SOURCES SOUGHT
A -- Omics in Latinos (OLa) - Genetic Analysis
- Notice Date
- 6/3/2011
- 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
- NIH-NHLBI-SS-12-12
- Archive Date
- 7/3/2011
- Point of Contact
- Paul C McFarlane, Phone: 301-435-0345, Deirdre Lyons, Phone: 301-435-9068
- E-Mail Address
-
pmcfarlane@mail.nih.gov, deirdre.lyons@nih.gov
(pmcfarlane@mail.nih.gov, deirdre.lyons@nih.gov)
- Small Business Set-Aside
- N/A
- Description
- MARKET SURVEY NOTICE NOTICE NUMBER -NIH-NHLBI-SS-12-12 PROJECT TITLE -Omics in Latinos (OLa) - Genetic Analysis BACKGROUND The National Heart, Lung, and Blood Institute (NHLBI) of the National Institutes of Health plans a new initiative is to identify rare and common genetic variants and to measure context dependent effects among members of Hispanic Community Health Study / Study of Latinos (HCHS/SOL) through analysis of large-scale high-throughput genotyping. The Hispanic Community Health Study / Study of Latinos (HCHS/SOL) is an ongoing multi-center epidemiologic study in Hispanic/Latino (hereafter “Hispanic”) populations initiated in 2006 to identify specific risk factors for multiple diseases and to determine the role of genes and environment, including acculturation, in the occurrence of disease. The study comprises 16,000 individuals of Hispanic origin, specifically Cubans, Dominicans, Puerto Ricans, Mexicans, and Central/South Americans. Participants aged 18-74 years (2/3 age 45+) are identified through household surveys and undergo a clinic exam that includes blood analytes, DNA extraction, EKG, ankle-brachial index, anthropometry, blood pressure, spirometry, and auditory, dental, and neurocognitive assessments. Participants also complete extensive sociodemographic, medical, and behavioral and lifestyle questionnaires that include questions on occupation, diet, physical activity, socioeconomic status, and various measures of acculturation. Annual follow-up interviews are conducted and endpoints in cardiovascular and lung disease are collected. To date, genetic studies of Hispanics have often focused on a single national origin, had disease-specific ascertainment, limited environmental and disease measures, and/or were underpowered to detect small to moderate genetic effects. HCHS/SOL, because of its study design, sample size, and multi-country-of-origin focus, addresses many of these concerns. In addition, HCHS/SOL has both study approval and appropriate informed consent for data sharing. PURPOSE AND OBJECTIVES The overall objective of OLa - Genetic Analysis is to identify genetic variants associated with measured phenotypes, disorders and diseases in The Hispanic Community Health Study / Study of Latinos (HCHS/SOL) through the application of analytical and statistical methods to large scale genotyping data that will be generated in advance of this project. The National Institutes of Health (NIH), National Heart, Lung, and Blood Institute (NHLBI), seeks a contractor to provide genotype data cleaning, an analytical pipeline that will integrate genome-wide genotypic information with phenotypic information from HCHS/SOL, and analysis and publication support for HCHS/SOL working groups. ANTICIPATED CONTRACT PERFORMANCE PERIOD A single contract is planned for award on or about August 20, 2012 with a performance period of 36 months. CAPABILITY STATEMENT GUIDELINES NHLBI is soliciting capability statements from all qualified Offerors demonstrating their ability to perform this research effort. At a minimum, Offerors must document capabilities in the following areas. 1.Maintain the confidentiality of the data received, produced, and distributed. 2.Provide secure backup of all data essential to the project, including but not limited to all genotyping data received (including raw data), HCHS/SOL study data received, analytical data space and output, and reports generated. 3.Provide personnel with expertise and experience in genetic analyses for data cleaning. 4.Provide personnel with expertise and experience in the secure physical and electronic transfer of large-quantities of genetic and phenotypic data. 5.Provide personnel with expertise in bi- and tri-admixed populations to provide sufficient recommendations for issues unique to these populations (including sample assignment within arrays and methodologies for allelic determination and QC unique to admixed and multinational populations). 6.Provide personnel and computational facilities in sufficient quantity to analyze 14-16,000 participant genotypes at minimum density of 2 million to a maximum density of 6 million SNPs. 7.Participate in a genotype cleaning team that will be convened to determine the final, official genotypes for inclusion into NCBI’s database of Genotypes and Phenotypes (dbGaP) upon receipt from NCBI (or the designated genotyping contractor). Composition of the genotype analysis team shall include the Contractor, and representation from NHLBI, HCHS/SOL, and NCBI. Outside experts may be included upon NIH and Contractor agreement. 8.With mutual consultation with NCBI, independently and concurrently produce cleaned genotype data of sufficient quality for inclusion into dbGaP. 9.Perform data cleaning including but not limited to: checks for Hardy-Weinberg equilibrium, Mendelian inconsistencies, degrees of relatedness, and inter-and intra-population allele frequencies. 10.Complete all activities of the genotype cleaning team within 60 days of raw data receipt to the contractor. 11.Work with NHLBI, NCBI, and HCHS/SOL to ensure that all genotype and phenotype data to be transmitted during the contract period have a common system of participant IDs to ensure successful matching between genotype and phenotype. 12.During the duration of this contract, the Contractor will inform NHLBI of novel analytical methods that may be in the interest of NHLBI and this project. Should NHLBI agree, adjustments can be made to the proposed analytical pathway. 13.Provide NHLBI with the names and activities of designated investigators sufficient to provide analytical support. The Contractor shall designate analytical centers from one or more sites for analytic support (consisting of salary, computational tools, software licensing, and relevant project infrastructure). Analysts named by the Contractor will work with designated subject matter HCHS/SOL working group members. Analysts should have prior publication in Heart, Lung, Blood, and/or Sleep traits or phenotypes. Experience should include high volume genetic analyses, population stratification, admixture mapping, candidate gene investigation, analyses of gene-gene and gene-environment interactions, CNV analyses, intra- and inter-population analyses, as well as the analysis of epidemiologic data (qualitative and quantitative) and the appropriate covariates. Familiarity with cross-analysis of genomics and metabolomics would be beneficial. Activities should be coordinated with HCHS/SOL to maximize the number and impact of publications during the year of protected publication rights, a 12 month period that begins following a dataset release on dbGaP, per NHLBI SHARe policy. Further details are found in Section IV of “Policy for Sharing of Data Obtained in NIH Supported or Conducted Genome-Wide Association Studies (GWAS).” Prioritization of traits and measures will be made for Heart, Lung, Blood and Sleep in conjunction with NHLBI. Should NHLBI find additional funding partners to broaden the analysis, the NHLBI will work with the Contractor to discuss the feasibility of expansion. 14.Produce a flow chart demonstrating the proposed analytical pathway with designation of software used, individuals involved, reports generated, and estimates of computational runtime. 15.In order to allow for sufficient scientific process, the Contractor shall coordinate collaborations among HCHS/SOL Investigators by organizing collaborative meetings either by teleconference or in person meetings amongst the WHI Investigators and selected NHLBI staff as designated jointly by the Contractor and NHLBI. The investigators will plan for one in-person meeting to be held per year for 3 years. {Note: For planning purposes assume in the Washington, D.C. area.} The Contractor will be responsible for travel of their analysts and support staff but not HCHS/SOL Investigators (unless they are Contractor designated analysts). 16.The Contractor shall perform data analyses and manuscript preparation for paper proposals generated by HCHS/SOL working groups. Contractors should base their response on 100 paper proposals over the contract period. 17.Provide Monthly Status Reports to the Project Office and designated committees. The Monthly Status Report shall summarize the status of the designated analyses, manuscripts written, and other metrics designated by the Project Office. Provide copies in Excel Spreadsheet and/or Word documents as well as in a FIPS approved standard such as PDF. Copies will be sent to NHLBI designated representatives as well as HCHS/SOL designated representatives. 18.Provide materials and information promptly and communicate with the Program Office and the host study frequently and regularly. 19.Receive and process data and samples from The Hispanic Community Health Study / Study of Latinos (HCHS/SOL), including: a. Verify and obtain records of Institutional Review Board approval(s) for the study prior to accepting genotypes for genetic analysis; b. Receive, track, and store accompanying data from the HCHS/SOL in preparation for analysis. 20.The organization’s Institutional Review Board (IRB) or equivalent must approve the Contractor for relevant analyses and handling phenotypic data and measures related to de-identified human subjects. Contract employees in contact with genetic or phenotypic data must provide Certification of Human Subjects Training prior to a contract award. RESPONSE GUIDELINES This notice will expire 15 calendar days from its posting. Respondents may provide written capability statements detailing their ability to perform the efforts described above (not to exceed 15 two-sided pages e.g. 30 single-sided pages, maximum) in an original and two (2) copies, to the named NHLBI Contracting Officer. Respondents shall indicate their business size, specifically if theirs is a small business under one of the socioeconomic programs identified in FAR Subpart 19. This is not a request for proposals and the Government is not required to solicit or award any contract as a result of this notice.
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