GenomeNext, LLC, a leader in genomic data management and integrated analysis, announced today that, through the “Intel Heads In The Clouds Challenge on Amazon Web Services (AWS)” with support from JHC Technology, and in conjunction with Nationwide Children’s Hospital, has benchmarked whole genome sequencing analysis at an unprecedented 1,000 genomes per day.
GenomeNext and Nationwide Children’s were challenged to perform analysis of the complete 1000 Genomes Consortium’s sequencing dataset in one week. This dataset consists of raw genomic sequence data from 2,504 individuals sampled across 26 different populations.
All 5,008 samples (2,504 whole genomes & 2,504 exomes) were analyzed on GenomeNext’s Platform, leveraging its proprietary genomic sequence analysis technology developed by Nationwide Children’s, operating on the AWS Cloud powered by Intel® Xeon™ processors.
The entire analysis was completed in one week, with as many as 1,000 genome samples being completed per day, generating close to 100TB of processed result files. The results of the analysis will be published in the coming months, and Dr. Peter White, director of Nationwide Children’s Biomedical Genomics Core, and his team found there was a high-degree of correlation with the original analysis performed by the Consortium, with additional variants potentially discovered during the analysis performed utilizing GenomeNext’s Platform.
“The successful completion of this proof-of-concept not only sets a groundbreaking timeframe for the analysis of a massive quantity of genomic data, but demonstrates the utility of the GenomeNext solution, eliminating the sequence analysis computational bottlenecks, enabling researchers and clinicians to keep pace with processing the magnitude of genomic data analysis required for population-scale genomics” said James Hirmas, CEO of GenomeNext.
GenomeNext believes this is the fastest, most accurate and reproducible analysis of a dataset of this magnitude. The goal is to integrate the new knowledge into GenomeNext’s analysis pipeline to assist researchers and clinicians in identifying rare pathogenic variants. Access to a growing and diverse repository of DNA sequence data, including the ability to integrate and analyze the data is critical to accelerating the promise of precision medicine. “We believe this dataset will become invaluable to genomic medicine as a whole and further catalyze the identification of disease causing genetic variants,” Hirmas said.
“At Nationwide Children’s we have a strategic goal to introduce genomic medicine into multiple domains of pediatric research and healthcare,” Dr. White said. “Rapid diagnosis of genetic disease can be critical in newborns, so our initial focus was to create an analysis pipeline that was extremely fast, but didn’t sacrifice clinical diagnostic standards of reproducibility and accuracy. Having achieved that, we discovered that a secondary benefit of this analysis pipeline was that it could be adapted for population scale genomic analysis.”
“Intel is proud of our work with GenomeNext and AWS to deliver these remarkable performance results with Nationwide Children’s Hospital,” said Ketan Paranjape, General Manager Life Sciences at Intel. “As we look to bringing precision medicine mainstream we will need to continue to work on solutions based on a converged infrastructure of compute, storage and networking products as well as optimized software packages that will enable population scale genomic analysis.”
“Analysis and bioinformatics pipelines need to be able to keep up with the new genomic data being generated as sequencing moves closer to clinical practice,” said Matt Wood, General Manager, Data Science at Amazon Web Services, Inc. “It's great to see that important projects such as this are able to take advantage of the scale and flexibility of the cloud, advancing and improving the delivery of care for patients worldwide."
An article describing GenomeNext’s novel parallelization strategy for human genome analysis was recently published in Genome Biology (http://genomebiology.com/2015/16/1/6/). Through implementation of this peer reviewed analysis method, the GenomeNext platform fully automates the analytical process, enabling an efficient, accurate and deterministic execution of all steps in the entire human genome analysis workflow.
The Software as a Service (SaaS) is offered through the company’s website, http://www.genomenext.com/. Alternative configurations, including private cloud and custom pipelines are considered upon request.
About GenomeNext - GenomeNext is a genomic informatics company dedicated to accelerating the promise and capability of predictive medicine and scientific discovery. We commercialize genomic analysis tools and integrated systems for the evaluation of genetic variation and function. Our advanced informatics and data management solutions are designed to simplify, expedite and enhance genetic analysis workflows. Our solutions provide the market with genomic data and analysis at an unprecedented combination of performance, quality, cost and scale without requiring the investment in high-performance computing resources and specialized personnel. Our proprietary platforms address a broad range of highly interconnected markets, including sequencing, genotyping, gene expression, and molecular diagnostics. Our customers include leading genomic research centers, academic institutions, government laboratories, and clinical research organizations, as well as pharmaceutical, biotechnology, agrigenomics, and consumer genomics companies.
© 2015 GenomeNext, LLC. GenomeNext is a trademark of GenomeNext, LLC. All rights reserved.
About Nationwide Children’s Hospital
Ranked 7th of only 10 children's hospitals on U.S. News & World Report’s 2014-15 “America’s Best Children’s Hospitals Honor Roll” and among the Top 10 on Parents magazine’s 2013 “Best Children’s Hospitals” list, Nationwide Children’s Hospital is one of the nation’s largest not-for-profit freestanding pediatric healthcare networks providing care for infants, children and adolescents as well as adult patients with congenital disease. As home to the Department of Pediatrics of The Ohio State University College of Medicine, Nationwide Children’s faculty train the next generation of pediatricians, scientists and pediatric specialists. The Research Institute at Nationwide Children’s Hospital is one of the Top 10 National Institutes of Health-funded free-standing pediatric research facilities in the U.S., supporting basic, clinical, translational and health services research at Nationwide Children’s. The Research Institute encompasses three research facilities totaling 525,000 square feet dedicated to research. More information is available at www.NationwideChildrens.org/Research.
About Intel Corporation
Intel is helping drive the life sciences evolution through a comprehensive approach that includes working with key players in the industry. Together, we are pursuing an end-to-end solution to the computing challenges faced in personalized care and the development of new plant and drug compounds. We draw on expertise spanning the entire compute continuum, from local high performance computing (HPC) clusters, big data analytics, cloud, and commercial and open source software initiatives, to mobile devices, smartphones, and sensors. www.intel.com/healthcare/bigdata
About JHC Technology, Inc.
JHC Technology is a Service Disabled, Veteran-Owned Small Business headquartered outside Washington, DC. JHC has been a leader in Amazon Web Services cloud solutions since 2010, supporting the Federal Government, Local Government, Non-Profits, and the Private Sector. We provide intelligent engineering and development services focused on disruptive technologies with core capabilities in cloud, virtualization, mobility, and collaboration. We deliver high performing subject matter experts to support clients in multiple industries, including defense, international trade, financial services, grant administration, science, and retail. JHC is an AWS Advanced Consulting Partner and Channel Reseller. For more information, visit www.jhctechnology.com.