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Mountain View, CA, United States

Patent
DNAnexus | Date: 2012-08-10

A repository of DNA sequence data is available online. A user can query the repository using a search term. Search results that are provided by the repository include information about studies, experiments, samples, and/or runs that are related to the search term. A user can select one or more of the displayed search results. Based on the user selection, the repository provides relationship(s) between the selected results and run(s). Runs may be associated with DNA sequence data. The determined relationship between the search term and any available DNA sequence data is displayed. The DNA sequence data may be obtained by the user using, for example, the FASTQ format and/or the SRA format.


HILDEN, Germany & MOUNTAIN VIEW, Calif.--(BUSINESS WIRE)--DNAnexus Inc., the leader in cloud-based genome informatics and data management, today announced that QIAGEN, a leading global provider of Sample to Insight solutions to transform biological materials into valuable molecular insights, has integrated the DNAnexus cloud genomics platform with Ingenuity Variant Analysis, QIAGEN’s leading variant interpretation solution. Researchers globally now have the ability to choose a sequencer independent, cloud-based solution for analyzing and interpreting their NGS data by uploading raw sequencing data into the scalable DNAnexus cloud platform and seamlessly generating uniquely actionable biological insights through QIAGEN’s Ingenuity Variant Analysis. “Adoption of QIAGEN’s universal bioinformatics solutions is growing rapidly as NGS becomes the norm for translational research in cancer and other diseases,” said Dr. Frank Schacherer, Vice President Discovery Genomics at QIAGEN. “The HIPAA-compliant DNAnexus Platform provides seamless and secure integration from the sequencer to QIAGEN bioinformatics tools where disease-focused researchers now have a complete solution to move rapidly from raw data to valuable insights.” Ingenuity Variant Analysis leverages expert, manually-curated literature and powerful Path-to-Phenotype™ capabilities to relate biological phenotype with human variation data. The DNAnexus Platform enables QIAGEN to run best practices secondary analysis in the cloud, providing a secure, reproducible, cost-effective, and scalable solution. In addition, the DNAnexus export tool enables customers to securely transfer variant data into QIAGEN’s Ingenuity platform automatically for downstream analysis, including annotation, interpretation, and variant reporting. Furthermore, while exploring variants inside of Variant Analysis, researchers can easily refer back to supporting information such as the mapped reads found in a BAM file on DNAnexus, and view this data along with the variant data inside of a genome browser. This integrated solution allows researchers to rapidly identify, prioritize, and validate the most promising variants for follow-up. Dr. Schacherer will be in attendance at this year’s American Society for Human Genetics in Baltimore to further discuss details of the partnership to Society members. “The DNAnexus Platform is becoming the go-to solution for data interpretation tool providers who are seeking a secure, compliant, and scalable environment on which they can deploy and expand their product offerings,” said Richard Daly, CEO of DNAnexus. “We are proud of the collaboration with QIAGEN, which allows clinical researchers to move seamlessly between the two environments providing a powerful new end-to-end analytical solution for genomic biomarker discovery and interpretation.” By providing the global network for genomic medicine, DNAnexus is removing barriers to genomic insight; whether those barriers are geographic boundaries that hinder collaborating across national borders, disparate organizations sharing and analyzing data together, or financial barriers for customers not looking to invest in additional IT infrastructure. DNAnexus combines expertise in cloud computing and bioinformatics to create the global network for genomic medicine. DNAnexus provides security, scalability, and collaboration for enterprises and organizations that are pursuing genomic-based approaches to health in order to accelerate medical discovery. DNAnexus is supporting customers around the world that are tackling some of the most challenging and exciting opportunities in human health. For more information please visit: https://dnanexus.com and follow us at @DNAnexus. QIAGEN N.V., a Netherlands-based holding company, is the leading global provider of Sample to Insight solutions to transform biological materials into valuable molecular insights. QIAGEN sample technologies isolate and process DNA, RNA and proteins from blood, tissue and other materials. Assay technologies make these biomolecules visible and ready for analysis. Bioinformatics software and knowledge bases interpret data to report relevant, actionable insights. Automation solutions tie these together in seamless and cost-effective molecular testing workflows. QIAGEN provides these workflows to more than 500,000 customers around the world in Molecular Diagnostics (human healthcare), Applied Testing (forensics, veterinary testing and food safety), Pharma (pharmaceutical and biotechnology companies) and Academia (life sciences research). As of June 30, 2015, QIAGEN employed approximately 4,400 people in over 35 locations worldwide. Further information can be found at http://www.qiagen.com.


MOUNTAIN VIEW, Calif.--(BUSINESS WIRE)--DNAnexus, a leader in genome informatics and data management, today announced a collaboration with The Human Genome Sequencing Center (HGSC) at Baylor College of Medicine, a world leader in large-scale sequencing and analysis solutions, to co-develop HgV, the next generation of the HGSC’s Mercury solutions pipeline. HgV is a comprehensive framework for large-scale high-throughput whole genome sequence analysis in the settings of precision medicine research and clinical applications. The HGSC’s Mercury pipeline is the core data-processing and variant-calling tool for the world’s largest cloud-based genome analysis projects, including the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium, the Alzheimer’s Disease Sequencing Project, and the Baylor-Hopkins Center for Mendelian Genomics. This pipeline is used in clinical studies to identify mutations from genomic data to determine the significance of these mutations as a cause of serious disease. HGSC continues to be at the forefront of technical innovation and bioinformatics development. Partnering with DNAnexus, HGSC’s team of bioinformatics experts have expanded their capability for rapid development and deployment of HgV to the broader research community via the leading cloud-based bioinformatics platform – DNAnexus. HgV is optimized for Illumina X Ten levels of throughput and whole-genome data processing, analytics, and collaboration. Drawing on extensive R&D of high-quality personal genomes and large disease cohorts, this platform will provide an improved alternative to existing methods and multiple protocols for comprehensive whole genomes: As the cost of whole genome sequencing (WGS) continues to decline and the quality increases, its use for novel discovery and to identify genetic disorders in the clinic is becoming routine. Although most identified disease-causing variants fall within the exome, WGS can identify non-coding variants and large, structural variants that may contribute to complex and common diseases, especially in cases that have proven elusive to exome analysis. DNAnexus sits at the forefront of cloud-based data security, compliance and controlled access. By co-developing with DNAnexus, the HGSC can deploy HgV into an investigative environment while leveraging extensive research experience. These efforts include establishing an exceptionally high-quality personal genome for testing, benchmarking and validating protocols, methods and tools. The raw sequence data from multiple platforms have been subject to deep variant calling, trio analysis, whole genome assembly, long-read structural variant analysis, and Mendelian prioritization, generating high-quality variants that can be used for future tool validation. HgV development includes specific emphasis on trackability, versioning and reproducibility to enable seamless transition into a CAP/CLIA environment. HgV is an open-source and fully configurable platform that will be equipped with pre-configured DNAnexus workflows for various use cases, including optimized speed, sensitivity, and accuracy. Designed with the Illumina HiSeq X Ten platform in mind, it provides a secure and scalable environment for single samples and multi-sample projects, allowing users to focus on interpreting their data rather than local IT infrastructure and data logistics. Through DNAnexus, this Data Commons model serves as a global framework for developers and downstream users to implement new methods, share data, provide feedback, and identify new collaborations. DNAnexus combines expertise in cloud computing and bioinformatics to create a global network for genomic medicine. DNAnexus provides security, scalability and collaboration for enterprises and organizations that are pursuing genomic-based approaches to health in order to accelerate medical discovery. DNAnexus is supporting customers around the world that are tackling some of the most challenging and exciting opportunities in human health. For more information, please visit: https://dnanexus.com and follow us at @DNAnexus.


News Article | August 5, 2015
Site: www.businesswire.com

MOUNTAIN VIEW, Calif.--(BUSINESS WIRE)--DNAnexus, the leader in cloud-based genome informatics and data management, today announced that the company was awarded a research and development contract by the U.S. Food and Drug Administration’s Office of Health Informatics to build precisionFDA, an open source platform for community sharing of genomic information. precisionFDA is a new approach for evaluating bioinformatics workflows, and is an integral part of the agency’s work in understanding diagnostic tests that incorporate next generation sequencing (NGS) technologies. FDA’s role under the White House’s Precision Medicine Initiative is to review the current regulatory landscape and develop a streamlined approach to evaluating NGS-based diagnostics. precisionFDA is being developed to offer test developers a flexible method for independently evaluating the accuracy and reproducibility of NGS analysis workflows, and to securely share results with collaborators and the FDA. precisionFDA will also support community efforts to crowdsource reference datasets, addressing the critical need for convenient, reproducible comparisons between results derived from the same biospecimen. DNAnexus expects that the platform will be broadly used by NGS-based test providers, standards-making bodies, pharmaceutical and biotechnology companies, health care providers, academic medical centers, research consortia, and patient advocacy groups. “DNAnexus is proud to be delivering precisionFDA and creating a community around open-source genomic analysis pipelines, reference data, and analytical processing resources,” said Richard Daly, CEO of DNAnexus. “The FDA has taken a leadership position in making President Obama’s Precision Medicine Initiative a reality, and the DNAnexus platform will enable the managing and sharing of genomic data at an unprecedented level.” Technical information on precisionFDA can be found on the DNAnexus blog. For more information on the FDA’s perspective on precisionFDA, visit http://blogs.fda.gov/fdavoice/index.php/2015/08/advancing-precision-medicine-by-enabling-a-collaborative-informatics-community/. DNAnexus combines expertise in cloud computing and bioinformatics to create the global network for genomic medicine. DNAnexus provides security, scalability and collaboration for enterprises and organizations that are pursuing genomic-based approaches to health in order to accelerate medical discovery. DNAnexus is supporting customers around the world that are tackling some of the most challenging and exciting opportunities in human health. For more information, please visit: https://dnanexus.com and follow us at @DNAnexus.


MOUNTAIN VIEW, Calif.--(BUSINESS WIRE)--DNAnexus, the global leader in genome informatics and data management, today announced that it has worked with Intel Corporation, the world’s largest semiconductor company, to deploy elPrep, a high-performance software tool for the preparation of genomic data for large-scale sequence analysis. The first use is by Janssen Research & Development, a division of Janssen Pharmaceutica, which is currently using elPrep in the settings of precision medicine research and clinical applications. It is the mission of Janssen R&D to discover and develop innovative medicines that ease patient’s suffering, and solve the most important unmet medical needs of our time. elPrep, developed by Janssen R&D, IMEC and Intel as part of the ExaScience Life Lab, was designed for preparing SAM/BAM/CRAM files for variant calling in next-generation sequence analysis workflows. The ExaScience Life Lab is a collaboration between IMEC, Intel, and Janssen Pharmaceutica to explore the application of high-performance computing to problems in the life sciences industry. IMEC is a world-leading nanoelectronics research center headquartered in Leuven, Belgium. “elPrep is completely compatible with existing tools and datasets, and can be used as a drop-in replacement for SAMtools and Picard to deliver a 6-10x performance enhancement,” according to Ketan Paranjape, General Manager Life Sciences at Intel Corporation. These results, shown with benchmarks executing elPrep on a 24-core server consisting of 12-core Intel Xeon E5-2690 processors, clocked at 2.6 GHz. “The DNAnexus platform has been designed to host a variety of genome sequencing tools and applications for clinical research and advancing genomic medicine,” said Richard Daly, CEO of DNAnexus. “We are proud to partner with Intel to bring the elPrep tool to the global DNAnexus network.” The ExaScience Life Lab has open-sourced elPrep on GitHub, and DNAnexus specific modifications are available in a public project on the DNAnexus platform. DNAnexus combines expertise in cloud computing and bioinformatics to create the global network for genomic medicine. DNAnexus provides security, scalability and collaboration for enterprises and organizations that are pursuing genomic-based approaches to health in order to accelerate medical discovery. DNAnexus is supporting customers around the world that are tackling some of the most challenging and exciting opportunities in human health. For more information, please visit: https://dnanexus.com and follow us at @DNAnexus.

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