SOLICITATION NOTICE
66 -- Genotyping Services
- Notice Date
- 6/16/2010
- Notice Type
- Combined Synopsis/Solicitation
- NAICS
- 334419
— Other Electronic Component Manufacturing
- Contracting Office
- Department of Agriculture, Agricultural Research Service, Procurement and Property Division, Acquisition Branch (DC), 1280 MARYLAND AVE SW, Portals Bldg, Rm 580C, Washington, District of Columbia, 202500310, United States
- ZIP Code
- 00310
- Solicitation Number
- 00812655600004KLN
- Archive Date
- 6/30/2010
- Point of Contact
- Kathy L Newton, Phone: 202-720-7478
- E-Mail Address
-
knewton@ars.usda.gov
(knewton@ars.usda.gov)
- Small Business Set-Aside
- N/A
- Description
- The United States Department of Agriculture (USDA), Agricultural Research Service (ARS) has a requirement for SNP Genotyping using the BovineSNP50. The contractor shall perform genotyping of each individual bovine DNA (284 each) with Illumina's BovineSNP50 BeadChip as indicated below: The following is the basic minimum objectives and contractor requirements: Purpose and Objectives of the Acquisition The goals of the Bovine Functional Genomics Laboratory (BFGL) are •• Use genotyping to determine the impact of particular areas in the bovine genome affecting important phenotypic traits. •• Build databases that enable imputation from lower density panels to high density genotype equivalents. Contractor Requirements The contractor shall perform genotyping of each individual bovine DNA with Illumina's BovineSNP50 BeadChip in accordance with the following: 1) Supply BovineSNP50 BeadChips from Illumina. 2) Organize shipping of chips from Illumina to the company. 3) Hybridize DNA (provided by ARS BARC) to the chips 4) Collect genotypes using the chips with supplied DNAs. Period of performance The period of performance will be the date of award through August 30, 2010. Government Responsibilities USDA ARS BARC will provide DNA from every pig to be SNP genotyped. Reporting Requirements and Deliverables The company must deliver complete data on genotypes by secure FTP to BFGL. The company must confirm progress by the 15 th of each month on data generation and completion of genotypes, and submission of data by secure electronic submission via a secure FTP site. Inspection and Acceptance Requirements The complete data on SNP allele data on genotypes must meet current quality control criteria for SNP data, including good signal to noise for signal data generated. All samples with call rates (total genotypes called for a sample)/ (total possible genotypes for that sample minus the number of zeroed markers) below 90% for SNP hybridization will be considered as "failures." Such samples will be examined to try to determine the reason for failure. Multiple contiguous poor samples on a chip are grounds to rerun the samples due to a chip problem and the contractor will arrange for all such samples to be rerun. Isolated single bad samples will be examined for sample contamination and signal strength. Sample contamination will be assessed visibly by plotting all x and y values for all markers on the same graph. Sample will be considered "contaminated or mixed sample" if it has more than three visible lobes. Samples will be considered as "poor quality or degraded" if the SNP hybridization signals are very low or non-existent lobes with a handful of abnormally strong markers. If "contaminated or mixed sample" or "poor quality or degraded sample" is noted then the contractor will request that a fresh aliquot of the sample be extracted and supplied to the contractor. All SNP genotype data will be reviewed for quality of SNP binding signal generated and the contractor shall repeat the analyses for data not meeting the criteria. The inspection and acceptance will be affirmed by the PHGC project members and the PHGC database managers. Please submit your quotes via email to Kathy.Newton@ars.usda.gov by noon EST on Tuesday, June 29, 2010.
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/USDA/ARS/PPB/00812655600004KLN/listing.html)
- Place of Performance
- Address: USDA-ARS, 10300 Baltimore Avenue, Beltsville, Maryland, 20705, United States
- Zip Code: 20705
- Zip Code: 20705
- Record
- SN02179253-W 20100618/100616235024-8fda539411bddd48077abe674c838bc1 (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
(may not be valid after Archive Date)
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