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News Article | December 24, 2016
Site: www.businesswire.com

MOUNTAIN VIEW, Calif.--(BUSINESS WIRE)--DNAnexus Inc., the global leader in genome informatics and data management, today announced that its cloud-based translational medicine platform was utilized in two important studies reporting data from the DiscovEHR collaboration between Geisinger Health System (GHS) and the Regeneron Genetics Center (RGC). These large-scale studies, which were published today in the journal Science, combined genomic data with electronic health records of more than 50,000 people and highlight the clinical and research value of integrating genetic and phenotypic data. “The idea of integrating genetic and phenotypic data to advance science and help patients has found palpable expression in the DiscovEHR program, powered by the DNAnexus translational medicine platform,” said David A. Shaywitz, MD, PhD, chief medical officer of DNAnexus. “It’s thrilling to see what can be accomplished when audacious champions commit their organizations to ambitious goals, and we’re privileged at DNAnexus to provide the platform capabilities that enable the vision to be implemented, science to be advanced, and improved care to be delivered.” Next-generation sequencing technologies have reduced the cost and increased the speed of DNA sequencing to the point where genome informatics is often the bottleneck. To address this issue, the DNAnexus translational medicine platform allows the RGC to analyze a massive volume of raw sequencing data rapidly and economically, enabling the processing of samples from more than 1,000 patients per week and the sharing of data easily and safely with collaborators such as GHS. The platform also provides a secure environment where genetic data can be combined with de-identified clinical data, paving the way for novel scientific insights. “These studies are a powerful example of how the DNAnexus platform is employed as the proven option at scale by organizations and consortia globally to integrate data, enable collaboration, and accelerate discovery,” said Richard Daly, chief executive officer of DNAnexus. Genomic data from these patients, all members of the Geisinger MyCode Community Health Initiative, have been linked to corresponding de-identified electronic health records, enabling the discovery of clinical associations supporting new and existing therapeutic targets. To date, 126,000 GHS patients have consented to participate in the MyCode initiative. Of those, 50,726 have had their exomes sequenced through the organization’s collaboration with RGC and analyzed on the DNAnexus translational platform. More than 200 patients –where disease-causing variants were found– have had results returned to them so far. These results were verified by an independent, certified lab and the results were delivered via established medical protocols. DNAnexus first deployed this secure translational platform in 2015 which enabled the combination and integrated analysis of genotypic and phenotypic data at scale. The two publications can be accessed via the Science website: “Distribution and clinical impact of functional variants in 50,726 whole-exome sequences from the DiscovEHR study” (DOI: 10.1126/science.aaf6814) “Genetic identification of familial hypercholesterolemia within a single U.S. health care system” (DOI: 10.1126/science.aaf7000) DNAnexus combines expertise in computing and bioinformatics to create the global network for genomics, operating in North America, Europe, Asia-Pacific (including China), South America, and Africa. The secure, scalable, and collaborative DNAnexus Platform helps thousands of researchers across a spectrum of industries – biopharmaceutical, bioagricultural, sequencing services, clinical diagnostics, government, and research consortia – accelerate their genomics programs globally. For more information on DNAnexus, please visit www.dnanexus.com or follow the company @DNAnexus.


News Article | December 9, 2016
Site: www.businesswire.com

MOUNTAIN VIEW, Calif.--(BUSINESS WIRE)--DNAnexus Inc., the global leader in genome informatics and data management, today announced that it has performed uniform reanalysis and mutation calling on the world’s largest pan-cancer dataset, encompassing 10,487 patients across 33 cancer types from The Cancer Genome Atlas (TCGA). TCGA is a joint effort of the National Cancer Institute (NCI), and the National Human Genome Research Institute (NHGRI). The mutation data has undergone additional quality control and filtering and is available as an open access dataset for download at the NCI Genomic Data Commons and on Synapse. The pipelines used are also fully available to researchers who wish to reproduce this TCGA mutation discovery via DNAnexus or a GitHub repository. “In the past, mutation calling for TCGA samples was primarily done for individual tumor types, with projects using different mutation callers or different versions of the callers, meaning the data wasn’t uniform,” said Carolyn Hutter, PhD, Program Director, Division of Genomic Medicine at the NHGRI. “We now believe the best way to do analysis is to have a uniform set of calls generated by multiple mutation callers, with quality control and filtering, across multiple cancer types. That’s why the TCGA team decided to go back and recall the over 10,000 exomes in TCGA and produce this multi-caller somatic mutation dataset.” The necessary compute resources for the mutation calling across cancer types was not in place at TCGA member institutes. Important requirements for the mutation calling project included patient security, a scalable environment that could handle tens of thousands of exomes, and reproducibility of results. The DNAnexus Platform had this capability. “This was a massive undertaking, and a prime example of the benefits of the DNAnexus Platform,” said Richard Daly, CEO of DNAnexus. “Over a four-week period approximately 1.8 million core-hours of computational time were used to process 400 TB of data to yield reproducible results. Now consistent data is available to researchers worldwide to interpret genomic features, oncogenic signatures, and potential treatment targets shared across multiple cancer types.” “Realigning TCGA data with a single methodology across new standardized mutation callers will make the tumor data much more relevant to the community. DNAnexus created uniform, and sensitive, analytical treatment through version-controlled analyses and tools, that would have been challenging to replicate at any single facility in a reasonable time frame,” said David Wheeler, PhD, Professor, Department of Molecular and Human Genetics at Baylor College of Medicine. “With this standardized set of mutation calls obtained by several callers, we’ll be able to identify genetic alterations contributing to cancer that are shared between tumors independent of the tissue-of-origin. We are optimistic that having access to such information will spur advancement in precision medicine.” Researchers now have access to the TCGA pipelines via the DNAnexus Platform in addition to a GitHub repository. DNAnexus works to ensure mechanisms for data access requests and vending data to approved requestors meets security standards for dbGaP and TCGA data in the cloud. DNAnexus combines expertise in computing and bioinformatics to create the global network for genomics, operating in North America, Europe, Asia-Pacific (including China), South America, and Africa. The secure, scalable, and collaborative DNAnexus Platform helps thousands of researchers across a spectrum of industries – biopharmaceutical, bioagricultural, sequencing services, clinical diagnostics, government, and research consortia – accelerate their genomics programs globally. For more information on DNAnexus, please visit www.dnanexus.com or follow the company @DNAnexus.


A computer application programming interface (API) for interacting with genomic data. Genomic data is stored by a genomic information provider using cloud-optimized, tabular structures in the form of genomic tables. A client computer may instruct, via API method calls, the genomic information provider to create a genomic table. Client computers may add genomic data to the genomic table via additional API method calls. A client computer may close the genomic table via an API method call. Once closed, client computers may retrieve genomic data based on genomic coordinates from the genomic table via API method calls. In this way, the transmission of genomic data via flat files can be avoided.


Patent
DNAnexus | Date: 2014-03-03

An ensemble predictor for characterizing uncharacterized genetic mutations is disclosed. A first set of genomic information representing a particular (e.g., harmful) mutation is obtained. The first set of genomic information is provided to a number of underlying mutation impact predictors. Predictions are obtained from the underlying predictors. The predictions predict whether the first set of genomic information represents the particular mutation. The predictions and the particular (known) mutation are provided to a logistic regression model, which provides a coefficient for each underlying predictor. A second set of (uncharacterized) genomic information is obtained. The second set of genomic information is provided to the underlying predictors. Predictions are obtained from the underlying predictors and are then weighted using the coefficients. A characterization (e.g., as harmful or not) of the second set of genomic information is provided by the ensemble predictor based on the weighted underlying predictions and may be displayed.


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.


Grant
Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 74.48K | Year: 2010

DESCRIPTION (provided by applicant): DNAnexus proposes to develop a complete solution for the identification and stratification of personal genetic variation from ultra-high-throughput sequencing projects. The solution will be implemented as a Web 2.0 service and online browsing tool that will integrate public data sources such as the 1000 genomes project, comparative information, and the ENCODE II project data. Users will be able to browse and stratify the identified variation in the context of these genomic annotations, and according to the likely functional impact. In Phase I of our project, we will develop a basic browser for displaying sequence reads that are mapped to a reference genome with our state-of-the-art read mapper. The browser will support viewing mate paired reads as well as display of the variation between these reads and the reference genome. It will facilitate the algorithmic development that we will perform during Phase II, and it will be the foundation for the more sophisticated variation browser also proposed in Phase II. In Phase II, we will develop algorithms for detecting genomic variation, and a state-of-the-art browser for viewing variation in the context of existing genome annotations, functional genomic and comparative genomic data. Our algorithms for detecting variation will support all major types of genomic variation, including SNPs, microindels, larger insertions and deletions, duplications, copy number variations, inversions, and translocations. Our algorithms will be based on state-of-the-art statistical and machine learning methodology for human genome resequencing. The DNAnexus browser will have two components: a list browser that displays variation as a list filtered and stratified by criteria that a user chooses, and a powerful GUI whose navigation capabilities are inspired by modern online tools such as Google Maps. PUBLIC HEALTH RELEVANCE: DNAnexus proposes to develop a complete solution for identifying and analyzing personal genetic variation for individuals whose genomes are sequenced using new sequencing technologies. Users will be able to browse an individual genome in the context of public data sources such as the 1000 genomes project, comparative information to other mammalian species, and functional data from the ENCODE II project.


MOUNTAIN VIEW, Calif.--(BUSINESS WIRE)--#NGS--Stanford Center for Genomics and Personalized Medicine (SCGPM) has adopted the DNAnexus Platform on the Microsoft Azure cloud for genomic processing and data management.


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.

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