inclusion…

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Monday, October 20, 2014

SMRT Sequencing for the HLA Complex: PacBio Goes to ASHI

This week marks the 40th annual meeting of the American Society for Histocompatibility and Immunogenetics, better known in the community as ASHI. The PacBio® team is looking forward to attending; after all, several organizations are now using Single Molecule, Real-Time (SMRT®) Sequencing specifically for resolving the incredibly complex genetic regions related to histocompatibility. Earlier this year, we announced that two leading HLA typing institutions had adopted SMRT Sequencing to untangle this highly polymorphic set of genes: Anthony Nolan, a UK-based blood cancer charity that started the world’s first bone marrow registry, and HistoGenetics, a pioneer that has used sequence-based typing…

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Wednesday, October 15, 2014

New Chemistry Boosts Average Read Length to 10 kb – 15 kb for PacBio® RS II

We are pleased to announce the launch of our new reagent kit, P6-C4, which represents the next generation of our polymerase as well as our chemistry. This kit replaces the P5-C3 chemistry and is recommended for all SMRT® Sequencing applications, including de novo assembly, targeted sequencing, isoform sequencing, minor variant detection, scaffolding, long-repeat spanning, SNP phasing, and structural variant analysis. P6-C4 continues the steady read length improvement our users have seen since the instrument first launched. With this new chemistry, average read lengths increase to 10 kb – 15 kb, with half of all data in reads 14 kb or…

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Friday, October 10, 2014

ASHG 2014: A New Look at the Human Genome with Long-Read Sequencing

Scientists around the world are getting ready for the annual meeting of the American Society of Human Genetics taking place October 18-22 at the San Diego Convention Center. We’re looking forward to a number of excellent presentations and posters, and are delighted to see that many of them will focus on applying Single Molecule, Real-Time (SMRT®) Sequencing to human studies. If you’ll be among those attending ASHG, be sure to attend our workshop, A New Look at the Human Genome – Novel Insights with Long-Read PacBio Sequencing, taking place 12:30 – 2:00 p.m. on Tuesday, October 21. Register in advance to…

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Thursday, October 9, 2014

New Brain Study Reveals Higher Molecular Diversity from Alternative Splicing

A new paper from scientists in Switzerland and the US adds to recent findings about diversity of neuronal transcripts in the mammalian brain. The authors report that this study was only possible using long reads from Single Molecule, Real-Time (SMRT®) Sequencing. “Targeted Combinatorial Alternative Splicing Generates Brain Region-Specific Repertoires of Neurexins,” from lead author Dietmar Schreiner, senior author Peter Scheiffele, and collaborators, was published this month in the journal Neuron. The researchers are from the University of Basel, ETH Zurich, and North Carolina State University. This is the second study on neurexin mRNA diversity using PacBio® sequencing. The team tackled…

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Monday, October 6, 2014

‘The Quality of PacBio Data Is Beyond Compare’: Eric Schadt on Applications of SMRT Sequencing to Human Genetics

As part of its continuing series on long-read sequencing, last week Mendelspod aired an engaging interview with Eric Schadt, Professor & Chair of Genetics and Genomic Sciences, and Director of the Icahn Institute for Genomics and Multiscale Biology at Mount Sinai. Having now spent three years in his role at the groundbreaking institute, he reports that they are making great progress in the quest to build better data-driven health profiles around individuals that may better guide healthcare choices. On short-read versus long-read sequencing Short-read sequencing technologies still maintain the advantage in terms of throughput, says Schadt, but there are a…

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Thursday, October 2, 2014

‘We’re Going to Find the Keys’: Dan Geraghty Discusses an Approach to Understanding Causal Genetic Variation

Dan Geraghty, a researcher at Fred Hutchinson Cancer Research Center and CEO of Scisco Genetics, has spent much of his career focused on the genetics of immune response. Recently he talked to Mendelspod host Theral Timpson as part of a continuing series of podcasts on the rise of long-read sequencing. Geraghty explained that while there have been decades’ worth of studies associating the genetics of the major histocompatibility complex (MHC), and the highly polymorphic HLA class 1 and 2 genes, we still haven’t found the key mutations for a variety of different autoimmune diseases such as type 1 diabetes, rheumatoid…

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