SOLICITATION NOTICE
B -- Sequencing of Blood Pressure Candidate Genes
- Notice Date
- 8/18/2009
- Notice Type
- Presolicitation
- 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)-2009-271-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)-2009-271-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 stroke and dementia, osteoporosis and arthritis, nutrition, diabetes, eye diseases, hearing disorders, lung diseases, and genetic patterns of common diseases. 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 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 regulation of blood pressure, a key risk factor for cardiovascular disease. Specifically, through resequencing 25 blood pressure candidate genes in 192 Framingham Heart Study participants at each extreme of the blood pressure distribution, we will identify genetic variants, both rare and common, that are distributed unevenly between the two extremes of blood pressure. We will then genotype a subset of 72 of these identified variant in 3840 Framingham participants, and based on these results, genotype 36 variants in an additional 3840 Framingham participants. The Broad resequencing facility will take DNA from the top 192 and bottom 192 individuals with high and low blood pressure, respectively (plus 16 HapMap control samples; 2 per pool), and put their DNA into 4 high BP pools and 4 low BP pools, respectively (48 individuals/pool). Sequencing will then be done on each of the 8 pooled sets of DNA. 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 then be done using next-generation sequencing (Illumina paired-end resequencing) for 25 genes with an estimated 50,000 base-pairs of target sequence with an average of 30x coverage (this can be scaled to lower coverage e.g. 15x which still has 70% sensitivity to an allele that occurs only once in 50 individuals). The initial sequencing will identify approximately 500 variants to be identified that need to be validated via individual genotyping. Results of individual sample genotyping (n=192 from 8 pools of 48 individuals) will be compared to the pooled genotypes from resequencing. For quality assurance purposes, we will plan to include 48 Framingham samples per pool (x8=384 unique samples) and put in 16 HapMap CEU unrelated samples (2 per pool) in order to have 384 total FHS individuals for follow-up and to be able to place any alleles identified into the haplotype context that we know from HapMap or 1000 Genomes Project. NHLBI will identify a set of variants that should be followed up by genotyping in 4000 Framingham Third Generation and 3500 Framingham Offspring Cohort participants. This stage of extension genotyping will be split into two stages to allow two pools (72 SNPs) to be genotyped in the 4000 individuals from the Framingham Third Generation Cohort as an initial screen with one pool of SNPs (36 SNPs) that appear promising in the Third Generation to be genotyped in 3500 Framingham Offspring Cohort participants in the second stage. Because of the way the plates fit we will conduct genotyping in 3840 individuals in the stage 1 extension and 3840 in the stage 2 extensions. I. Contractor Requirements A.Contractor will provide sequence variant information on 384 individuals for 25 genes/gene regions to be specified by Dr. Levy (CPS/NHLBI) B.Contractor will provide genotyping services to genotype in 3840 DNA samples a total of 72 SNPs to be identified by Dr. Levy. C.Contractor will provide genotyping services to genotype in 3840 additional DNA samples a total of 36 SNPs (derived from the 72 described in “B”) to be identified by Dr. Levy. D.The Contractor will provide high quality genotyping results with a.a call rate in excess of 98% b.reproducibility in excess of 99% c.Mendelian error rate (among first degree relatives) of less than 1% E.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. 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 return 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 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.Mendelian error rate (among first degree relatives) of less than 1%. C.Dr. Shih-Jen Hwang, NHLBI/CPS will inspect and accept the 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)-2009-271-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.
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/NIH/NHLBI/NHLBI-PB-(HL)-2009-271-DDC/listing.html)
- Place of Performance
- Address: Bethesda, Maryland, 20774, United States
- Zip Code: 20774
- Zip Code: 20774
- Record
- SN01916407-W 20090820/090819001008-1b8d9555ad196b40c5f0551597b3a2f0 (fbodaily.com)
- Source
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