SOLICITATION NOTICE
B -- Sequencing of Genes Underlying MI and Coronary Artery Calcium
- Notice Date
- 8/17/2009
- Notice Type
- Combined Synopsis/Solicitation
- NAICS
- 541712
— Research and Development in the Physical, Engineering, and Life Sciences (except 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)-2009-272-DDC
- Archive Date
- 9/8/2009
- Point of Contact
- Deborah - Coulter, Phone: (301) 435-0368
- E-Mail Address
-
dc143b@nih.gov
(dc143b@nih.gov)
- Small Business Set-Aside
- N/A
- Description
- This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in FAR 12.6 as supplemented with additional information included in this notice. This announcement constitutes the only solicitation and a separate written solicitation will not be issued. This solicitation number is NHLBI-PB-(HL)-2009-272-DDC and is issued as a Request for Quotation (RFQ). The solicitation/contract will include all applicable provisions and clauses in effect through Federal Acquisition Circular 2005-35. The North American Industry Classification (NAICS) Code is 541712 and the business size standard is 500 employees. This acquisition is being conducted using Simplified Acquisition Procedures in accordance with FAR Part 13. However, this solicitation is not set aside for small business. It is the intent of the National Institutes of Health (NIH) National Heart, Lung and Blood Institute, Office of Acquisition (OA), to procure the services from Massachusetts Institute Of Technology/Broad Institute, 77 Massachusetts Avenue Building E19-750, Cambridge, MA 02144, to provide the following DNA Sequencing in according with the statement of work. 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 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 carotid-artery ultrasound and computerized tomography of the coronary arteries have been evaluated and integrated into ongoing protocols. While pursuing the study's established research goals, the NHLBI and the Framingham investigators have expanded 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 myocardial infarction, stroke and dementia, as well as risk factors for these conditions, including hypertension, hyperlipidemia and diabetes. This project seeks to identify genetic sequence variations underlying coronary atherosclerosis, detected by computed tomography testing as coronary artery calcium, as well as early onset myocardial infarction (MI). MI is a leading cause of death and morbidity in men and women, and thrombosis in coronary atherosclerotic plaque is the overwhelmingly common etiology. In recent genomewide association studies of MI, a specific region in chromosome 9p21 as well as several other genes/loci have been implicated in MI, and these loci are also noted to be associated with CAC in a meta-analysis of six cohorts (N=10,000 participants) including the Framingham Heart Study. We propose to conduct targeted sequencing of three of these genes—PHACTR1, CXCL12, and MIA3—in 292 Framingham Heart Study participants, 94 participants with high levels of CAC, 94 participants with prior early onset MI, and 94 subjects free of CAC or history of MI. The Broad re-sequencing facility will conduct sequencing of DNA from each of the 292 individuals. Sequencing will be performed using 1 mcg of DNA, which provides enough material for validation genotyping and repeat analysis of any failed samples. Sequencing will be conducted using next-generation sequencing (Illumina paired-end resequencing). I. Contractor Requirements A.The Contractor will provide sequence variant information on 288 individuals for 3 genes/gene regions selected by Dr. O’Donnell (CPS/NHLBI)—PHACTR1, CXCL12, MIA3. B.The Contractor will provide sequencing services to sequence the gene regions for PHACTR1, CXCL12, MIA3 in 288 DNA samples. C.The Contractor will provide high quality sequencing results with a.a call rate in excess of 80% b.reproducibility in excess of 99% D.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. E.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. F.Contractor will specify any special packaging, marking, or shipping instructions for plates to be shipped for genotyping. G.Each DNA sample received will be identified by the Contractor using the identifiers provided by NHLBI. II. 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. III. Reporting Requirements and Deliverables A.Contactor will provide genotyping results 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.Contractor will maintain the DNA plates in the event additional genotyping is required. IV. Program Management and Control Requirements No special management or control systems are required under this contract. V. Inspection and Acceptance Requirements A.Inspection and Acceptance of genotyping results will be performed at NHLBI/CPS/Genome Group B.Acceptance of sequence data and genotype will be based on successful call rate and its compatibility with established standards as outlined in Section I, Contractor Requirements: a.a call rate in excess of 98% b.reproducibility in excess of 99% C.Inspection, acceptance and analysis of sequence data will be conducted by Dr's Andrew Johnson and Shih-Jen Hwang. We expect to receive sequence data on all genomic regions with >= 98% call rate in the research participants studied. We will further examine the sequence data we receive for consistency with preselected SNPs in the sequenced gene regions that we have previously genotyped. For any subjects with < 98% call rate for the preselected SNPs, we will confer with the Broad sequencing group and determine together whether tailored resequencing is or is not indicated D.Drs. Shih-Jen Hwang and Andrew Johnson will inspect and accept all deliverables. The required period of performance is schedule for twelve months. The sole source justification is based on the fact that the Broad Institute development and has conducted several large-scale proof-of-principle experiments assessing the characterization of next-generation resequencing technologies as applied to pooled samples, achieving dramatic efficiency in bringing large-scale resequencing technology to bear on the larger sample sizes required to recognize low-frequency alleles that contribute to human disease. The Broad Institute has an established track record of technological expertise to accomplish the aims of this project. These resources will be paired with the genetic data management expertise of the Broad Institute. There are relatively few commercial or academic laboratories with both the sequencing and the genotyping capabilities of the Broad Institute, which can complete the work scope for this project in a short time frame. The Broad Institute has the capabilities of doing so with high throughput, and using the minimum sample amount of DNA (well below the threshold for our DNA Committee allowance). On other Framingham projects, the Broad has demonstrated excellent QC and reliability. In addition, the Broad Institute has a number of collaborations with Framingham investigators and has extensive experience using Framingham DNA and plate sets. For another Framingham project using the exact same DNA samples as proposed in this project, the Broad has also amplified Framingham DNA samples, and those samples can be used for this project if they pass the necessary QC steps required for resequencing (those samples have passed QC for genotyping). The offeror must include a completed copy of the following provisions: 1) FAR Clause 52.212-1 Instructions to Offerors Commercial; 2) FAR Clause 52.212-2, Evaluation Commercial Items. 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. The following factors shall be used to evaluate offers: Technical Evaluation and Price. 3) FAR Clause 52.212-3, Offeror Representations and Certifications Commercial Items; 4) FAR Clause 52.212-4, Contract Terms and Conditions Required To Implement Statues or Executive Orders Commercial Items, Contract Terms and Conditions Commercial Items; and 5) FAR Clause 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders Commercial Items Deviation for Simplified Acquisitions. 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 requirement. 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 quotations however; all responses received within five (5) days from the date of publication of this synopsis will be considered by the Government. A determination by the Government not to compete this proposed acquisition is based upon responses to this notice and is solely for the purpose of determining whether to conduct a competitive acquisition. The offeror must include in their quotation, the unit price, the list price, shipping and handling costs, the delivery period after contract award, the prompt payment discount terms, the F.O.B. Point (Destination or Origin), the Dun & Bradstreet Number (DUNS), the Taxpayer Identification Number (TIN), and the certification of business size. Note: In order to receive an award from the NHLBI contractors must have a valid registration in the Central Contractor Registration (CCR) www.ccr.gov. The clauses are available in full text at http://www.arnet.gov/far. Interested vendors capable of furnishing the government with the item specified in this synopsis should submit their quotation to the below address. Quotations will be due five (5) calendar days from the publication date of this synopsis or by August 24, 2009, 7:30am, Eastern Standard Time. The quotation must reference Solicitation number NHLBI-PB-(HL)-2009-272-DDC. All responsible sources may submit a quotation, which if timely received, shall be considered by the agency. Quotations must be submitted in writing to the National Heart, Lung and Blood Institute 6701 Rockledge Blvd., Room Suite 6100, Bethesda, Maryland 20892, Attention: Deborah Coulter. Faxed copies will not be accepted. Emails will be accepted.
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