HGSC deploys its Mercury variant-calling pipeline on the DNAnexus cloud platform; processes 3,751 whole genomes and 10,771 exomes using 2.4 million core-hours with a peak of 20,800 cores; makes Mercury and results available to 300 researchers participating in the global CHARGE Consortium
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 HGSC’s 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 project’s 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.
DNAnexus is powering the genomics revolution with an enterprise-level solution that combines cloud computing with advanced bioinformatics. The DNAnexus team is made up of experts in software, computational biology, and genetics who are on a mission to establish DNAnexus at the center of a growing ecosystem of scientific and clinical research, and diagnostic efforts in personalized medicine. For more information please visit https://dnanexus.com.
Colin Sanford, 203-340-2441