GGP HD 150K

The custom, high density GeneSeek® Genomic Profiler (GGP-HD) for dairy utilises Illumina Infinium® chemistry and features nearly 150,000 SNPs for more accurate evaluation of genetic merit, genome-wide selection, comparative genetic studies, and higher density imputation.

The GGP BeadChip, built on the highly informative Illumina 7k BeadChip, also offers the most informative SNPs from the Illumina Bovine 50k and 770k BeadChips. Utilising the best content from all three Illumina chips, all for a low, affordable price, PLUS comprehensive parentage, disease and trait relevant SNPs.

  • More information. Includes approximately 42,000 of the most informative SNPs from the original Illumina Bovine 50k. 74,000 SNPs overlap with the original GGP-HD bovine and greater than 25,000 SNPs from the GGP-LD array are included. The remaining 23,000 SNPs come directly from the Illumina 777k array.
  • Uniform coverage.The average SNP spacing within the genome is approximately 19 kb (the Illumina 50k chip has average spacing at 49.4 kb for comparison), with a higher concentration on the telomeric regions of the chromosome. A majority of the SNPs were specifically chosen for high minor allele frequency values and uniform genome coverage for a majority of the Bos taurus breeds.
  • Verify Parentage. Includes all commonly utilised USDA parentage SNPs, plus hundreds of SNPs to enable conversion of ISAG microsatellite parentage data.
  • Custom content. Contains 700 putative functional variants/splice site mutations derived from whole genome sequencing data from a variety of beef and dairy breeds.

Packed with new custom content

The GGP-HD 150K contains additional markers that have been shown to have an impact on disease susceptibility and performance in various breeds of dairy cattle. These markers include:

  • ATP binding cassette sub family G member 2 (ABCG2)
  • Beta casein A2/A3
  • Beta casein variants
  • Beta lactoglobulin
  • Bovine leukocyte adhesion deficiency (BLAD)
  • Brachyspina syndrome (BY)
  • Citrullinemia
  • Coat colour including dominant red
  • Complex vertebral malformation (CVM)
  • Diacylglycerol O-acyltransferase 1 (DGAT1)
  • Dilated-cardiomyopathy
  • Factor XI
  • Fish-odour syndrome
  • Growth hormone receptor (BGHR1)
  • Holstein fertility haplotypes 1,3,4
  • Horned/Polled
  • Jersey fertility haplotype (JH1)
  • Kappa Casein
  • Mulefoot
  • Spinal dysmyelination (BSD)
  • Spinal muscular atrophy (SMA)
  • Uridine monophosphate synthase (DUMPS)
  • Weaver syndrome
  • Yellow fat

Looking to the future

Neogen is continuously adding on newly discovered content to add even more value to the GGP-HD 150K for dairy. Newly added content includes:

  • Holstein Cholesterol Deficiency (HCD)
  • Brown Swiss Fertility Haplotype 2 (BH2)
  • Ayrshire Fertility Haplotype 1 (AH1)

Technical Information