SOLICITATION NOTICE
A -- High Throughput Genotyping and DNA Sequencing for Studying the Genetic Contributions to Human Health and Disease
- Notice Date
- 9/15/2015
- 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-HG-2016-17-DL
- 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
- The National Heart, Lung, and Blood Institute (NHLBI) on behalf of the National Human Genome Research Institute (NHGRI) is seeking a Contractor to perform high throughput genotyping and DNA sequencing services for a seven (7) year period to support the Center for Inherited Disease Research (CIDR) program. The purpose of this announcement is to provide a Pre-Solicitation Notice for the release of Solicitation No. HHS-NIH-NHLBI-CSB-HG-2016-17-DL. THIS IS A SYNOPSIS. THIS IS NOT A SOLICITATION. 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. Mandatory Criterion: Please note that there will be a mandatory criterion in the RFP regarding the place of performance of the contract. The offeror must 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 mandatory criterion must be met at the time of submission of proposals. This is not a Request for Proposal (RFP) and the Government is not committed to award a contract pursuant to this announcement. This advertisement does not commit the Government to award a contract. The RFP will be available on the FedBizOpps Web page at http://www.fedbizopps.gov. Prospective offerors are responsible for downloading the RFP and all attachments. The offeror is responsible for monitoring the FedBizOpps Web page for the release of the solicitation and any amendments. The RFP will be available from the FedBizOpps on or about September 30, 2015.
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/NIH/NHLBI/HHS-NIH-NHLBI-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
- SN03887429-W 20150917/150916000809-c10bfc54a368643f52db52acdcbea19b (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
(may not be valid after Archive Date)
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