Supply of Custom SNP Chips for the Livestock Sector and Associated Ancillary Services

Description

The Contracting Authority provides a genotyping management service for farmers, AI companies, herd books and research institutes that includes sample management through to genomic evaluation results. Information obtained from SNP arrays is used to provide an additional source of information to calculate the genetic merit of an animal. Lot 1: The Contracting Authority requires the SNP chips and associated services to meet minimum technical specification set out in Table 1 below, these are indicative requirements subject to change: Table 3.1.1: Indicative minimum requirements for the technical specifications. 1. SNP Chips must be capable of delivering genotypes of between 50,000 to 65,000 bovine genomic variants per sample identified by the Contracting Authority. 2. The data files must be reported in a format suitable for importing into the Contracting Authority’s database and at a minimum include: 3.1.1.2.1 Genotype report 3.1.1.2.2 DNA report 3.1.1.2.3 Sample map 3.1.1.2.4 SNP map 3. The data included in the genotype reports must be in a format suitable for importing into the Contracting Authority’s database and at a minimum include: 3.1.1.3.1 SNP Name; 3.1.1.3.2 Sample ID; 3.1.1.3.3 Allele1 Forward; 3.1.1.3.4 Allele2_Forward; 3.1.1.3.5 Allele1 AB; 3.1.1.3.6 Allele2 AB; 3.1.1.3.7 Allele1 TOP; 3.1.1.3.8 Allele2 TOP; 3.1.1.3.9 X intensity; 3.1.1.3.10 Y intensity; 3.1.1.3.11 BAF; 3.1.1.3.12 Allele log ratio; 4. The data included in the DNA report must be in a format suitable for importing into the Contracting Authority’s database and at a minimum include: 3.1.1.4.1 Sample ID; 3.1.1.4.2 Number of NoCalls; 3.1.1.4.3 Number of Calls; 3.1.1.4.4 Call Rate; 3.1.1.4.5 AA Frequency; 3.1.1.4.6 AB Frequency; 3.1.1.4.7 BB Frequency; 5. The data included in the Sample Map report must be in a format suitable for import into the Contracting Authority’s database and at a minimum include: 3.1.1.5.1 Sample ID; 3.1.1.5.2 Gender; 3.1.1.5.3 Plate; 3.1.1.5.4 Well; 6. The data included in the SNP Map report must be in a format suitable for import into the Contracting Authority’s database and at a minimum include: 3.1.1.5.1 SNP ID; 3.1.1.5.2 Chromosome; 3.1.1.5.3 Position; 3.1.1.5.4 SNP Type 7. Additional data, QC and genotype metrics and / or reports may be specified prior and during the contract.