SOURCES SOUGHT
A -- High Throughput Genotyping and DNA Sequencing for Studying the Genetic Contributions to Human Disease Renewal 2012 – 2017
- Notice Date
- 9/8/2011
- 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
- HHS-NIH-NHLBI-SBSS-HG-12-20
- Point of Contact
- Jeffrey A Williams, Phone: (301) 435-0331
- E-Mail Address
-
williamsja2@nhlbi.nih.gov
(williamsja2@nhlbi.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 all 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; 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. The applicable NAICS code for this notice is 541712. An organization that is not considered a small business under the applicable NAICS code shall not submit a response to this notice. Background The Center for Inherited Disease Research (CIDR) is a program dedicated to providing high quality, high throughput genotyping in support of efforts to locate and identify genes responsible for human disease and health. The identification of the locations of genes that predispose to or are responsible for a variety of human diseases will greatly benefit the programs of the National Institutes of Health. By identifying these genes, the function of their gene products in normal and disease states can be studied. New DNA-based diagnostic methods can be developed and tested in clinical trials. Ultimately, identification of the genes can illuminate the biochemical and physiological pathways that have become deranged in these disorders and thus provide insights that may be crucial to developing both preventive and therapeutic interventions, thereby improving the public health. CIDR is a program established and supported by fourteen NIH Institutes: National Human Genome Research Institute (NHGRI), National Cancer Institute, National Institute of Dental and Craniofacial Research, National Institute of Neurological Disorders and Stroke, National Institute of Child Health and Human Development, National Eye Institute, National Institute of Environmental Health Sciences, National Institute on Aging, National Institute of Deafness and other Communication Disorders, National Institute of Mental Health, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institute on Alcohol Abuse and Alcoholism and the National Institute on Drug Abuse. NHGRI provides the scientific and administrative oversight for the center. Purpose and Objectives The purpose of this acquisition is to provide high quality, high throughput human and mouse genotyping services, high throughput exome and whole genome DNA sequencing, whole genome DNA methylation measurements and the ability to produce data in a setting of a laboratory certified under the standards of the Clinical Laboratory Improvement Amendments (CLIA). Services to be provided will 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 fourteen participating Institutes. Services to be provided : (1) Single nucleotide genotyping (SNP) to allow whole genome linkage scans of at least 10,000 human samples per year. (2) SNP genotyping using custom designed assay for 96 to 500,000 user selected SNPs on ~36,000 samples per year. (3) Fixed content genotyping on platforms capable of scoring 500,000 to 5,000,000 uniformly spaced loci to allow SNP whole genome association scans of ~100,000 human samples per year. These assays shall be designed to capture >90% of the variation in human DNA when taking human linkage disequilibrium into account, for the purposes of genome-wide association studies. This measure should be calculated for each of the three major human ancestral groups. (4) SNP genotyping of human immune response genes using ~200,000 SNPs on ~8,000 samples per year. (5) SNP genotyping using ~ 200,000 SNPs covering the genes in human metabolism in ~35,000 samples per year (6) SNP genotyping of up to ~1500 SNPs in ~5,000 mouse DNA samples per year. (7) Measure DNA methylation in human samples using arrays that cover 10,000 to 250,000 potential sites of methylation in the human genome in ~15,000 samples per year. (8) Carry out whole exome sequencing of human DNA for ~1,000 exomes per year. (9) Carry out whole genome sequencing on human and mouse DNA for ~40 samples per year. (10) 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. (11) 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. (12) Use of pedigree structure information to test for inheritance errors, misattributed parentage, and incorrect gender assignments, all of which might point to sample mix-ups. (13) Provide opportunity for investigators who submit their projects to CIDR to replace problematic DNA samples that do not pass pre-testing quality control before production genotyping is undertaken. (14) Accurate quality control reporting for each project and an annual summary over 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. (15) 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. (16) Ability to provide results and all quality control metrics on CD-ROM or electronic media in a format mutually agreed upon by the CIDR Program and the submitting Investigator. (17) Provide 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. (18) Ability to receive and interpret electronically encoded family and pedigree structure information. (19) Capacity to receive >150,000 DNA samples per year from submitting investigators in multi-well, barcode encoded plates. (20) Ability to aliquot, dilute, test, store and genotype these DNA samples without cross-contamination. (21) 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. (22) Ability to provide SNP genotyping results in a CLIA approved manner upon request for clinical studies. Anticipated Period of Performance June 1, 2012 through May 31, 2017 Capability Statement/ Information Sought NHLBI is interested in soliciting capability statements from all qualified small businesses demonstrating their ability to perform this research effort. At a minimum prospective Offerors must document capabilities in the following areas: (1) Evidence of availability and skill of staff, including project management, to provide all of the services listed above and including the associated 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. (2) Evidence of ability to hire and retain senior staff with the necessary qualifications and requisite certifications from the American College of Medical Genetics. Past experience importing and/or implementing 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 academic appointments in a university or government-based organized research unit (Department, Branch, Institute or Center) specializing in genetics research. (3) 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. (4) Demonstrated prior experience in high throughput genotyping of DNA samples at a rate of >80,000 samples per year. (5) Demonstrated ability to provide SNP genotyping service on at least two different platforms, with SNP sets ranging in size from 96 SNPs to >~5,000,000 SNPs genotyped per sample. Ability to provide SNP genotyping results on up to 5,000 SNPs per sample in a CLIA approved manner, when requested by the submitting investigator. (6) Demonstrated experience in using high throughput genome sequencing technologies (such as "NextGen" or massively parallel sequencing) to produce data on the human exome and whole genome sequencing for organisms in which a reference genome sequence is publicly available. (7) The ability to analyze exome and whole genome sequence data to identify common and novel variants in the sequence (8) Demonstrated experience with depositing the large scale data sets produced from SNP and sequencing projects into NIH's data repositories such as dbGAP. Information Submission Instructions The NHLBI asks that the capability statement not exceed 20 single sided or 10 double sided pages in length. Three (3) copies of the capability statement must be received at the following address no later than September 23, 2011 at 3:00 PM EST.: National Institutes of Health, National Heart, Lung, and Blood Institute, Office of Acquisitions, Rockledge II- Room 6114, 6701 Rockledge Drive - MSC 7902, Bethesda, MD 20892-7902 (use 20817 for express mail), Attention: Jeffrey Williams, Contracting Officer. Capability statements may also be emailed (as a Word document or PDF) to: Jeffrey Williams at williamsja2@nhlbi.nih.gov Do not include budget information. When submitting this information, please refer to the Small Business Sources Sought Notice HHS-NIH-NHLBI-SBSS-HG-12-20. Responses that do not adhere to these guidelines will not be considered. This notice will close 15 days from the date of posting. Questions may be directed to the Contract Specialist, Jeffrey Williams, williamsja2@nhlbi.nih.gov, 301-435-0331. 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 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).
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