The United States Department of Agriculture (USDA), Agricultural Research Service (ARS) has a requirement for SNP Genotyping 1209.  The contractor shall perform genotyping of each individual pig DNA (300 each) with Illumina's Porcine SNP60 BeadChip as indicated below:

The following is the basic minimum objectives and contractor requirements:

Purpose and Objectives of the Acquisition

The goals of the Porcine Host Genetics Consortium (PHGC) are

••          Use genotyping and phenotyping tools to determine if there are host genes that control resistance/susceptibility to porcine respiratory and the reproductive syndrome virus (PRRSV) infection

••          Verify genetic variation in response to PRRSV, via improved health, survivability and growth

••          Identify relative importance of different phenotypes, and their heritability, that predict response to PRRSV infection

Contractor Requirements

The contractor shall perform genotyping of each individual pig DNA with Illumina's Porcine SNP60 BeadChip in accordance with the following: 

1) Supply Porcine SNP60 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 all 300 supplied DNA's.

[JL1] Period of performance

The period of performance will be February 8, through May 30, 2010.

Government Responsibilities

USDA ARS BARC will provide DNA samples from every pig to be SNP genotyped. 

Reporting Requirements and Deliverables

The company must deliver complete data on genotypes by secure FTP to PHGC manager and PHGC project members as affirmed by PHGC database managers.

The company must confirm progress monthly on data generation and completion of genotypes, and submission of data by secure electronic submission via a secure FTP site, to PHGC project members. 

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 [email protected] by noon EST on 2/08/2010.[JL1] 

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