Computational Challenges of Genome Wide Association Studies (GWAS)
Request for Proposals 2007

DEADLINE EXTENSION for last date for submission of proposals:  January 31, 2008, 10:00 AM PST

Background

Genome-wide association studies (GWAS) aims to correlate patterns of genomic variation with phenotypes such as response to drugs, disease, aging, or the expression of genetic disorders. The National Institutes of Health sees GWAS as “laying the groundwork for an era of personalized medicine.” Microsoft Research seeks to aid researchers, scientists and clinicians in this endeavor.

The scientific community has generated and stored datasets for broad usage. Tools for data analysis have been created and deployed. However, researchers are hampered by data inconsistencies and algorithm performance. There is also a need to remove obstacles to collaboration and promote results sharing. This request for proposals (RFP) focuses on encouraging the development of computational solutions ranging from data access and database federation to human computer interactions (HCI) and algorithm parallelization.

Combining clinical and phenotype data with enabling solutions in this area will ultimately help in the prediction of disease and patient care—in particular for common diseases for which there is a genetic predisposition such as diabetes, asthma, cancer and heart disease. Successful proposals will address the limitations of existing systems and facilitate solving a specific genomic research question.

Goals & Objectives

The ultimate objective of this RFP is to accelerate the rate of discovery of common genetic factors that influence health and disease. Specific goals include, but are not limited to the following areas:

Data Access
Development of applications and online interfaces that enable researchers to access new and existing genomic data sources in faster and more and intuitive ways. Of particular interest are systems that combine access to publically available genomic databases, such as dbGaP, with data-access models. This includes tools for data search, federation, query optimization, sorting and filtration for SNP and expression data.

Data Standardization
Enabling standardized, interoperable capture of genomic data. This includes analysis of existing systems and new solutions, as well as methods of lossless data federation.

Tool Development
Enabling the development and improvement of analytic algorithms for GWAS. This includes interfaces that enable access to these tools more ubiquitously and simultaneously enables higher throughput through optimization and parallelization.

Data Visualization
Creation of new or improvement of existing data visualization tools to be deployed in the analysis of genomic data. These tools should facilitate the identification and extraction of patterns in order to help identify relationships between different components of genomic data. Ideally these applications would be integrated with existing genomic analysis tools.

Awards

The total amount available under this request for proposals (RFP) is $700,000. Microsoft Research anticipates making approximately 4-5 awards averaging $150,000, with a maximum of $200,000 for any single award. All awards will be made in $US. Awards are generally made as unrestricted gifts to the institution. Outside the United States other local restrictions may apply to the terms of the award. For current policy regarding non-U.S. countries, please refer to http://research.microsoft.com/ur/us/fundingopps/faq.aspx

For all awards, payment of indirect costs (“overhead”) is not permitted.

Microsoft Research will take into account the reasonableness of the amount requested in any proposal in light of stated deliverables, local costs, etc., and reserves the right to fund proposals at an amount lower than requested if appropriate.

Awards are made for the purpose of seed-funding larger initiatives, proofs of concept, or demonstrations of feasibility. It is important to understand that funding will continue after the first year only in exceptional circumstances, and that the principal investigators should therefore make every effort to leverage Microsoft Research funds as one component of a diverse funding base in a larger or longer-running project.

Eligibility

Conditions of eligibility listed below will be strictly adhered to, so please read them carefully. Proposals not meeting all these criteria will not be considered.

1. The proposing institution must be either:
   1. An accredited degree-granting college or university (or international equivalent) with non-profit status and awarding degrees at the baccalaureate level or above.
   2. A research institution with non-profit status.
2. All qualifying institutions are eligible without regard for geographic location.
3. An institution will be awarded a maximum of one gift per RFP, regardless of the number of proposals submitted from the institution. Collaborative proposals embracing multiple groups across the organization are encouraged.
4. Proposals that are incomplete, inaccurate, request funds in excess of the maximum award available, or are otherwise not responsive to the terms and conditions of this RFP will, at the sole discretion of Microsoft Research, be excluded from consideration.
5. Proposals from or on behalf of persons participating in the evaluation process for this RFP will not be considered.
6. Proposals should evidence a commitment to make all results arising from a funded project (including all intellectual property in those results) broadly available by either:
   1. dedicating such results to the public domain through publication, presentation or upload to data repositories; or
   2. making the results available under a non-restrictive license that allows modification and redistribution without any significant restrictions or conditions, including so-called “reach through” provisions that require publication of source code. An example of an acceptable license is the BSD license available at http://www.opensource.org/licenses/bsd-license.html, whereas GPL and LGPL licenses are not acceptable.
7. Proposals should evidence willingness to contribute any resulting curriculum material to the MSDN Academic Alliance Repository at http://www.msdnaacr.net/curriculum/facetmain.aspx.
8. The receiving institution must agree that awards made as unrestricted gifts, will not be subject to indirect costs or overhead charges and these may not be included in the budget for the proposed project.
9. While the use of Microsoft technologies is not a condition of this RFP, any proposal relying exclusively on non-Microsoft technologies should provide a justification for why this must be the case. Please note that ordinary use of Microsoft Office applications will not be compelling in itself, although innovative uses of Office applications (or the use of applications such as SQLServer, Visual Studio, C#, .NET and Windows Presentation Foundation) are acceptable and encouraged. We are not able to provide support for the development of exclusively Java or LINUX-based applications. Use of non-Microsoft applications on Windows, cross-platform development, and interoperability with other operating systems and applications are all encouraged.

Submission Process

Proposals will be accepted in electronic form only at http://microsoft.redwhale.com. Proposals submitted to Microsoft Research will not be returned. Microsoft Research cannot assume responsibility for the confidentiality of information in submitted proposals. Therefore, proposals should not contain information that is confidential, restricted or sensitive. Microsoft Research reserves the right to make public proposals that receive awards, except those portions containing budgetary or personally identifiable information.

The submission process includes two parts.

1. Brief summary and contact information. Applicants must provide full contact information for principal investigators, amount requested, and a brief abstract. This information will be submitted through a web form as part of the submission process.
2. Complete proposal containing full detail on the proposed project. 7 pages maximum, 10pt. font or larger, double-spaced, in either Microsoft Word or PDF format. Exceeding 7 pages may result in disqualification.

Proposals should address each of the items listed below under separate numbered headings:

1. Problem Statement: What is the problem or curriculum area addressed by the proposal and why is it important? What is the potential contribution to the field of the project if successful? Cite relevant work in the field as appropriate.
2. Expected outcomes: What tangible assets, if any, will be created or produced as a result of the proposed project? How will the results of this project be disseminated to others?
3. Schedule: When is the project to be completed? What milestones will be used to measure progress of the project and when will they be completed? (If the project described is part of a larger ongoing research program, estimate the time for completion of this project only).
4. Use of Funds: Provide a budget ($US) describing how the award will be used, including purchases of hardware or software, salaries, and other costs. Microsoft software or licenses requested should be listed in the budget, but the cost should be given as zero dollars. The budget does not have to be detailed, and should be presented as a table with the total budget request clearly indicated. Please note that, because awards are made as unrestricted gifts, Microsoft policy prohibits the payment of indirect cost (“overhead”).
5. Use of Microsoft Technologies: Describe the Microsoft tools and technologies (if any) to be used in this project. If software is to be developed, give details of the tools to be used, the number of software developers and the proposed timescale. Does the software to be developed require the incorporation of code from commercial or public-domain libraries? If so, please give details.
6. Research Question Addressed: Give a brief summary of the current state of the art in this field, including references where appropriate and how the proposed project will address a specific research question.
7. Dissemination and Evaluation: How will the results of this project be evaluated (if appropriate), and how will they be disseminated to others? Under what general license terms will the results be made available?
8. Other Support: Including other contributions to this project (cash, goods or services), if any, but not including such things as use of university facilities otherwise provided on an ongoing basis. Please note: authors of winning proposals will be required to submit an original letter on department letterhead certifying the commitment of any additional or matching support described in the proposal.
9. Qualifications of Principal Investigator: Include a brief description of any relevant prior research, teaching, publication or other professional experience. A detailed vita or list of publications is not required.

Please do not submit any confidential materials to Microsoft.

Selection Process and Criteria

All proposals in compliance with the eligibility criteria and received by the deadline will be peer-reviewed by a panel of subject-matter experts chosen by Microsoft Research, and which may include experts from outside the company. Based on evaluations by the review panel, Microsoft Research will select the most worthy proposals for funding. Microsoft Research reserves the right to fund winning proposals at an amount greater or less than the amount requested, up to the stated maximum amount for individual awards. Due to the volume of submissions and for legal reasons, Microsoft Research cannot provide individual feedback on proposals that are not funded.

Authors (including co-investigators) of winning proposals will be required to grant Microsoft permission for the use of their name, image, institutional affiliation and related professional information in press releases or other forums for publication of their award. Microsoft Research may also request assistance with the preparation of posters, slides or other materials, and periodic reports on the status of funded projects.

All proposals will be evaluated based upon the following criteria:

1. Well-defined goals and objectives that, if achieved, have the potential to have a significant impact on research in genome wide association studies. There should be at least one research question addressed by the project.
2. Realistic Timescale for the goals to be achieved. It should be possible to complete the goals within the timescale of the funded project, and where appropriate placed into the context of milestones in a larger or longer-running project.
3. Potential for wide dissemination and use of intellectual property created, including specific plans for publications, conference presentations, distance learning, etc., as well as plans to distribute content in multiple formats or languages.
4. Ability to complete the project including the adequacy of resources available, reasonableness of timelines, and number and qualifications of identified contributors.
5. Leveraging of other resources: preferential consideration will be given to proposals utilizing additional sources of funding to build larger or longer-running projects and/or leveraging other projects or resources in the field.

Schedule and Deadlines

Please be advised that we are obligated to strictly adhere to the deadline date and time. The application system will not accept submissions after the deadline has expired. Exceptions to this policy cannot be granted. It is advisable to upload your submission well in advance of the deadline.

Additional Resources

Please address any questions to “ktolle[at]microsoft[dot]com”. Please put “GWAS RFP” in the subject line of your e-mail message to ensure a prompt and proper response.

Microsoft Word version of this document