SOLICITATION NOTICE
A -- Caerphilly Co-hort Genotyping
- Notice Date
- 9/5/2014
- 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
- HHS-NIH-NHLBI-CSB-(HV)-2014-229-NR
- Archive Date
- 9/27/2014
- Point of Contact
- Nora I Rivera, Phone: (301) 435-0712
- E-Mail Address
-
nr85c@nih.gov
(nr85c@nih.gov)
- Small Business Set-Aside
- N/A
- Description
- NOTICE OF INTENT TO AWARD INTRODUCTION: THIS IS A PRE-SOLICITATION NON-COMPETITIVE (NOTICE OF INTENT) SYNOPSIS TO AWARD A PURCHASE ORDER WITHOUT PROVIDING FOR FULL OR OPEN COMPETITION. The National Heart, Lung, and Blood Institute (NHLBI), Office of Acquisitions (OA), intends to award a firm fixed price purchase order on a noncompetitive sole source basis to Mount Sinai Hospital Mount Sinai Hospital, Clinical Genomics Centre at 600 University Ave. Room 6-423 Toronto, Ontario M5G 1X5 Canada is to support the genetic mapping of DNA collected as part of the Caerphilly Study in Men by genotyping and quality control services for 1,235 DNA samples with whole-genome SNP mapping genotyping product. BACKGROUND: The Cardiovascular Epidemiology & Human Genomics Branch of the National Heart, Lung, and Blood Institute of the National Institutes of Health, is involved in the study of blood diseases and genetic associations for measurable blood traits. As part of the research, the lab requires genotyping of genetic markers (SNPs: single nucleotide polymorphisms) in human samples, which enables analyses for genetic associations to uncover new risk genes. In particular the lab is focused on hemostatic and thrombotic factors including platelets and seeks to conduct genetic studies in human population cohorts that have these relatively uncommon phenotypes measured. The Caerphilly Study in Men (CaPs) is one such cohort having among the largest samples in the world with DNA (genetic material) and having measured phenotypes including platelet reactivity. That study is composed of U.K./British biobanked samples and has been ongoing for more than 30 years. This study provides some complementarity and collaborative opportunity with another U.K.-based project (the UK Biobank). The resulting data of the proposed work will also relate to existing project data in the Framingham Heart Study on the genetics of platelet reactivity and hemostatic factors and blood cell counts. The lab is thus requesting the purchase of SNP genotyping arrays (Biobank arrays designed for the UK Biobank project) and the service to perform genotyping assays in order to continue valuable research. Genetic research approval in CaPs is granted under the South East Wales Research Ethics Committee (ref #05/WSE02/131). The current project has been reviewed by the NHLBI OCA and the OHSRP with the final determination Excluded from IRB Review (OHSRP #12535). JUSTIFICATION: The sole source determination is based on the need to continue developing two existing active protocols with the exact brand name power injector in order to avoid introducing new variables that could potentially invalidate existing quantitative analysis already developed under the two protocols that have been active since 2007. REQUIREMENT: Genotyping of 1,235 DNA samples with a whole-genome SNP mapping genotyping product is required. This product must include modern content (based on information from major population genetics databases in the last 1 year) since this content has been rapidly changing. The content should include rare variation recently discovered, as well as functional ("loss of function") genetic variation. This is to improve the discovery of high impact large effect genetic variants. Also, it may provide compatibility with other project effort in different DNA samples which have focused on rare variation content (exome sequencing and exome chip projects). Complementary content to existing BioBank projects such as the UK BioBank project is highly desirable to maximize opportunities for future collaboration and use of results. 1. Coordinate shipping and receiving of DNA sample from Caerphilly Study resource lab: a. Barcode sample plates to be used for DNA samples and ship to Caerphilly Study resource lab. b. Handle receipt of DNA aliquots from Caerphilly Study resource lab in accordance to good laboratory practices. 2. Follow good lab practices to reduce the risk of mix-ups from the point of receipt. 3. Complete DNA genotyping on all 1,235 samples with a genome-wide SNP genotyping product (chip or array) that meets specifications (high proportion of common and rare variation tagged/covered based on up-to-date human genetic variation maps; inclusion of enhanced content for "loss of function" and other rare variation discovered in recent sequencing projects; complementary content to existing large scale UK projects (e.g., the UK BioBank) to leverage use of the data). 4. Conduct and complete sample and variant QC analyses including negative control samples, positive control samples, sample and variant call rates, analysis of duplicate samples, gender-mismatch checks, measurements of genotype quality including Hardy-Weinberg Equilibrium calculations 5. Complete quality control checks and re-genotype on all failed samples. 6. The result will be a large computed dataset which reflects a data matrix approximately 1,235 X 800,000 (988 million entries) of individuals and their genotypes for specific genetic markers. The raw and processed data will be returned by the vendor to the government and verify successful delivery. 7. Respond to technical support questions following delivery of results. 8. Provide access to platform-specific bioinformatics and annotation resources specific to the product vendor (e.g., Affymetrix or Illumina chip annotation files or genotype calling software) that allow the Government to verify or repeat the genotype calling and annotation results. REGULATORY AUTHORITY This acquisition is conducted under the authority of the Federal Acquisition Regulations (FAR) Subpart 13.106-1(b) Soliciting from a single source (for purchases not exceeding the simplified acquisition threshold) and only one responsible source and no other supplies or services will satisfy agency requirements. ADDITIONAL INFORMATION Industry Classification (NAICS) Code is 541712 Research and Development Physical, Engineering, Life Sciences (except Biotechnology), and the Small Business Size Standard is $25.5M. The acquisition is being conducted under FAR Part 13, Simplified Acquisition Procedures; therefore the requirements of FAR Part 6, Competitive Requirements, are not applicable (FAR Part 6.001). The resultant award will include all applicable provisions and clauses in effect through the Federal Acquisition Circular (FAC) 05-72 (January 30, 2014). This synopsis is not a request for competitive proposals. However, interested parties may express their interest and capability by responding to this notice. Responses to this notice shall contain sufficient information to establish the interested parties' bona-fide capabilities for fulfilling the requirement and include: unit price, 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. All offerors must have an active registration in the System for Award Management (SAM) www.sam.gov. 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. The information received will normally be considered solely for the purposes of determining whether to proceed on a non-competitive basis or to conduct a competitive procurement. All responses must be received by September 12, 2014 at 9:00am EST and must reference the pre-solicitation number DHHS-NIH-NHLBI-CSB-(HV)-2014-229-NR. Responses shall be submitted electronically to Nora I. Rivera, Contacting Officer, riverani@nhlbi.nih.gov OR hard copy to the National Heart, Lung, and Blood Institute, Office of Acquisitions, COAC Services Branch, 6701 Rockledge Drive, Room 6112, Bethesda, Maryland 20892-7902, Attention: Nora I. Rivera. Faxes will not be accepted. Responses will only be accepted if dated and signed by an authorized company representative. All responsible sources may submit a bid, proposal, or quotation with the capability statement which shall be considered by the agency.
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