SOURCES SOUGHT
A -- Genotyping Services
- Notice Date
- 1/9/2006
- Notice Type
- Sources Sought
- NAICS
- 541710
— Research and Development in the Physical, Engineering, and Life Sciences
- 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, MD, 20892-7902
- ZIP Code
- 20892-7902
- Solicitation Number
- Reference-Number-NHLBI-PB-2006-091-MKL
- Response Due
- 1/19/2006
- Archive Date
- 2/3/2006
- Description
- THE NATIONAL HEART, LUNG, AND BLOOD INSTITUTE (NHLBI) is conducting a market survey to determine the availability and potential technical capability of small businesses to provide large-scale SNP high-quality genotyping, including, but not limited to: obtaining the samples, ordering the genotyping assays, obtaining reagents, genotyping SNPs, repeating failed genotyping reactions, genotyping additional SNPs to compensate for those that failed, assessing genotype quality, analyzing the data to produce a clean data set, transferring the data, and indirect, facilities, and/or administration services. The Statement of work is as follows: Objectives: The overall objective of this project is to identify genetic variants associated with heart, lung, blood and sleep (HLBS) disorders and diseases through the application of large-scale genotyping for genome-wide association analyses. In collaboration with the National Center for Biotechnology Information (NCBI), the National Heart, Lung and Blood Institute is developing a data resource that will integrate genome-wide genotypic information with phenotypic information from multiple NHLBI studies. Following its development, access will be provided to the scientific community to perform genome-wide association analyses and thus identify genetic variants that are correlated with HLBS disorders and diseases. The contractor will perform four major tasks: 1) sample receipt and handling; 2) large-scale genotyping of a panel of 500,000 (500K) or more assays (including quality control measures during production to identify genotyping errors and sample mix-ups) in about 16,200 samples from designated NHLBI studies; 3) data cleaning (including but not limited to checks for Hardy-Weinberg equilibrium and Mendelian inconsistencies); and 4) transfer of each of the completed and cleaned data sets to the NCBI for data integration and ultimately data dissemination. Background Information: Although linkage analysis and positional cloning have produced remarkable results for single-gene disorders, results are inconsistent for common disorders due to their multifactorial nature. Genetic contributions to major HLBS disorders are increasingly recognized as complex, heterogeneous, and difficult to identify and replicate. The lack of success of linkage studies is due to a combination of factors, including the moderate heritability and heterogeneous nature of common, complex traits, the inability of a set of markers spaced an average of 10 million base pairs apart to obtain complete information about inheritance, the imprecision of study phenotypes, and inadequate sample sizes. Candidate gene studies have identified genes that contribute to complex disorders, but these studies rely on predicting correct gene or genes based on biological hypotheses and/or the location of the candidate gene in a region previously identified by linkage analysis. The candidate gene approach is not able to fully explain the genetic basis of the disease because the pathophysiology is not clearly understood for most complex disorders. Genome-wide association studies introduce an efficient and comprehensive approach to finding causal variants for disorders and/or diseases without making assumptions about the genomic location of the variants. NHLBI population studies represent an enormous investment in the etiologic investigation of HLBS disorders. Sophisticated, rigorous measures of subclinical disease, such as carotid ultrasonography, polysomnography, echocardiography, spirometry, cardiac and cerebral MRI, and coronary calcium, have been performed in many of these studies, such as the Framingham Heart Study (http://www.nhlbi.nih.gov/about/framingham/index.html ,often repeatedly. They thus provide valuable research opportunities for performing genome-wide association analyses with objectively measured, often asymptomatic, disease at a stage early enough to prevent progression to clinical events, disability, and death. Positive genetic associations can be followed by candidate gene analyses as well as functional genetic studies to assess the actual effect of the gene variant in the biologic system. Detailed Description of the Technical Requirements: The successful Contractor shall: (1) Provide personnel with expertise and experience in large-scale genotyping, general laboratory management, and quality control (QC) (used here and throughout encompassing quality assurance and quality control activities). (2) Provide personnel with expertise and experience in sample receipt, tracking, handling and storage; develop and implement procedures for these activities. (3) Provide personnel with expertise and experience in genetic analyses for data cleaning. (4) Provide personnel with expertise and experience in the secure transfer of large-quantities of genetic data. (5)Provide raw data and coding information to the Project Office or its designee on request in a complete and timely manner. (6) Provide Monthly Status Reports to the Project Office and Steering Committee. The Monthly Status Report shall summarize the status of the genotyping, the monthly QC data, the monthly production, completeness, call rates and error rates. (7) Maintain the confidentiality of the data received or produced. (8) Provide secure backup of all data essential to the project, including but not limited to all genotyping data generated, study data received, sample tracking and storage information, and QC information. (9) Receive and process data and samples from the Framingham Heart Study cohort (approximately 9,000 samples), including: a. Verify and obtain records of Institutional Review Board approval for the study prior to accepting samples for genotyping; b. Receive, track, and store DNA samples and accompanying data from the Framingham Heart Study in preparation for genotyping. (10) Initiate genotyping of a panel of 500K or more assays on all samples received (approximately 9,000) within the first two months of contract award. (11) Complete genotyping of the 500K or more panels on all samples received (including quality control measures during production to identify genotyping errors and sample mix-ups) ? at a maximum cost of $1,300 per sample. (12) Perform data cleaning (including but not limited to checks for Hardy-Weinberg equilibrium and Mendelian inconsistencies). Transfer a complete, cleaned data set to NCBI within six months of initiation. (13) Based on the requirements of NHLBI, request and receive data and samples from the other designated NHLBI studies (approximately 7,200 samples total), including: Verify and obtain records of Institutional Review Board approval for each study prior to accepting samples for genotyping. b. Receive, track, and store DNA samples and accompanying data from the designated NHLBI studies in preparation for genotyping. (14) Initiate genotyping of a panel of 500K or more assays on samples received from each designated NHLBI study (approximately 7,200 samples total) within two months of the receipt of samples. (15) Complete genotyping of the 500K or more panels on all samples received (including quality control measures during production to identify genotyping errors and sample mix-ups). (16) Perform data cleaning (including but not limited to checks for Hardy-Weinberg equilibrium and Mendelian inconsistencies). Transfer a complete, cleaned data set to NCBI within six months of initiation. The Contractor must be approved for handling human DNA. Contract employees in contact with human DNA or data derived from these human subjects must provide Certification of Human Subjects Training prior to a contract award. The anticipated period of performance is three (3) years from the date of the award. It is expected that the contract award will occur on or about September 1, 2006. THERE IS NO SOLICITATION AT THIS TIME. This request for capability information does not constitute a request for proposals and submission of any information in response to this market survey is purely voluntary; the Government assumes no financial responsibility for any costs incurred. The applicable North American Industry Classification System (NAICS) code assigned to this procurement is 541710, Research & Development Support Services, with a size standard of 500 Employees, over the last 3 years. If your organization has the potential capacity to perform these contract services, please provide the following information: 1) Organization name, address, email address, Web site address and telephone number as well as size and type of ownership for the organization, i.e., small business, Small Disadvantaged Business, 8(a), woman-owned, Historically Underutilized Business Zone (HUBZone) concern, Veteran, and/or Service-disabled Veteran; and 2) Tailored capability statements addressing the particulars of this effort, with appropriate documentation supporting claims of organizational and staff capability. Organizations responding to this market survey should keep in mind that only focused and pertinent information is requested. If significant subcontracting or teaming is anticipated in order to deliver technical capability, organizations should address the administrative and management structure of such arrangements to demonstrate that small business prime contractors can maintain labor, technical, and management control of the project, meeting the "limitation on subcontracting" imposed on small business set-asides. Taking into account the magnitude of the scope of this effort, organizations also should address the capacity of their financial infrastructure to deliver contract performance. Although no geographic restriction is anticipated, responding organizations should indicate how the organization would coordinate with the agency to provide support for multiple study sites. The Government will evaluate the capability information using the following criteria: 1)Documented experience with large-scale genotyping of panels of 500,000 assays or more per sample, call rates, and error rates for each project. 2) Expertise and experience of key personnel: Expertise and experience of proposed personnel and organization in large-scale genotyping, and data management. Commitment and capability of offerors to: provide low cost genotyping in quantity and quality required and adequate plans for quality control during production and genetic analyses for data cleaning. 3) Genotyping method and throughput: Adequacy of the genotyping platform in performing the amount of genotyping described in the workscope. Feasibility of proposed plan to genotype at or better than the capacity, cost, and error rate specified. Demonstration of appropriate understanding of use and problems associated with the methods and materials proposed, including reproducibility, accuracy, efficiency, capacity, and success rate. 4) Feasibility of the proposed informatics management plan for organizing and integrating genotype results into a secure database. Documented efficiency and security of the existing database system to be used or modified including data tracking, data synchronization, data transfer and interoperability, and backup of electronically-based information. 5) Equipment and Facilities: Availability and adequacy of facilities and equipment including but not limited to genotyping equipment, computing facilities, sample storage facilities and backup plans, the physical security of data, samples, communications, and equipment. Plans for replacing, maintaining and repairing equipment. Interested firms responding to this survey are encouraged to structure capability statements in the order of the area of consideration noted above. Responding firms should provide three (3) copies of a tailored capability statement to the above noted address within ten (10) business days from the date of publication of this notice. This market survey is being conducted through the FedBizOpps to reach the widest possible audience and to gather current market information.
- Place of Performance
- Address: Bethesda, Maryland
- Zip Code: 20892
- Country: USA
- Zip Code: 20892
- Record
- SN00963276-W 20060111/060109211731 (fbodaily.com)
- Source
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FedBizOpps Link to This Notice
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