Akaza Research to develop gene expression repository for the Harvard Brain Tissue Resource Center at McLean Hospital

Cambridge, MA – July 17, 2003 – Akaza Research, announced that it has been contracted by the Harvard Brain Tissue Resource Center (HBTRC) at McLean Hospital (Belmont, MA) to develop the National Brain Databank, a public gene expression repository to provide the neuroscience community with data generated by microarray experiments conducted on human brain tissue of patients with psychiatric and neurological disorders.

The Harvard Brain Tissue Resource Center, or “Brainbank”, was established at McLean Hospital to serve as a federally funded resource for the collection and distribution of human brain specimens for research. As a designated “NIH National Resource”, the Brainbank provides a vital public service by collecting and disseminating postmortem brain tissue samples to the neuroscience research community. These brain tissues are typically related to neurological disorders including Huntington's, Parkinson's, and Alzheimer's, psychiatric disorders like schizophrenia and manic-depression (bipolar disorder), as well as normal control specimens which are essential for comparative work. Collectively, these samples are used for a wide variety of applications, including receptor binding, immunocytochemistry, in situ hybridization, virus detection, polymerase chain reaction (PCR), DNA sequencing, mRNA isolation, and a broad range of neurochemical assays.

The unique public mandate of the Brainbank combined with its growing repository of over 5,800 human brain samples places the Brainbank in a unique position to provide high quality data on its cohort samples to the research community. With this project developed in conjunction with Akaza Research, the Brainbank seeks to establish a publicly accessible gene expression repository, the National Brain Databank, to collect and disseminate the results of and data from postmortem studies of neurological and psychiatric disorders. The web-based repository will be designed to provide researchers and investigators with secure and selective access to collections at the Brainbank, including the McLean 66 cohort, along with gene expression profiles, diagnostic reports, demographic data, and brain tissue images. Dr. Francine Benes, director of the Brainbank and the Laboratory of Structural Neuroscience at McLean Hospital mentions that “since limited brain tissue cannot be easily replenished, providing physical samples to all investigators is clearly less effective than capturing and disseminating high quality electronic datasets extracted from gene expression profiling through the National Brain Databank. While many researchers will continue to request physical biological samples, the online repository can benefit a wider community of neuroscientists.”

Both the NIH and the neuroscience community have recently introduced “Statements on Sharing Research Data” (http://datasharing.net), while there has been emerging consensus and ongoing debate on the benefits and approach for sharing data among neuroscience researchers. Dr. Nitin Sawhney, Chief Scientific Officer at Akaza Research and the project lead on the National Brain Databank, mentions that “while the debate over data sharing is important, individual research organizations should take a clear position and adopt policies appropriate to their own institutional context and research mandates, keeping in mind the shared objectives of the neuroscience community. Given the specialized needs of individual researchers and institutions as well as the nature of their research experiments, it seems pragmatic to develop smaller, distributed databases that can be tied together through interoperable standards, thereby providing a broader, but unified network of resources to the neuroscience community.”

Dr. Sawhney notes that “microarray data standards will be essential to develop the National Brain Databank into an interoperable repository for gene expression data. In the past, the exchange of gene expression data among databases has been difficult due to lack of sufficient information on the microarray experiments provided in the published data and lack of unified standards, procedures and formats. However, with the emergence of microarray data standards include MIAME and MAGE-ML we can begin to develop repositories that provide complex experimental data in usable formats for researchers everywhere.” Dr. Sawhney is conducting a technical feasibility study and will lead the design of the system architecture and user interface.

The repository will be developed to be scaleable and extensible, created using open source platforms including the Java J2EE application framework, MAGE object model, and PostgreSQL database, such that it can be generalized and replicated for other neuroscience datasets. The repository will facilitate submission, validation and curation of gene expression data and related metadata for Brainbank tissue samples. Extensive visual and hierarchical queries using multiple views of brain regions and diagnostic criteria will allow interactive browsing and retrieval of datasets. The project will evaluate and implement open data sharing standards that support dissemination and collaboration on studies of neurological disorders, while providing secure access to data in strict compliance with HIPAA guidelines.

The first public beta release of the repository is scheduled in January 2004, while working prototypes will be evaluated in the interim with select neuroscience researchers in conjunction with the HBTRC scientific advisory board.

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