SPECIAL NOTICE
B -- Genetic Analysis (Genotyping) Services
- Notice Date
- 8/21/2008
- Notice Type
- Special Notice
- NAICS
- 541711
— Research and Development in Biotechnology
- 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
- NHLBI-PB(HL)-2008-244-DCH
- Response Due
- 9/3/2008 9:00:00 AM
- Archive Date
- 9/18/2008
- Point of Contact
- Debra C. Hawkins,, Phone: (301) 435-0361
- E-Mail Address
-
dh41g@nih.gov
- Small Business Set-Aside
- N/A
- Description
- THIS IS A NOTICE OF INTENT, NOT A REQUEST FOR A PROPOSAL. A SOLICITATION DOCUMENT WILL NOT BE ISSUED AND PROPOSALS WILL NOT BE REQUESTED. The National Heart, Lung, and Blood Institute (NHLBI) Office of Acquisitions (OA), intends to negotiate and award a contract on a noncompetitive sole source basis to Illumina, Inc. 9885 Towne Centre Drive, San Diego, California 92121-1975. The intent of this procurement is to acquire FastTtrack Genetic Analysis (Genotyping) services using the Illumina iSelect Infinium custom genotyping array. The genotyping services are in support of the ongoing “Genotyping of Candidate Gene Variants for Blood Pressure and Cardiovascular Disease” project as performed in accordance with the statement of work. The sole source determination is based upon the use of these particular whole genome genotyping kits from Illumina, Inc., as it relates to the ongoing “Genotyping of Candidate Gene Variants for Blood Pressure and Cardiovascular Disease” project which is a subset of the Framingham Heart Study Offspring and Third Generation cohorts. In order to avoid the introduction of new variables into the experimental results and to avoid long delays resulting from retesting of products from other potential suppliers, we must continue to purchase the genotyping kits from Illumina, Inc. Also, in order to maintain the continuity of the methodologies used for the initial genotyping, an award to any other source for this follow-on contract would result in a substantial duplication of cost to the Government that is not expected to be recovered through competition. This action is under the authority of 41 U.S.C. 253(c)(1), as set forth in FAR 6.302-1 and HHSAR 306-302-1. Only one responsible source and no other supplies or services will satisfy agency requirements. Interested parties may identify their interest and capability to respond to the requirement or submit proposals. This notice of intent is not a request for competitive proposals. However, all responses received within 15 days after publication of this synopsis will be considered by the Government. A determination by the Government not to compete this proposed contract based upon responses to this notice is solely within the discretion of the Government. Information received will normally be considered solely for the purpose of determining whether to conduct a competitive procurement. The period of performance of this requirement is September 2008 through September 2013. It is estimated that 5,950 SNPs in each of 7,379 subjects are required for the project. Brief History/Purpose/Description of Project Cardiovascular disease (CVD) is the leading cause of death and serious illness in the United States. In 1948, the Framingham Heart Study under the direction of the National Heart Institute (now known as the National Heart, Lung, and Blood Institute; NHLBI) -- embarked on an ambitious project in health research. At the time, little was known about the general causes of heart disease and stroke, but the death rates for CVD had been increasing steadily since the beginning of the century and had become an American epidemic. The objective of the Framingham Heart Study was to identify the common factors or characteristics that contribute to CVD by following its development over a long period of time in a large group of participants who had not yet developed overt symptoms of CVD or suffered a heart attack or stroke. The Framingham Heart Study continues to make important scientific contributions by enhancing its research capabilities and capitalizing on its inherent resources. New diagnostic technologies, such as echocardiography (an ultrasound examination of the heart), carotid-artery ultrasound, bone densitometry (for monitoring osteoporosis), and computerized tomography of the coronary arteries, are evaluated and integrated into ongoing protocols. While pursuing the study's established research goals, the NHLBI and the Framingham investigators are expanding their research into other areas such as the role of genetic factors in CVD. Framingham investigators also collaborate with leading researchers from around the country and throughout the world on projects in stroke and dementia, osteoporosis and arthritis, nutrition, diabetes, eye diseases, hearing disorders, lung diseases, and genetic patterns of common diseases. This project seeks to characterize genetic variation involved in key heart, lung, blood, and sleep disorders by extending knowledge gained from the recent genotyping of common genetic variation by the NHLBI Framingham SHARe project. Specifically, we will define the role of genetic variants more likely to have functional effects on gene products by targeting single nucleotide polymorphisms (SNPs) that have been implicated in altered gene expression (eSNPs), alterations in copy numbers (cSNPs), or alterations in amino acid sequence of proteins, known as nonsynonymous SNPs (nSNPs). Through bioinformatics approaches, we have identified several thousand eSNPs, cSNPs, and nSNPs. In addition, we will use some of the genotyping capacity of this project to type promising SNPs identified through recent resequencing projects (Levy and Newton-Cheh; O’Donnell and Newton-Cheh). Those SNPs include synonymous and non-synonymous coding variants, frame-shift and nonsense variants (stop codons), and many non-coding variants. Last, we also will target for genotyping SNPs found to be associated with disease traits in genomewide association analyses of SHARe data or other published association studies. In general, we will target for genotyping those SNPs that were not genotyped as part of SHARe and for which imputation to the HapMAp SNP set was imperfect. We plan to genotype 7600 SNPs of interest in the entire DNA plate set from the Framingham Heart Study Offspring and Third Generation cohorts (total n=7357) in order to determine which, if any variants are associated with heart, lung, blood, and sleep phenotypes in the general population. Identifying genetic variants that are robustly associated with these traits may provide insight into the genetic contributions to disease, which would further the cause of personalized medicine by allowing for diagnosis of susceptible individuals and for the identification of novel therapeutic targets for treatment of disease. This project involves the contractor performing genotyping of SNPs to be identified by Dr. Levy, Dr. O’Donnell and members of their CPS research team. The SNPs will be genotyped in plate sets from the Framingham Heart Study Offspring and Third Generation cohorts with a total sample size of approximately 7,357. The period of performance is September 2008 through September 30, 2013 The statement of work is as follows: Contractor Requirements A.The contractor will provide genotyping services to genotype 7600 SNPs to be identified by NHLBI. The contractor will process NHLBI samples at contractor location using the iSelect Infinium Custom Genotyping array. B.The Contractor will provide high quality genotyping results with: 1.a call rate in excess of 98%; 2.reproducibility in excess of 99%; 3.Mendelian error rate (among first degree relatives) of less than 1% C.The Contractor will accept for genotyping SNPs for which Reference Sequence (RefSeq) accession numbers (rs numbers) are available as well as SNPs for which no accession number is available, but for which flanking sequence is provided. In such cases NHLBI will provide the flanking sequence information in FASTA format. The Contractor will review the requested assays and return SNP Score files to NHLBI. D.Quality control measures will be applied by the Contractor and genotyping results from each genotype plate will be accompanied by quality control information reflecting call rate, reproducibility rate, and other appropriate measures of quality. E.The contractor will specify any special packaging, marking, or shipping instructions for plates to be shipped for genotyping. F.Each DNA sample received will be identified by the Contractor using the identifiers provided by NHLBI. Government Responsibilities A.Using blinded replicates and family structure data, NHLBI will inspect the results provided by the Contractor and review them for fulfillment of the quality control measures stipulated above (Section IA). SNPs that do not fulfill quality metrics will be identified by NHLBI (Dr. Hwang at the NHLBI Framingham Heart Study). The Contractor will be notified about genotyping quality failure within 30 days of receipt by NHLBI of the final genotyping results files. NHLBI will be credited for any SNPs that do not meet specified quality measures. B.NHLBI will provide to the Contractor plates with standard concentrations of DNA and identifiers for each plate. In addition, NHLBI will provide a list of identifiers for each DNA sample within each plate. Reporting Requirements and Deliverables A.Genotyping results will be returned by Contractor to NHLBI in a standard format in a nonproprietary database in which each SNP is identified by standard accession number or by FASTA number when an accession number is not available. B.Return of genotyping by the Contractor will be accompanied by summary quality control measures for each DNA plate and for the project overall. C.Genotyping will be returned to NHLBI within 10-12 weeks of receipt DNA samples and a final SNP list from NHLBI. D.The contractor will maintain the DNA plates in the event additional genotyping is required. The North American Industry Classification System (NAICS) code applicable to this requirement is 541711– Research and Development in Biotechnology, size standard 500 employees. This acquisition is being conducted in accordance with the requirements of the Federal Acquisition Regulations (FAR) Part 13 – Simplified Acquisition Procedures, Subpart 13.5 – Test Program for Certain Commercial Items. Therefore, the following FAR Clauses are applicable to this requirement: FAR Clause 52.212-1 Instructions to Commercial Offerors, applies to this acquisition. FAR Clause 52.212-2, Evaluation Commercial Items, applies to this acquisition. As stated in FAR Clause 52.212-2 (a), The Government will award a contract resulting from this solicitation to the responsible offeror whose offer conforming to the solicitation will be most advantageous to the Government, price and other factors considered. Technical Evaluation Factors are (1) available technology to perform genotyping services using BeadArray technology; (2) availability of necessary facilities to perform work; and (3) cost per sample. FAR Clause 52.212-3, Offeror Representations and Certifications Commercial Items, applies to this acquisition, and the offeror must include a completed copy in its response. FAR Clause 52.212-4, Contract Terms and Conditions - Commercial Items, applies to this acquisition. FAR Clause 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders -- Commercial Items, applies to this acquisition. Responses to this announcement, must reference synopsis number NHLBI-PB(HL)-2008-244-DCH, and must be submitted electronically to Debra C. Hawkins hawkinsd@nhlbi.nih.gov, National Heart, Lung, and Blood Institute, Office of Acquisitions, Procurement Branch, 6701 Rockledge Drive, Suite 6042, Bethesda, MD 20892-7902.
- Web Link
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FedBizOpps Complete View
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- Place of Performance
- Address: Contractor' site, San Diego, California, 92121-1975, United States
- Zip Code: 92121-1975
- Zip Code: 92121-1975
- Record
- SN01646928-W 20080823/080821221344-02f8575146cf65aa2fbf9edc52b092ce (fbodaily.com)
- Source
-
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