TY - JOUR
T1 - Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds
AU - Schaefer, Robert J.
AU - Schubert, Mikkel
AU - Bailey, Ernest
AU - Bannasch, Danika L.
AU - Barrey, Eric
AU - Bar-Gal, Gila Kahila
AU - Brem, Gottfried
AU - Brooks, Samantha A.
AU - Distl, Ottmar
AU - Fries, Ruedi
AU - Finno, Carrie J.
AU - Gerber, Vinzenz
AU - Haase, Bianca
AU - Jagannathan, Vidhya
AU - Kalbfleisch, Ted
AU - Leeb, Tosso
AU - Lindgren, Gabriella
AU - Lopes, Maria Susana
AU - Mach, Núria
AU - da Câmara Machado, Artur
AU - MacLeod, James N.
AU - McCoy, Annette
AU - Metzger, Julia
AU - Penedo, Cecilia
AU - Polani, Sagi
AU - Rieder, Stefan
AU - Tammen, Imke
AU - Tetens, Jens
AU - Thaller, Georg
AU - Verini-Supplizi, Andrea
AU - Wade, Claire M.
AU - Wallner, Barbara
AU - Orlando, Ludovic
AU - Mickelson, James R.
AU - McCue, Molly E.
N1 - Publisher Copyright:
© 2017 The Author(s).
PY - 2017/7/27
Y1 - 2017/7/27
N2 - Background: 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. Results: 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. Conclusions: 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.
AB - Background: 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. Results: 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. Conclusions: 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.
KW - Equine genomics
KW - Linkage disequilibrium
KW - SNP chip
KW - SNP discovery
KW - SNP informativeness
KW - SNP validation
KW - SNP-tagging
KW - Variant recalibration
KW - Whole genome sequence
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U2 - 10.1186/s12864-017-3943-8
DO - 10.1186/s12864-017-3943-8
M3 - Article
C2 - 28750625
AN - SCOPUS:85026226414
SN - 1471-2164
VL - 18
JO - BMC Genomics
JF - BMC Genomics
IS - 1
M1 - 565
ER -