SOURCES SOUGHT
B -- Exome Analysis
- Notice Date
- 6/18/2013
- Notice Type
- Sources Sought
- NAICS
- 541511
— Custom Computer Programming Services
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Heart, Lung and Blood Institute, Rockledge Dr. Bethesda, MD, Office of Acquisitions, 6701 Rockledge Dr RKL2/6100 MSC 7902, Bethesda, Maryland, 20892-7902
- ZIP Code
- 20892-7902
- Solicitation Number
- HHS-NIH-NHLBI-CSB-(Hg)-SBSS-2013-180-DLM
- Archive Date
- 7/20/2013
- Point of Contact
- Dorothy Maxwell, Phone: 301-435-0352
- E-Mail Address
-
maxwelld@mail.nih.gov
(maxwelld@mail.nih.gov)
- Small Business Set-Aside
- N/A
- Description
- This is a Small Business Sources Sought notice. This is NOT a solicitation for proposals, proposal abstracts, or quotations. The purpose of this notice is to obtain information regarding: (1) the availability and capability of qualified small business sources; (2) whether they are small businesses; HUBZone small businesses; service-disabled, veteran-owned small businesses; 8(a) small businesses; veteran-owned small businesses; woman-owned small businesses; or small disadvantaged businesses; and (3) their size classification relative to the North American Industry Classification System (NAICS) code for the proposed acquisition. Your responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible. An organization that is not considered a small business under the applicable NAICS code should not submit a response to this notice." A. Background: The National Institute of Health (NIH) is the nation's leading medical research agency and the primary Federal agency conducting, supporting and making medical discoveries that improve people's health and save lives. The National Institutes of Health Undiagnosed Disease Program (UDP) is a trans-National Institute of Health (NIH) initiative that focuses on the most puzzling medical cases referred to the NIH Clinical Center in Bethesda, Md. It was organized by the National Human Genome Research Institute (NHGRI), the NIH Office of Rare Diseases Research (ORDR) and the NIH Clinical Center. Many medical specialties from other NIH research centers and institutes contribute the expertise needed to conduct the program, including endocrinology, immunology, oncology, dermatology, dentistry, cardiology and genetics, among the dozens of participating senior attending physicians. A longstanding medical condition that eludes diagnosis by a referring physician can be considered undiagnosed and may be of interest to this clinical research program. The exome analysis pipeline developed at UDP uses trio data to identify the total set of mutations in the pro-band genome, as well as their pattern of inheritance from the parents. While the pipeline is implemented at NIH, the current version of the code is suboptimal for high throughput analysis in a cluster environment B. Purpose and Objectives: The purpose of this requirement is to provide a robust methodology for analysis of the UDP exomes according to and improving upon the methodology developed by the UDP. Specifically, this involves the reimplementation and refinement of the current UDP exome analysis pipeline, implementation of tools to identify medium-scale indels (20-10,000bp), and novel Alu retrotranspositions, and development of tools for prioritizing potentially causative variants based on phenotypes. These objectives support the research needs of the UDP through generating tools that can then lead to the characterization of causes of new and rare diseases. C. Scope of Work: The Contractor shall provide: 1) reimplementation of the UDP Trio NGS Analysis pipeline; 2) improvements to UDP pipeline by identifying additional types of variation; 3) implementation of variant prioritization techniques and data visualization; 4) exome data processing; and 5) an integration of these with the UDP work flow. Specifically the contractor shall: 1. Provide reimplementation and refinement of the current UDP analysis pipeline. 2. Perform implementation of the iteration of parental chromosome inference to improve alignment quality and reduce False-Negative calls. 3. Perform implementation of a Smith-Waterman based realignment, or direct read re-assembly to improve alignment quality proximal to identified insertion/deletion (indel) variants. 4. Identify medium-length indels, we will implement within the UDP pipeline developed in D1 the PRISM tool developed by us previously (http://compbio.cs.toronto.edu/prism) 5. Identify novel Alu retrotranspositions we will implement within the UDP pipeline developed in D1 the Alu-Detect tool being developed by us (http://compbio.cs.toronto.edu/aludetect) 6. Install and configure the Exomizer software (developed by collaborators Smedley and Robinson) at CCM. Enable the integration of Exomizer into the UDP pipeline 7. Add all resulting data (variants and prioritizations) to the MedSavant database, and make the data available to the UDP using remote access protocols. 8. The above pipeline, consisting of steps D1-D3, will be run on all exomes provided by the UDP. This is estimated at 500 exomes (200 probands) per year. 9. Develop APIs for communication of the above with the UDP process management infrastructure (LIMS). 10. Develop and supply required algorithms, software tools to accomplish the above as well as assist in the implementation of these tools in the UDP work flow (LIMS). 11. Supply a platform for analysis of UDP exomes according to the UDP requirements as specified above. 12. Supply results with qualified interpretations in formats appropriate to the process management systems and for facilitation of other collaborations. D. Projects: 1. Project P1 : Reimplementation of the UDP Trio NGS Analysis pipeline Rationale: The exome analysis pipeline developed at UDP uses trio data to identify the total sets of mutations of proband genome as well as their pattern of inheritance from the parents. While the pipeline is implemented at NIH, the current version of the code is suboptimal for high throughput analysis in a cluster environment. Deliverables: • Reimplementation of current UDP analysis pipeline at CCM - making it compatible with local scheduler to speed up analysis. • Implementation of the iteration of parental chromosome inference to improve alignment quality and reduce False-Negative calls. • Implementation of a Smith-Waterman based realignment, or direct read re-assembly to improve alignment quality proximal to identified insertion/deletion (indel) variants. 2. Project P2 : Improvements to UDP pipeline by identifying additional variant types Rationale: The UDP pipeline, in its current state, is optimized for identification of small-scale variation (SNPs and small indels, < 20bp), and large-scale Copy Number Variants (through the use of arrays). Simultaneously, the current pipeline does not allow for the identification of medium-scale indels (20-10,000bp), and novel Alu retrotranspositions. Deliverables: • To identify medium-length indels, we will implement within the UDP pipeline developed in P1 the PRISM tool developed by us previously (http://compbio.cs.toronto.edu/prism) • To identify novel Alu retrotranspositions we will implement within the UDP pipeline developed in P1 the Alu-Detect tool being developed by us (http://compbio.cs.toronto.edu/aludetect) 3. Project P3 : Implementation of Variant Prioritization and Data Visualization Rationale: To enable easier identification of causative variants within UDP-sequenced genomes we will utilize methodologies to help prioritize potentially causative variants based on phenotypes indicated for each patient using the Exomizer software, and provide visualization of resulting data and analyses through MedSavant. Deliverables : • Install and configure the Exomizer software. Enable the integration of Exomizer into the UDP pipeline • All resulting data (variants and prioritizations) will be added to the MedSavant database, and will be made available to the UDP using remote access protocols. 4. P4: Exome Data Processing Deliverables: The above pipeline, consisting of steps P1-P3, will be run on all exomes provided by the UDP. E. Other considerations: 1. The Contractor is required to provide reports, record methods, and materials as appropriate to the highest scientific standards. These materials, methods and results will be shared will agreed upon UDP collaborators. 2. The Government will provide the data for analysis of the effectiveness of the tools being developed; this includes phenotypes and exome data. 3. No government property will be provided in the performance of the requirement. 4. The Government will not furnish any facilities or provide space in the performance of the requirement. 5. The desired results, end items or functions of the project are: (1) a stable and robust platform for analysis of UDP exomes according to the criteria pioneered within the UDP; (2) Integration of this analysis with the tools being developed by the Monarch consortium and with the untargeted analyses of UDP patient samples; and (3) Research collaborations conducted via Videoconferences, email communications, shared professional presentations, posters and publications. Grand Round presentations at the Contractor's location and the NIH Clinical Center may also occur. F. Anticipated Period of Performance: Twelve (12) months from the date of award. G. Capability Statement /Information: Interested parties are expected to review this notice to familiarize itself with the requirements of this project. Failure to do so will be at your firm's own risk. The following information shall be included in the capability statement: 1. A general overview of the respondents' opinions about the difficulty and /or feasibility of the potential requirement, and any information regarding innovative ideas or concepts. 2. Information in sufficient details of the respondents' (a) staff expertise, including their availability, experience, and formal and other training; (b) current in-house capability and capacity to perform the work; (c) prior completed projects of similar nature; (d) corporate experience and management capability; and (e) examples of prior completed Government contracts, references, and other related information. 3. The respondents' DUNS number, organization name, address, point of contact, and size and type of business (e.g., 8(a), HUBZone, etc) pursuant to the North American Industry Classification System (NAICS) code: 541511 Custom Programming Services, small business size standard is $25.5M. 4. Any other information that may be helpful in developing or finalizing the requirements of the potential acquisition. 5. The capability statement shall not exceed 20 single-sided pages (including all attachments, resumes, charts, etc.) presented in single-space and using a 12-point font size minimum, in either Microsoft Word or Adobe Portable Document Format (PDF), with 8-1/2 by 11 inch paper size, and 1 inch top, bottom, left and right margins. 6. All proprietary information should be marked as such. Statements should also include an indication of current certified small business status; this indication should be clearly marked on the first page of your capability statement (preferably placed under the eligible small business concern's name and address). Responses will be reviewed only by NIH personnel and will be held in a confidential manner. H. Closing Statement : The capability statement should be submitted electronically (via email) to Dorothy Maxwell, Contract Specialist, at maxwelld@mail.nih.gov, on or below June 28, 2013, 7:30 AM, EST. All responses must be received by the specified due date and time in order to be considered. This Sources Sought Notice (SS) is for information and planning purposes only and shall not be construed as a solicitation or as an obligation on the part of the National Heart, Lung, and Blood Institute (NHLBI).The NHLBI does not intend to award a contract on the basis of responses nor otherwise pay for the preparation of any information submitted. As a result of this notice, the NHLBI may issue a Request for Quote (RFQ). THERE IS NO SOLICITATION AVAILABLE AT THIS TIME. However, should such a requirement materialize, no basis for claims against NHLBI shall arise as a result of a response to this notice or the NHLBI's use of such information as either part of our evaluation process or in developing specifications for any subsequent requirement. " Disclaimer and Important Notes". This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization's qualifications to perform the work. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, a pre-solicitation synopsis and solicitation may be published in Federal Business Opportunities. However, responses to this notice will not be considered adequate responses to a solicitation. Confidentiality. No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s)."
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/NIH/NHLBI/HHS-NIH-NHLBI-CSB-(Hg)-SBSS-2013-180-DLM/listing.html)
- Place of Performance
- Address: NIH Undiagnosed Disease Program Center, Bethesda, Maryland, 20892, United States
- Zip Code: 20892
- Zip Code: 20892
- Record
- SN03092334-W 20130620/130618234750-19e72cd7e3e99b04065b77a40a7ec40b (fbodaily.com)
- Source
-
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