SOURCES SOUGHT
A -- High Throughput Genotyping and DNA Sequencing for Studying the Genetic Contributions to Human Health and Disease
- Notice Date
- 3/20/2015
- 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-SBSS-CSB-HG-2016-17-DL
- Archive Date
- 4/21/2015
- Point of Contact
- Deirdre Lyons, Phone: 3014359068, Lynn Furtaw, Phone: 8434168457
- E-Mail Address
-
deirdre.lyons@nih.gov, lynn.furtaw@nih.gov
(deirdre.lyons@nih.gov, lynn.furtaw@nih.gov)
- Small Business Set-Aside
- N/A
- Description
- 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. Background: The Center for Inherited Disease Research (CIDR) is a centralized facility that performs directed research and provides a suite of services and deliverables all focused on understanding the genetic contribution to human phenotypes. These services are provided to qualified Principal Investigators (PIs) in consultation with NIH institutes who are affiliated with the CIDR program. Services provided by CIDR include genotyping, DNA sequencing, epigenomic analyses, statistical genetics services and the deposition of data into NIH data repositories. CIDR resources and expertise are made available to qualified scientific investigators through competitive peer review by a chartered CIDR Access Committee (CAC). All applications are evaluated by the CAC for scientific merit. The application and the CAC's recommendations are reviewed by the Board of Governors (BOG), which is comprised of NIH staff. The BOG determines which projects are granted access to CIDR. All applications require prior approval from an NIH Institute liaison before a proposal is submitted to CIDR. CIDR was established in 1996 through a sole-source contract to Johns Hopkins University. Originally supported by seven NIH Institutes, it is now funded by twelve NIH Institutes with NHGRI providing scientific and administrative oversight. Purpose and Objectives: This proposed acquisition is a renewal of the CIDR program with an anticipated period of performance of seven years. The purpose of this acquisition is to provide: 1) high quality, high throughput human and mouse genotyping services (via custom designed arrays and whole genome arrays), 2) next generation high throughput DNA sequencing services consisting of the direct sequencing of selected genomic regions, whole exome sequencing and whole genome DNA sequencing, 3) epigenetics services including DNA methylation arrays and whole genome bisulfite DNA sequencing, and 4) the ability to produce data in a laboratory certified under the standards of the Clinical Laboratory Improvement Amendments (CLIA). Services to be offered include expertise in statistical genetics and genomic analysis using methods designed to find the genetic basis for disease. These services will support extramural and intramural research programs funded by the twelve participating Institutes. The acquisition also contains a significant research and development component. As existing technologies improve, enhancements shall be evaluated and adopted. The acquisition also includes tasks related to the ongoing evaluation of new technologies that may significantly increase the efficiency and yield of genetic studies. Project Requirements: Services to be performed include: a. Single nucleotide genotyping (SNP) to allow whole genome linkage scans of at least 10,000 human samples per year. b. SNP genotyping using custom designed assay for 96-500,000 user selected SNPs on 100,000 samples per year. c. Fixed content genotyping on platforms capable of scoring 500,000 to 5,000,000 uniformly spaced loci to allow SNP whole genome linkage scans of 200,000 human samples per year. These assays shall be designed to capture >~90% of the variation in human DNA samples from the three major continental populations (Asian, African and European) using appropriate metrics that take human linkage disequilibrium into account. These platforms will be used to carry out genome-wide association studies. d. SNP genotyping using 10,000- 200,000 SNPs covering focused sets of genes to address specific biological questions, e.g., genes related to human metabolism, human pharmacogenetic targets, human immune response genes, human cancer genes. Capacity should be available to analyze 35,000 samples per year with these fixed content arrays. e. SNP genotyping of up to ~1500 SNPs in 10,000 mouse DNA samples per year. f. Measurement of DNA methylation in human samples using arrays that cover 10,000-500,000 potential sites of methylation in the human genome in 15,000 samples per year. g. Whole exome sequencing of human DNA for 8,000 samples per year. h. Whole genome sequencing of human and mouse DNA for 200 samples per year. i. Consultation on statistical genetics questions including power estimates for assessing sample size requirements before production genotyping is carried out, and analysis of genotyping data after production genotyping is complete. j. Strict quality control to include testing of all samples for adequacy of amount and quality of DNA prior to full genotyping and produce genotypes to DNA fingerprint each sample as it enters the lab. k. Use of pedigree structure information to test for inheritance errors, misattributed parentage, incorrect gender assignments and the de novo occurrence of mutations. l. Opportunity for Principal Investigators (PIs) to replace problematic DNA samples that do not pass pre-testing quality control before DNA sequencing or production genotyping is undertaken. m. Accurate quality control reporting for each project and an annual summary of all projects on missing data, pedigree structure errors, and blind duplicate error rates, using either available software or designing and implementing novel software to generate these reports. n. Databases for laboratory information management (tracking samples and reagent usage, DNA and reagent quality control), collecting genotyping results, and analyzing genotypes for data quality control metrics. o. System-wide data security and data back-up in a secure location off-site that is specially designed to provide protection from physical damage to storage media. p. Ability to receive and interpret electronically encoded family and pedigree structure information. q. Capacity to receive >250,000 DNA samples per year from submitting investigators in multi-well, barcode encoded plates. r. Ability to aliquot, dilute, test, store and genotype these DNA samples without cross-contamination. s. Expertise in evaluating and implementing novel genotyping technologies and work flow procedures in order to keep CIDR's methodology up to date and cost effective. t. Ability to provide SNP genotyping or DNA sequencing results in a CLIA compliant workflow upon request for clinical studies. Anticipated period of performance: The anticipated period of performance for this requirement is May 1, 2016 to April 30, 2023. Other important considerations: The NAICS code for this requirement is 541712 with a size standard of 500 employees. Capability statement/Information sought: Small business concerns that believe they possess the capabilities necessary to undertake this requirement should submit a tailored capability statement that clearly details the ability to perform the required services described in this notice. Capability Statements should include the following: 1. Evidence of the firm's status as a small business under NAICS code 541712. 2. Evidence that a firm can either provide laboratory facilities within a 100 mile radius of the NIH in Bethesda, MD or occupy the Government leased facility in the TRIAD building in Baltimore, MD. This will be a mandatory criterion in the RFP. 3. Evidence of availability and skill of staff, including those with laboratory, project management and bioinformatics experience to provide all of these services including sample and reagent handling, tracking and reagent and sample quality control using a Laboratory Information Management system, high throughput production genotyping, analysis to provide data quality control assessments, statistical genetics expertise in study design and data analysis, and database management. 4. Evidence of ability to hire and retain senior staff with the necessary qualifications and requisite certifications from the American College of Medical Genetics that would allow for CLIA certified genetic testing. Past experience importing and/or implement highly technical genotyping methods, work flow procedures, to implement and apply state-of-the-art statistical genetics programs for study design and data analysis, and to import or create novel computer algorithms and programs in support of the goals of the CIDR Program. These qualifications are to include having 3 -5 years of genetics and molecular biology research experience applying these methods. 5. Evidence of prior experience in providing the database support, data back-up, and data analysis required for linkage and association studies involving tens of thousands of samples and millions of thousands of loci. 6. Demonstrated prior experience in high throughput genotyping of DNA samples at a rate of >100,000 samples per year. 7. Demonstrated ability to provide SNP genotyping service on at least two different platforms, with SNP sets ranging in size from a 96 SNPs to >~5,000,000 SNPs genotyped per sample. Ability to provide SNP genotyping results on up to 5,000 SNPs per sample using a CLIA certified/compliant pipeline, when requested by the submitting investigator. 8. Demonstrated experience in using high throughput genome sequencing technologies ("Next Generation" sequencing) to produce data on the selected regions of a genome, the human exome and whole genome sequencing for organisms in which a reference genome sequence is publicly available. 9. The ability to analyze and align exome and whole genome sequence data to identify common and novel variants in the sequence. 10. Demonstrated experience with depositing the large scale data sets produced from SNP and sequencing projects into accessible databases such as those hosted by the National Center for Biotechnology Information. Information Submission Instructions - this should include but not be limited to the following information: Capability statements are not to exceed 20 single-sided pages (including all attachments, charts, etc.), using a 12-point font size. 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. All capability statements sent in response to this SOURCES SOUGHT notice must be submitted electronically (via email) to Deirdre Lyons, Contract Specialist, at lyonsde@mail.nih.gov in either MS Word, or Adobe Portable Document Format (PDF), by Monday, April 6, 2015, 1:00 PM, EST. All responses must be received by the specified due date and time in order to be considered. Disclaimer and Important Notes: This notice does not obligate the Government to award a contract 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-SBSS-CSB-HG-2016-17-DL/listing.html)
- Place of Performance
- Address: Within 100 miles of the NIH, Bethesda, Maryland, 20815, United States
- Zip Code: 20815
- Zip Code: 20815
- Record
- SN03674486-W 20150322/150320234730-51e3959fde09d87fe9de0e8fcc42cae0 (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
(may not be valid after Archive Date)
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