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Wednesday, October 5, 2016

Diploid Assembly of Korean Genome Reveals Population-Specific Variation and Novel Sequence

In a paper published today in Nature, scientists from Seoul National University, Macrogen, and other institutions present the de novo genome assembly for a Korean individual. The effort used SMRT Sequencing and other technologies to generate the assembly, fully phase all chromosomes, and perform detailed analyses of structural variation and other elements. In the process, the team generated novel sequence data that helps fill gaps in the human reference genome and continues the trend of developing important new population-specific resources. The work, reported in “De novo assembly and phasing of a Korean human genome,” was contributed by lead authors Jeong-Sun…

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Monday, November 9, 2015

Steven Marsh from Anthony Nolan Discusses the Past and Future of Donor Matching

Mendelspod host Theral Timpson recently interviewed Professor Steven Marsh, Director of Bioinformatics at the Anthony Nolan Research Institute, a UK-based organization dedicated to improving the outcomes of bone marrow transplantation and host to the world’s first bone marrow registry. Prof. Marsh and his team have dramatically improved the resolution of HLA typing — one of the methods used for matching compatible donors with transplant recipients — using long, accurate reads from PacBio sequencing. Their fascinating conversation covers the past, present, and future of HLA typing — highlights are below. Short History of HLA Typing — There’s a Lot More Diversity…

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Tuesday, July 21, 2015

Webinar: Anthony Nolan’s Neema Mayor Reports on HLA Typing with Long Reads

Following the recent paper about HLA typing from scientists at Anthony Nolan Research Institute, we thought readers might enjoy this webinar from Neema Mayor, a scientist at the institute and lead author on the paper. The video offers a great foundation on HLA typing for beginners as well as more detailed information about typing technologies for advanced users. (Learn more about the institute's plans for HLA typing in this GenomeWeb article.) Named for Anthony Nolan, a young boy whose need for a bone marrow transplant spurred his mother to start the world’s first registry of potential donors, the institute focuses…

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Thursday, June 25, 2015

SMRT Data Delivers for Next-Generation HLA Typing at Anthony Nolan Research Institute

A new publication in PLoS One from authors at Anthony Nolan’s Research Institute describes a feasibility study for HLA typing using SMRT® Sequencing. The research institute, where the world’s first bone marrow registry started in 1973, is part of the UK-based charity dedicated to improving the outcomes of bone marrow transplantation. Scientists at Anthony Nolan are leaders in HLA typing, which is an important step in matching a bone marrow or stem cell donor to a patient in need. The Anthony Nolan team adopted the PacBio® system last year, and this publication reflects its efforts to test and establish the…

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Tuesday, January 20, 2015

Looking Ahead: The 2015 PacBio Technology Roadmap

By Jonas Korlach, Chief Scientific Officer All of us at Pacific Biosciences are very proud of the momentum SMRT® Sequencing achieved in 2014, especially due to the more than 500 customer publications now in the literature describing its many applications. We remain deeply thankful to all the scientists who have applied our technology to gain new insights into genomes, transcriptomes, and epigenomes. By applying SMRT Sequencing to a wide variety of applications, our customers are demonstrating that long, unbiased reads have brought about new quality standards for many fields of genomic research. This exciting level of scientific activity and collaboration…

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Tuesday, December 16, 2014

At ASHI 2014, SMRT Sequencing Meets HLA Typing with Great Results

Earlier this fall, we headed to Denver for ASHI, or the annual meeting of the American Society for Histocompatibility and Immunogenetics. Though we’d attended this conference in the past, this was our first year having an exhibit hall booth and workshop, both of which were enthusiastically received by the conference attendees. Even though it’s a fairly recent development for scientists to apply the PacBio® sequencing platform to analyze the HLA genes, which are often used in histocompatibility research studies, there were already many great examples and exciting data generated by users on the PacBio platform. Our luncheon workshop on fully…

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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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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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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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Tuesday, May 13, 2014

A New Approach for HLA Typing: SMRT Sequencing

Two recent news announcements demonstrate the utility of our Single Molecule, Real-Time (SMRT®) Sequencing technology in the challenging realm of HLA typing.  HLA typing — or analysis of genes in the human leukocyte antigen region of the human genome — is of critical importance for research in tissue transplantation matching, autoimmune disease-association studies, drug hypersensitivity research, and other applications. But analyzing those genes, which are highly polymorphic and contain thousands of alleles that code for proteins important in recognizing foreign antigens, has proven difficult with most technologies. Use of Sanger or short-read sequencing technologies has required other methods for confirmation…

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