SOURCES SOUGHT
A -- Caerphilly Co-hort Genotyping
- Notice Date
- 8/27/2014
- Notice Type
- Sources Sought
- 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)-SBSS-2014-229-NR
- Archive Date
- 9/19/2014
- 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
- Sources Sought Notice No.: HHS-NIH-NHLBI-CSB-(HV)-SBSS-2014-229-NR Title: Genotyping Caerpilly Study in Men DNA Samples This is a Small Business Sources Sought notice. This is NOT a solicitation for proposals, proposal abstracts, or quotations. The purpose of this notice is to obtain information regarding: (1) the availability and capability of qualified small business sources; (2) whether they are small businesses; HUBZone small businesses; service-disabled, veteran-owned small businesses; 8(a) small businesses; veteran-owned small businesses; woman-owned small businesses; or small disadvantaged businesses; and (3) their size classification relative to the North American Industry Classification System (NAICS) code for the proposed acquisition. Your responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible. An organization that is not considered a small business under the applicable NAICS code should not submit a response to this notice." A. Background The National Institute of Health (NIH) is the nation's leading medical research agency and the primary Federal agency conducting, supporting and making medical discoveries that improve people's health and save lives. The Cardiovascular Epidemiology & Human Genomics Branch in the National Heart, Lung, and Blood Institute at NIH, is involved in the study of blood diseases and genetic associations for measurable blood traits. Genotyping of genetic markers (SNPs: single nucleotide polymorphisms) in human samples, which enables analyses for genetic associations to uncover new risk genes in a part of the research performed. 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 [see Framingham SHARe and OMNI cohort genotyping projects, and Johnson et al., Nat Gen 2010:42(7)]. 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). B. Purpose and Objectives Genotyping of 1,235 DNA samples is required with a current generation mapping array which includes excellent content for genetic mapping in human populations and includes rare variant and functional variant content (i.e., variants derived from exome sequencing and other recent projects). The purpose is to enable genetic mapping in the U.K. based Caerphilly Study in Men cohort which has valuable and rare phenotype data collected. The objectives are to enable genetic mapping studies, cross-validation studies to existing U.K.-based and European ancestry studies (e.g., studies in the Framingham Heart Study Gen1/2/3) as well as studies of heritability, methodological and risk prediction studies. A further objective in line with mandates on Federal funding of genetic projects is to provide a genetic resource that will be available for other scientists to utilize in the future (via the European Genome-Phenome Archive). Genotype results for ~821,000 human genetic variants will be generated in 1,235 Caerphilly Study in Men DNA samples and returned to investigators. Quality control procedures will be observed and repeated data acquisition will be performed if there are any failing samples. Government scientists will link and analyze the genotypes in association with phenotypes. This data will allow government scientists the ability to make new discoveries. The benefits of the project are that they will enable genetic mapping studies of clinical, subclinical and drug-response related phenotypes. In particular rare and functional variants may have higher penetrance and potential clinical effect. These efforts may lead to the discovery of new genes or help in the validation of genes from other studies, and may in turn suggest new drug targets or possible genetic modifiers of treatment or therapeutic strategies in cardiovascular disease. C. Scope of Work 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. D. Deliverables: The vendor will provide bi-weekly updates on the sample progress and genotyping. The vendor will provide an initial overview of genotyping and QC results upon completion. Raw and processed data will be delivered to the government on all, or nearly all, 1,235 DNA samples. Quality control and basic annotation information will be provided (e.g., sample and SNP call rates, SNP positions and identifiers, allele frequencies, cluster or other calling confidence metrics, gender checks, negative controls, positive controls) to assess genetic variant QC and conduct downstream analyses. E. Government Responsibilities: The Government will facilitate the provision of DNA samples from the CaPs source laboratory to the vendor (e.g., pay shipping costs). The Government will review resulting data for its quality assurance to determine if any remedies are needed. F. Inspection and Acceptance Requirements: The Government investigator will inspect data QC reports from the vendor. These will include primary measures of overall sample call rates (% success) and variant call rates (% success), as well as specific analysis outcomes such as suspected gender mismatches; positive, negative and duplicate control samples; monomorphic rates; and Hardy-Weinberg equilibrium outliers. G. Other considerations 1. The Contractor is required to provide reports, record methods, and materials as appropriate to the highest scientific standards. These materials, methods and results will be shared with agreed upon collaborators. 2. No government property will be provided in the performance of the requirement. 3. The Government will not furnish any facilities or provide space in the performance of the requirement. 4. The desired results, end items or functions of the project are: (1) high quality genotyping results on the CaPs DNA with currently relevant SNP panels including high coverage of European ancestry common and rare variation, putative functional variation from recent sequencing projects and known disease variation; (2) Integration of CaPs genotype-phenotype analyses with existing and ongoing genotype-phenotype analyses primarily in the Framingham Heart Study; and (3) Research collaborations conducted via Videoconferences, email communications, shared professional presentations, posters and publications. H. Anticipated Period of Performance All genotyping and QC will be completed and delivered by August 30, 2015. I. Capability Statement /Information Interested parties are expected to review this notice to familiarize itself with the requirements of this project. Failure to do so will be at the interested parties' own risk. The following information shall be included in the capability statement: 1. A general overview of the respondents' opinions about the difficulty and /or feasibility of the potential requirement, and any information regarding innovative ideas or concepts. 2. Information in sufficient details of the respondents' (a) staff expertise, including their availability, experience, and formal and other training; (b) current in-house capability and capacity to perform the work; (c) prior completed projects of similar nature; (d) corporate experience and management capability; and (e) examples of prior completed Government contracts/purchase orders 3., references, and other related information. 4. The respondents' DUNS number, organization name, address, point of contact, and size and type of business (e.g., 8(a), HUBZone, etc) pursuant to the North American Industry Classification System (NAICS) code: NAICS 541712,Research and Development Physical, Engineering, Life Sciences (except Biotechnology), small business size standard is $25.5M. 5. Any other information that may be helpful in developing or finalizing the requirements of the potential acquisition. 6. The capability statement shall not exceed 20 single-sided pages (including all attachments, resumes, charts, etc.) presented in single-space and using a 12-point font size minimum, in either Microsoft Word or Adobe Portable Document Format (PDF), with 8-1/2 by 11 inch paper size, and 1 inch top, bottom, left and right margins. 7. All proprietary information should be marked as such. Statements should also include an indication of current certified small business status; this indication should be clearly marked on the first page of your capability statement (preferably placed under the eligible small business concern's name and address). Responses will be reviewed only by NIH personnel and will be held in a confidential manner. J. Closing Statement The capability statement should be submitted electronically (via email) to Nora I. Rivera, Contracting Officer, riverani@nhlbi.nih.gov, on September 4, 2014, 8:30 AM, EST. All responses must be received by the specified due date and time in order to be considered. Facsimiles are not accepted. This Sources Sought Notice (SS) is for information and planning purposes only and shall not be construed as a solicitation or as an obligation on the part of the National Heart, Lung, and Blood Institute (NHLBI). The NHLBI does not intend to award a purchase order on the basis of responses nor otherwise pay for the preparation of any information submitted. As a result of this notice, the NHLBI may issue a Request for Quote (RFQ). THERE IS NO SOLICITATION AVAILABLE AT THIS TIME. However, should such a requirement materialize, no basis for claims against NHLBI shall arise as a result of a response to this notice or the NHLBI's use of such information as either part of our evaluation process or in developing specifications for any subsequent requirement. "Disclaimer and Important Notes. This notice does not obligate the Government to award a contract/purchase order or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization's qualifications to perform the work. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, a pre-solicitation synopsis and solicitation may be published in Federal Business Opportunities. However, responses to this notice will not be considered adequate responses to a solicitation. Confidentiality. No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s)."
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/NIH/NHLBI/HHS-NIH-NHLBI-CSB-(HV)-SBSS-2014-229-NR/listing.html)
- Place of Performance
- Address: TBD, United States
- Record
- SN03483374-W 20140829/140828022637-0adfb02003ca5a475cc625a3447a9d42 (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
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