DNAnexus

DNAnexus is an American genomics technology company that provides cloud-based infrastructure for storing, managing, analyzing, and sharing DNA sequence data. Founded in 2009 as a Stanford University spin-off, the company was created in response to the computational and data-management demands generated by next-generation DNA sequencing. Its platform combines cloud storage, scalable computing, bioinformatics applications, workflow execution, and collaboration tools so that research organizations and clinical laboratories can process large genomic datasets without building all of the required infrastructure internally. The company’s initial technology was designed for DNA sequence analysis and supported common bioinformatics tasks such as read mapping, RNA sequencing analysis, ChIP-seq processing, and genomic variant analysis. Its infrastructure has used Amazon Web Services for computational workloads and storage. The platform model allows users to bring sequencing data into a managed environment, run analysis applications and pipelines, preserve intermediate and final results, and share data or workflows with collaborators. This positioning places DNAnexus between conventional laboratory informatics systems, bioinformatics software vendors, and general-purpose public-cloud providers. DNAnexus became associated with large-scale genomics computing through projects involving academic research organizations and sequencing consortia. In 2013, it worked with the Human Genome Sequencing Center at Baylor College of Medicine on a cloud-based analysis involving thousands of whole human genomes and exomes for the CHARGE consortium. The project demonstrated the use of public-cloud infrastructure for a workload involving hundreds of terabytes of genomic data and millions of core-hours of computation. The company also pursued public-data and clinical applications. In 2011, after uncertainty surrounding future funding for the National Center for Biotechnology Information’s Sequence Read Archive, DNAnexus worked with Google to create a cloud-hosted mirror and a new interface for accessing the archive. That hosting effort ended in 2012 after NCBI indicated that it would continue funding the database, although DNAnexus continued to provide a search and browsing interface for the NCBI-hosted resource. In 2012, the company announced work with Geisinger Health System and the University of California, San Francisco, to adapt its technology for clinical medicine. In 2013, it began offering its platform as a service to clinical testing laboratories, extending its target market beyond academic genomics. DNAnexus has also sought to build an application ecosystem around its platform. A developer program launched in 2013 was intended to help software developers create applications that could run within the DNAnexus environment. The company has financed its expansion through venture investment, including early funding from First Round Capital, K9 Ventures, and SoftTech VC, a $15 million round announced in 2011, and a further $15 million Series C round announced in 2014. Its public profile has centered on genomic data infrastructure rather than consumer genetic testing, sequencing instruments, or pharmaceutical products.

DNAnexus was established in early 2009 as a spin-off from Stanford University. Its founders were Stanford professors Serafim Batzoglou and Arend Sidow, together with Stanford computer scientist Andreas Sundquist. The founding premise was that the rapid adoption of DNA sequencing was creating a bottleneck in computing, storage, reproducibility, and collaboration. Rather than requiring each research group to assemble its own servers and software environment, DNAnexus sought to provide a managed cloud platform for genomic data. The company obtained $1.55 million in early venture financing from First Round Capital, K9 Ventures, and SoftTech VC. In April 2010, it launched a cloud-based sequence-data service. The service was designed to support both storage and computational analysis, using public-cloud resources to scale workloads according to the size of a project. Its applications included read mapping, RNA-seq, ChIP-seq, and analysis of genomic variants. Amazon Web Services served as the underlying infrastructure for important workloads. In 2011, DNAnexus attracted additional attention through both hiring initiatives and financing. It announced a $15 million funding round in October, with participation from Google Ventures, TPG Biotech, First Round Capital, SoftTech VC, K9 Ventures, and Felicis Ventures. Around the same period, it responded to concerns about the possible loss of funding for NCBI’s Sequence Read Archive. Working with Google Cloud Storage, DNAnexus developed a mirror of the archive and a new web interface. The hosted copy contained more than 350 terabytes of sequence data. NCBI later confirmed continued support for the archive, and DNAnexus ceased hosting the mirror in June 2012, while continuing to offer search and browsing functionality for the NCBI-hosted database. The company broadened its clinical and translational ambitions in 2012. It announced collaboration with Geisinger Health System and the University of California, San Francisco, to adapt its technology for clinical medicine. In 2013, it made its platform available as a service to clinical testing laboratories. That move reflected a shift from serving primarily as research infrastructure toward supporting regulated or clinically oriented genomic workflows, although the available reference material does not establish the full scope of the company’s later regulatory offerings. DNAnexus also invested in platform extensibility. In June 2013, it introduced a developer program intended to help third parties build applications that could run on the platform. The approach aimed to make the company’s environment useful not only as a hosted analysis service but also as a foundation for specialized bioinformatics tools and workflows. A major demonstration of the platform’s scalability came in October 2013, when DNAnexus announced a collaboration with the Human Genome Sequencing Center at Baylor College of Medicine. The partners analyzed 3,751 whole human genomes and 10,771 exomes for the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium. The work used Amazon Web Services, approximately 2.4 million core-hours, and generated about 430 terabytes of data. It was presented as the largest cloud-based genomics analysis completed at that point. In January 2014, DNAnexus announced a $15 million Series C financing round involving Claremont Creek Ventures, First Round Capital, Google Ventures, and TPG Biotech. The financing supported the company’s continued development as a genomics data platform. Publicly documented materials in the supplied references provide limited detail about later corporate events, ownership, current leadership, revenue, or financial performance. The company’s documented identity remains that of a cloud-based genomic data analysis and management provider serving research and clinical users.

1. 2014Series C financing announced

   DNAnexus announced a $15 million Series C round led by existing and new venture investors.

   Source
2. 2013Clinical laboratory service introduced

   The company began offering its platform as a service to clinical testing laboratories.

   Source
3. 2013Large-scale Baylor genomics analysis completed

   DNAnexus and Baylor reported cloud analysis of thousands of genomes and exomes for the CHARGE consortium.

   Source
4. 2012Clinical medicine collaboration announced

   DNAnexus announced work with Geisinger Health System and UCSF to adapt its platform for clinical applications.

   Source
5. 2011Major venture financing announced

   The company announced a $15 million funding round from a group of technology and biotechnology investors.

   Source
6. 2011Sequence Read Archive mirror project announced

   DNAnexus partnered with Google to develop a cloud-hosted mirror and interface for NCBI's Sequence Read Archive.

   Source
7. 2010Cloud sequence-data service launched

   DNAnexus launched its cloud-based service for genomic sequence data in April.

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8. 2009Company founded as a Stanford spin-off

   DNAnexus was founded by Stanford-affiliated researchers and a computer scientist to address the infrastructure requirements of large-scale DNA sequence analysis.

   Source

A cloud-based genomics data and bioinformatics platform for research organizations, sequencing programs, and clinical laboratories.

• DNAnexus PlatformGenomics cloud platform2010

  DNAnexus Platform is the company’s core cloud environment for genomic data storage, management, analysis, workflow execution, and collaboration. It is designed to let researchers and clinical laboratories run computationally intensive sequencing workflows using scalable cloud infrastructure rather than maintaining equivalent local systems. Documented capabilities include applications for read mapping, RNA-seq, ChIP-seq, and genomic variant analysis, along with tools for handling large datasets and sharing results.

• Sequence Read Archive search and browsing interfaceGenomic data discovery2011

  DNAnexus developed a web interface for searching and browsing sequence data associated with the National Center for Biotechnology Information’s Sequence Read Archive. The company also worked with Google on a large cloud-hosted mirror when the archive’s future funding was uncertain. After NCBI continued funding the archive and DNAnexus ended the mirror-hosting effort, the interface remained part of the company’s documented contribution to access and discovery around the public resource.

• Clinical genomics platform serviceClinical laboratory informatics2013

  Beginning in 2013, DNAnexus offered its cloud platform as a service to clinical testing laboratories. The service extended the company’s research-oriented genomic analysis capabilities into clinical laboratory settings, where sequence data must be processed, interpreted, stored, and shared as part of testing workflows. The supplied references do not specify the complete product name or the later regulatory status of this offering.

• 2013Developer program

  International

  DNAnexus launched a program to help software developers create applications that could run on its genomics platform, supporting an ecosystem approach around cloud-based bioinformatics.

  Outcome. The supplied reference confirms the program’s launch but does not document participation levels or subsequent commercial results.

  Source

• 2013Expanded platform into clinical testing laboratoriesStrategy

  After collaboration with Geisinger Health System and UCSF on clinical applications, DNAnexus sought to extend its technology beyond academic research.

  What changed. The company began offering its cloud-based platform as a service to clinical testing laboratories for DNA sequence analysis.

  Aftermath. This broadened the documented target market to include clinical genomics and laboratory informatics users.

  Source
• 2012Ended hosting of the Sequence Read Archive mirrorStrategy

  DNAnexus had worked with Google to host a mirror of NCBI’s Sequence Read Archive after concerns that NCBI funding might be discontinued.

  What changed. After NCBI announced that it would continue funding the archive, DNAnexus stopped hosting the mirrored dataset and continued providing a search and browsing interface.

  Aftermath. The decision aligned the company’s role with the NCBI-hosted archive while preserving a user-facing discovery function.

  Source

• 2014DNAnexus announces $15 million Series C financing

  DNAnexus announced Series C financing from Claremont Creek Ventures, First Round Capital, Google Ventures, and TPG Biotech.

  Other
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• 2013DNAnexus launches clinical laboratory platform service

  DNAnexus began offering its cloud platform as a service to clinical testing laboratories for DNA sequence data analysis.

  Product launch
  Source
• 2013DNAnexus and Baylor report large-scale cloud genomics analysis

  The companies reported a cloud-based analysis of 3,751 whole human genomes and 10,771 exomes for the CHARGE consortium, using Amazon Web Services infrastructure.

  Other
  Source
• 2012DNAnexus ends hosted Sequence Read Archive mirror

  The company stopped hosting the Sequence Read Archive mirror after NCBI indicated that it would continue funding the archive, while retaining a search and browsing interface.

  Other
  Source
• 2012DNAnexus expands toward clinical genomics

  DNAnexus announced a partnership with Geisinger Health System and the University of California, San Francisco, to develop applications of its technology in clinical medicine.

  Other
  Source
• 2011DNAnexus announces $15 million venture funding round

  DNAnexus announced a funding round backed by Google Ventures, TPG Biotech, First Round Capital, SoftTech VC, K9 Ventures, and Felicis Ventures.

  Other
  Source
• 2011DNAnexus works with Google on a Sequence Read Archive mirror

  DNAnexus announced work with Google Cloud Storage to host a mirror and interface for the National Center for Biotechnology Information's Sequence Read Archive.

  Other
  Source
• 2010DNAnexus launches cloud-based sequence data service

  The company introduced its cloud service for managing and analyzing DNA sequence data.

  Product launch
  Source

1. DNAnexus
2. DNAnexus official website