Present And Future Of Genomic Test Reporting In The Cattle Industry.

Abstract A series of custom low density (LD) SNP genotyping platforms have been created over the years. Recognized by the GeneSeek Genomic Profiler (GGP) nomenclature, these SNP arrays have increased in size as new versions were created, such as: GGP-LD-v1 (n = 8,762), GGP-LD-v2 (n = 20,057), GGP-LD-v3 (n = 26,151), GGP-LD-v4 (n = 30,108), and GGP Bovine 50K (n = 47,843), all of which contained a base of the Illumina Bovine LD array (n = 7,931) and then added SNPs to provide maximum information content (Shannon Entropy) and optimal genomic coverage into target populations without specific restrictions on overlap to historical commercial arrays such as the Illumina Bovine 50K (n = 54,001). Our approach has been to select SNP content which originated on the Illumina Bovine HD array (n = 777,962) or the GGP F250 functional SNP array (n = 221,115). This approach produced GGPs which: 1) have a larger number of SNPs that meet quality control metrics for minor allele frequency and Hardy-Weinberg segregation testing; 2) have superior imputation accuracy to the Illumina HD array in target populations; and 3) have causative SNPs or SNPs in closer LD with causative mutations for functional genomics studies and increased utility across populations. These design features have not always been utilized by users of the GGP portfolio. In some cases, users have imputed from GGP content back to the Illumina Bovine 50K SNP content within their population because that was the earliest process they developed in their evaluation system. This approach ignores the innovation and potential utility designed into the GGP chips for breeders within those organizations. We do not look back to prior SNP arrays for content definition for the purpose of bridging content from current arrays to the past. Instead, our vision is to continue to innovate, on a routine basis, which SNPs we provide to customers, so that their genetic evaluations can continue to evolve and improve into the future.