Category Archives: Transhuman News

MOUNTAIN VIEW, Calif. & HOUSTON--(BUSINESS WIRE)--

The Human Genome Sequencing Center (HGSC) at Baylor College of Medicine and DNAnexus today announced a broad collaboration focused on advancing the state-of-the-art in the large-scale clinical analysis of genomic data. Through this collaboration, the HGSC has adopted the DNAnexus enterprise cloud platform to power its Mercury pipeline, a semi-automated and modular set of tools for the analysis of next-generation sequencing data in both research and clinical contexts. The collaborators also worked with Amazon Web Services (AWS) to process data from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium using the Mercury pipeline, generating 430TB of results and making them available to hundreds of researchers participating in this global project.

The HGSCs Mercury pipeline identifies mutations from genomic data, setting the stage for determining the significance of these mutations as a cause of serious disease and is used as the core variant-calling pipeline for the CHARGE Consortium. The CHARGE Consortium is aimed at better understanding how human genetics contributes to heart disease and aging. The CHARGE Consortium has a longstanding collaboration with the HGSC to fuel disease gene discovery. These discoveries are instrumental in understanding disease and aging in mechanistic detail, enabling the development of new medical interventions and analysis tools.

The management and analysis of genomes at the scale needed to appropriately power clinical studies requires computational infrastructure that exceeds the capacity of most institutional resources, said Jeffrey Reid, Ph.D., Assistant Professor, Department of Molecular and Human Genetics, Baylor College of Medicine. Working with DNAnexus and Amazon Web Services, we were able to rapidly deploy a cloud-based solution that allows us to scale up our support to researchers at the HGSC, and make our Mercury pipeline analysis data accessible to the CHARGE Consortium, enabling what will be the largest genomic analysis project to have ever taken place in the cloud.

The CHARGE project involves more than 300 researchers across five institutions around the world analyzing the genome sequence data of over 14,000 individuals (3,751 whole genomes and 10,771 exomes), requiring approximately 2.4 million core-hours of computational time and some 860 TB of storage. At the projects peak, HGSC used the DNAnexus platform to spin up more than 20,000 cores on-demand in order to run the CHARGE data through the Mercury analysis pipeline. During this period, HGSC was running the largest genomics analysis cluster in the world, hosted by AWS.

Many large-scale population studies to date have been limited in scope by a lack of the necessary compute power; this is a real hindrance in realizing the full promise of genomic medicine, said Richard Daly, CEO of DNAnexus. The DNAnexus platform offers research and clinical enterprises the requisite computational resources that allow them to focus on the data and provide the ability to share and collaborate in a secure compliant environment. Through this collaboration with the HGSC and Amazon Web Services, 300 scientists can now perform downstream analyses on these invaluable health and aging data at a scale not previously possible.

DNAnexus provides an enterprise-focused API-based platform-as-a-service that enables clinical and research enterprises to efficiently move their analysis pipelines into the cloud, using their own algorithms alongside industry-recognized tools and reference resources to create customized workflows in a secure, cost-effective and compliant environment. With DNAnexus, labs of any size can build and run their data analysis applications and workflows from anywhere in the world, and work securely with research and clinical collaborators.

For more information please visit: https://dnanexus.com/usecases-charge.

About the Human Genome Sequencing Center at Baylor College of Medicine, (HGSC)

As one of three U.S. Centers that contributed to the Human Genome Project, the HGSC played a pivotal role in the emergence of genomics as a core discipline in modern biomedical and translational research, and has been at the forefront of technical innovation and testing of next-generation sequencing technologies. The HGSC is also a leader in developing large-scale sequencing and analysis solutions, and has emerged as a world leader in the analysis of personal genomes and the introduction of genomics into medicine. For more information please visit:https://www.hgsc.bcm.edu.

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DNAnexus and the Human Genome Sequencing Center at Baylor College of Medicine Announce Ultra Large-Scale Collaboration ...

The Wellcome Trust is piling almost 10 million additional funding into transformational upgrades to its Genome Campus conference facilities in the Cambridge UK medical technology cluster.

The Conference Centre will look to host an increased programme of events that attract wider audiences including school children as part of the Campuss public engagement strategy.

Planning consent has just been granted for the 9.7 million project, known as the Kitchen Garden Enclosure; the design is reminiscent of the famous glass ceiling in the British Museum and will include a new exhibition centre, modern meeting rooms and a bar.

Groundbreaking for this major new project will begin in January and is due to be completed by December 2014. All facilities at the Conference Centre are due to be opened by January 2015.

In total the Conference Centre will have undergone a 19 million renovation to modernise and improve all available facilities. This project is set to improve the international reputation of the Wellcome Trust Conference Centre, and celebrates the communication, collaboration, achievement and creativity of the overall Genome Campus, according to Linda Prior, sales and marketing manager at the Conference Centre

She said: Not only will this place us at the forefront of the scientific conferences sector, but also the development will better integrate us into the wider vision of the Genome Campus.

This new building work will see the current cloisters and grassed areas opened up and enclosed under a spectacular glass roof to create a multi-use space for both day and evening activities.

The roof, which is the central feature of the build, is designed to create a light and elegant space through the transparent and translucent areas of glass panelling above.

By opening up the area surrounding the auditorium, the Conference Centre will create space sufficient to support exhibitions both fixed and temporary, poster sessions, catering and a relaxation area for delegates and speakers.

David Davison, director of the Wellcome Trust Genome Campus, said: We welcome the development of the Kitchen Garden Enclosure on campus, which will complement perfectly the public engagement activities of both the Wellcome Trust Sanger Institute and EMBL-EBI.

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£19m Genome Campus overhaul targets global business

Next spring, students at local high schools will dive into the study of the marine bacterium Kytococcus sedentarius, thanks to a $1.1 million National Science Foundation grant to UB.

Stephen Koury and his colleagues in the School of Medicine and Biomedical Sciences, received the grant to educate regional high school teachers and recruit high school students to pursue careers in STEM (science, technology, engineering and mathematics) fields. The new program focuses on bioinformatics, an interdisciplinary field that uses software tools to store, retrieve, organize and analyze biologic information. Bioinformatics is a field of rapid growth that provides tools for better health care through improvement in prevention, detection, diagnosis and treatment of diseases.

Koury, research assistant professor in the Department of Biotechnical and Clinical Laboratory Sciences, notes that new jobs on the Buffalo Niagara Medical Campus likely will require training in biotechnology and bioinformatics; the new program will provide a pipeline for educator and student recruitment, training and mentorship in STEM fields at the high school level.

For us to be successful, we need to create the environment where children not only want to get involved, but want to stay in Buffalo, says Norma Nowak, professor of biochemistry, director of science and technology at UBs New York State Center of Excellence in Bioinformatics and Life Sciences, and associate professor of oncology at Roswell Park Cancer Institute. This needs to be the spark that lights the fire.

Over the next three years, the grant will allow 450 high school students and 90 teachers to conduct and present scientific research in bioinformatics. The program will involve educators and students from 13 counties, including Niagara, Erie, Chautauqua, Cattaraugus, Wyoming, Genesee, Orleans, Monroe, Livingston, Allegany, Ontario, Wayne and Steuben.

The educational program will begin with a two-week workshop at UB, where high school teachers will receive training in microbial genome annotation. The teachers then will pass on their new skills to selected students in their schools, with support from UB faculty and staff.

During the first semester, students will be introduced to basic aspects of genetics and genomics. They also will receive career mentoring through a partnership with the New York State Area Health Education Center System (AHEC), a unit of UBs Department of Family Medicine that addresses health care workforce needs.

The second semester will focus on conducting Web-based research in microbial annotation through a program called IMG-ACT, a bioinformatics tool kit available through the U.S. Department of Energys Joint Genome Institute. The program will end with a capstone symposium at which students will present the results of their research to university faculty, researchers and employers in the biosciences fields.

For many local students, this will be their first real-world taste of scientific experimentation. And since its an unscripted project, students will learn to rely on themselves, rather than the specific direction of instructors.

We cant say for sure what they should find, says Koury. They will actually be doing a research project, and by the time they are done, they will probably be the expert on the particular gene sequence they have studied. It will give them that joy of discovery.

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Genome project fosters bioinformatics education in high schools