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Type of publication: Journal Article
Type of document: Full Paper

Year: 2017

Authors: Schaefer, RJ; Schubert, M; Bailey, E; Bannasch, DL; Barrey, E; Bar-Gal, GK; Brem, G; Brooks, SA; Distl, O; Fries, R; Finno, CJ; Gerber, V; Haase, B; Jagannathan, V; Kalbfleisch, T; Leeb, T; Lindgren, G; Lopes, MS; Mach, N; da Câmara Machado, A; MacLeod, JN; McCoy, A; Metzger, J; Penedo, C; Polani, S; Rieder, S; Tammen, I; Tetens, J; Thaller, G; Verini-Supplizi, A; Wade, CM; Wallner, B; Orlando, L; Mickelson, JR; McCue, ME

Title: Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds.

Source: BMC Genomics. 2017; 18(1):565

Authors Vetmeduni Vienna:

Brem Gottfried
Wallner Barbara

Vetmed Research Units
Institute of Animal Breeding and Genetics, Unit of Molecular Genetics
Institute of Animal Breeding and Genetics, Unit of Reproductive Biology

To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array.Using whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of ~5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of ~2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of ~670 thousand SNPs (MNEc670k), was designed for genotype imputation.Here, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.

Keywords Pubmed: Animals
Gene Frequency
Genotyping Techniquesmethodsstandards
Linkage Disequilibrium
Oligonucleotide Array Sequence Analysismethodsstandards
Polymorphism, Single Nucleotide
Reference Standards
Whole Genome Sequencing

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