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

• Published in: BMC genomics Vol. 18; no. 1; p. 565
• Main Authors: Schaefer, Robert J, Schubert, Mikkel, Bailey, Ernest, Bannasch, Danika L, Barrey, Eric, Bar-Gal, Gila Kahila, Brem, Gottfried, Brooks, Samantha A, Distl, Ottmar, Fries, Ruedi, Finno, Carrie J, Gerber, Vinzenz, Haase, Bianca, Jagannathan, Vidhya, Kalbfleisch, Ted, Leeb, Tosso, Lindgren, Gabriella, Lopes, Maria Susana, Mach, Núria, da Câmara Machado, Artur, MacLeod, James N, McCoy, Annette, Metzger, Julia, Penedo, Cecilia, Polani, Sagi, Rieder, Stefan, Tammen, Imke, Tetens, Jens, Thaller, Georg, Verini-Supplizi, Andrea, Wade, Claire M, Wallner, Barbara, Orlando, Ludovic, Mickelson, James R, McCue, Molly E
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 27.07.2017; BioMed Central; BMC
• Subjects: Animal and Dairy Science; Animals; Arrays; Chromosomes; Density; DNA sequencing; Equine genomics; Equus caballus; Gene Frequency; Gene polymorphism; Gene sequencing; Genetic diversity; Genetic variance; Genomes; Genomics; Genotype; Genotype & phenotype; Genotypes; Genotyping; Genotyping Techniques - methods; Genotyping Techniques - standards; Horses; Horses - genetics; Husdjursvetenskap; Linkage Disequilibrium; Nucleotide sequence; Nucleotide sequencing; Nucleotides; Oligonucleotide Array Sequence Analysis - methods; Oligonucleotide Array Sequence Analysis - standards; Polymorphism; Polymorphism, Single Nucleotide; Quality; Reference Standards; Single nucleotide polymorphisms; Single-nucleotide polymorphism; SNP chip; SNP discovery; SNP-tagging; Variant recalibration; Whole genome sequence; Whole Genome Sequencing; SNP informativeness; SNP validation; Equine genomics; Linkage disequilibrium; SNP chip; Whole genome sequence; Variant recalibration; SNP discovery; SNP-tagging
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-017-3943-8

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.