SOLICITATION NOTICE
B -- The reimplementation and refinement of the current UDP exome analysis pipeline.
- Notice Date
- 7/2/2013
- Notice Type
- Combined Synopsis/Solicitation
- 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)-2013-197-DLM
- Archive Date
- 7/24/2013
- 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
- i. This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in Subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; proposals are being requested and a written solicitation will not be issued. ii. The solicitation number is NHLBI-CSB-(HG)-2013--DLM and the solicitation is being posted as a request for proposal (RFP). Offerors shall submit their proposals no later than 7:30 a.m. Eastern Standard Time (EST) on July 9, 2013. iii. A statement that the solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2005-68, June 26, 2013. iv. The associated North American Industry Classification System (NAICS) code for this is 541511 Custom Programming Services; small business size standard is $25.5M. This acquisition is being conducted in accordance with the procedures of Simplified Acquisition Procedures (Simplified Acquisition Threshold of $150,000.00) as set forth in FAR Part 13. v. 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 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 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. A. 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 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. B. Contract 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. C. 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. D. Anticipated Period of Performance Twelve (12) months from the date of award. vi. NIH/UDP is located at 9 Memorial Drive, Bethesda, Maryland 20892. vii. The FAR Provision 52.212-1, Instructions to Offerors -- Commercial, applies to this acquisition and is hereby incorporated by reference. All Federal Acquisition Regulations (FAR) clauses may be viewed at http://acquisition.gov/comp/far/index.html. viii. EVALUATION OF PROPOSALS: The Government will evaluate proposals that are determined technically acceptable in accordance with the Technical Evaluation factors. The Government intends to award a single contract from this solicitation. The Government reserves the right not to award a contract. Evaluation of Proposals: The Government reserves the right to make an award without discussions based solely upon initial proposals. EVALUATION FACTORS: 1. Ability to implement the UDP exome analysis pipeline and refine it; 2. Ability to improve the UDP exome analysis pipeline by the addition of tools for identifying medium length indels and retrotransposition events; 3. Ability to provide a stable and cost effective platform to host the UDP exome data and support exome analysis by UDP personnel; 4. Ability to integrate phenotype characteristics into the analysis of UDP exome data and to coordinate that with the Monarch consortium; and 5. Ability to support the curation of phenotypes in HPO terms using a user friendly Web-based interface A. Price (This will be Firm-Fixed Price): An evaluation of the offeror's price proposal will be made to determine if proposed prices are realistic for the work to be performed, reflect a clear understanding of the requirements, and are consistent with the technical proposal. Reasonableness determinations will be made by determining if competition exists, by comparing proposed prices with established commercial or GSA price schedules (if applicable), and/or by comparing proposed prices with the Independent Government Cost Estimate (IGCE). ix. In accordance with FAR Clause 52.212-3, Offeror Representations and Certifications - Commercial Items, offerors must complete annual representations and certifications on-line at https://www.sam.gov/portal/public/SAM/. x. FAR clause 52.212-4, Contract Terms and Conditions - Commercial Items applies to this Acquisition. xi. FAR clause 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders - Commercial Items applies to this Acquisition. xii. The Defense Priorities and Allocations System (DPAS) and assigned rating does not apply to this acquisition. Offerors shall submit their proposals no later than 7:30 a.m. Eastern Standard Time (EST) on July 9, 2013. The proposal must reference the RFP Number: NHLBI-CSB-(HG)-2013-197-DLM. All responsible offerors may submit a proposal, which if timely received, shall be considered by the agency. Proposals can be emailed to the Contracting Specialist, Dorothy Maxwell at maxwelld@nhlbi.nih.gov; Quotations shall not be deemed received by the Government until the quotation is entered into the e-mail address inbox set forth above. Faxed proposals will NOT be accepted. Offerors' proposals shall not be deemed received by the Government until the proposal is entered into the e-mail address inbox set forth above. All quotes shall contain the following: 1. Name of Contracting Organization; 2. Contract Number (for subcontracts, provide the prime contract number and the subcontract number); 3. Contract Type; 4. Total Contract Value and Discounts; 5. Description of Requirement; 6. Contracting Officer's Name and Telephone Number; 7. North American Industry Classification System (NAICS) Code; and 8. DUNS Number. Offerors must complete annual representations and certifications on-line at https://www.sam.gov/portal/public/SAM/.
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/NIH/NHLBI/HHS-NIH-NHLBI-CSB-(HG)-2013-197-DLM/listing.html)
- Place of Performance
- Address: NIH, 9 Memorial Drive, Building 9, Bethesda, Maryland, 20892, United States
- Zip Code: 20892
- Zip Code: 20892
- Record
- SN03106189-W 20130704/130702235638-13b68dd09fbbc82634c089df6a71ecaf (fbodaily.com)
- Source
-
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