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illumina® OvineSNP50 Genotyping BeadChip v2

52,152 SNP coverage of the Ovine genome including scrapie

Weatherbys Scientific have collaborated with illumina® to validate and release the new illumina® OvineSNP50 Genotyping BeadChip v2. This new SNP chip has been validated using 17 different sheep breeds from 456 animals. Scrapie Genotyping is now possible on this SNP chip via a subset of 4 specific scrapie probes that have demonstrated 100% concordance with control samples.

Compatible with your existing Ovine SNP data sets

Adopting the illumina® OvineSNP50 Genotyping BeadChip v2 is risk free. Our analysis has demonstrated backward compatibility to the illumina OvineSNP50 v1 chip, with genotype concordance of >99.9% between versions. Furthermore a reproducibility rate of >99.9% across all 52,152 SNPs ensures consistent integrity of genotypes generated when using illumina® OvineSNP50 Genotyping BeadChip v2.

Fast and Efficient

illumina® OvineSNP50 Genotyping BeadChip v2, routinely 10 workings days.  The chip utilizes illumina XT chemistry which is processed within a robust proprietary workflow which we have used to deliver over 2 million high quality genotypes in 5 years.  We have the capacity and expertise to support your SNP genotyping project providing rapid genotype delivery and additional values adds including parental verification, breed composition and genetic traits all delivered within 5 days of genotypes, to answer all your questions and drive precision breeding.

Technical Specifications
Species: Ovine
Manufacturer: illumina / Co-validated with Weatherbys Scientific
Chemistry: XT
Chip Format: 96 sample format
Illumina Based SNP Content: 52,152
Content Overlap – Ovine v1 and Ovine v2: 52,135
Minor Allele Frequency (MAF) across breeds:

MAF was determined using 456 animals across 17 different breeds, with sample numbers per breed ranging from 2 to 66 (Table 1).

Table 1: Minor allele frequencies across a total of 17 Ovine breeds for 52,152 SNP content. Number of SNPs with a minor allele frequency greater than a0.05 and b0.25 respectively.

Breed Samples Average MAF MAF >0.05a MAF >0.25b
Belclare 58 0.2491 44977 27169
Beltex 51 0.2365 42764 25059
Charollais 31 0.2617 46153 28358
NZ Suffolk 38 0.2416 44142 26407
NZ Texel 44 0.2532 45247 27685
Border Leicester 8 0.1567 31658 18102
Easy Care 8 0.2238 42942 26318
Hampshire Down 6 0.2315 42758 28278
Highlander 6 0.2524 44898 31377
Mayo Connemara 5 0.2562 44960 28136
Primera 4 0.2202 39191 28550
Shropshire 2 0.1984 30706 30706
Suffolk 66 0.2277 41960 24249
Swaledale 11 0.2361 41911 25198
Texel 26 0.2425 44192 26699
Vendeen 46 0.2345 42821 25306
Merino 46 0.2735 47776 30580
Overall/Average 456 0.2350 42297 26952
Chromosomal Coverage of 52,152 SNPs