Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds
Abstract 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 dev...
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| Format: | Article |
| Language: | English |
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BMC
2017-07-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-017-3943-8 |
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Article |
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DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Robert J. Schaefer Mikkel Schubert Ernest Bailey Danika L. Bannasch Eric Barrey Gila Kahila Bar-Gal Gottfried Brem Samantha A. Brooks Ottmar Distl Ruedi Fries Carrie J. Finno Vinzenz Gerber Bianca Haase Vidhya Jagannathan Ted Kalbfleisch Tosso Leeb Gabriella Lindgren Maria Susana Lopes Núria Mach Artur da Câmara Machado James N. MacLeod Annette McCoy Julia Metzger Cecilia Penedo Sagi Polani Stefan Rieder Imke Tammen Jens Tetens Georg Thaller Andrea Verini-Supplizi Claire M. Wade Barbara Wallner Ludovic Orlando James R. Mickelson Molly E. McCue |
| spellingShingle |
Robert J. Schaefer Mikkel Schubert Ernest Bailey Danika L. Bannasch Eric Barrey Gila Kahila Bar-Gal Gottfried Brem Samantha A. Brooks Ottmar Distl Ruedi Fries Carrie J. Finno Vinzenz Gerber Bianca Haase Vidhya Jagannathan Ted Kalbfleisch Tosso Leeb Gabriella Lindgren Maria Susana Lopes Núria Mach Artur da Câmara Machado James N. MacLeod Annette McCoy Julia Metzger Cecilia Penedo Sagi Polani Stefan Rieder Imke Tammen Jens Tetens Georg Thaller Andrea Verini-Supplizi Claire M. Wade Barbara Wallner Ludovic Orlando James R. Mickelson Molly E. McCue Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds BMC Genomics Equine genomics Whole genome sequence SNP-tagging SNP chip Variant recalibration SNP discovery |
| author_facet |
Robert J. Schaefer Mikkel Schubert Ernest Bailey Danika L. Bannasch Eric Barrey Gila Kahila Bar-Gal Gottfried Brem Samantha A. Brooks Ottmar Distl Ruedi Fries Carrie J. Finno Vinzenz Gerber Bianca Haase Vidhya Jagannathan Ted Kalbfleisch Tosso Leeb Gabriella Lindgren Maria Susana Lopes Núria Mach Artur da Câmara Machado James N. MacLeod Annette McCoy Julia Metzger Cecilia Penedo Sagi Polani Stefan Rieder Imke Tammen Jens Tetens Georg Thaller Andrea Verini-Supplizi Claire M. Wade Barbara Wallner Ludovic Orlando James R. Mickelson Molly E. McCue |
| author_sort |
Robert J. Schaefer |
| title |
Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds |
| title_short |
Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds |
| title_full |
Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds |
| title_fullStr |
Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds |
| title_full_unstemmed |
Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds |
| title_sort |
developing a 670k genotyping array to tag ~2m snps across 24 horse breeds |
| publisher |
BMC |
| series |
BMC Genomics |
| issn |
1471-2164 |
| publishDate |
2017-07-01 |
| description |
Abstract 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. |
| topic |
Equine genomics Whole genome sequence SNP-tagging SNP chip Variant recalibration SNP discovery |
| url |
http://link.springer.com/article/10.1186/s12864-017-3943-8 |
| work_keys_str_mv |
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doaj-04b87937b039413b87f3bf369e812a522020-11-25T00:10:11ZengBMCBMC Genomics1471-21642017-07-0118111810.1186/s12864-017-3943-8Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breedsRobert J. Schaefer0Mikkel Schubert1Ernest Bailey2Danika L. Bannasch3Eric Barrey4Gila Kahila Bar-Gal5Gottfried Brem6Samantha A. Brooks7Ottmar Distl8Ruedi Fries9Carrie J. Finno10Vinzenz Gerber11Bianca Haase12Vidhya Jagannathan13Ted Kalbfleisch14Tosso Leeb15Gabriella Lindgren16Maria Susana Lopes17Núria Mach18Artur da Câmara Machado19James N. MacLeod20Annette McCoy21Julia Metzger22Cecilia Penedo23Sagi Polani24Stefan Rieder25Imke Tammen26Jens Tetens27Georg Thaller28Andrea Verini-Supplizi29Claire M. Wade30Barbara Wallner31Ludovic Orlando32James R. Mickelson33Molly E. McCue34Department of Veterinary Population Medicine, College of Veterinary Medicine, University of MinnesotaCentre for GeoGenetics, Natural History Museum of Denmark, University of CopenhagenMaxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of KentuckySchool of Veterinary Medicine, University of California-DavisUnité de Génétique Animale et Biologie Intégrative- UMR1313, INRA, Université Paris-SaclayThe Robert H. Smith Faculty of Agriculture, Food and Environment, The Koret School of Veterinary Medicine, The Hebrew UniversityInstitute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine ViennaDepartment of Animal Science, University of FloridaInstitute for Animal Breeding and Genetics, University of Veterinary MedicineLehrstuhl für Tierzucht der Technischen Universität MünchenSchool of Veterinary Medicine, University of California-DavisSwiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and AgroscopeSchool of Life and Environmental Sciences, Faculty of Veterinary Science, University of SydneyInstitute of Genetics, University of BernDepartment of Biochemistry and Molecular Biology, School of Medicine, University of LouisvilleInstitute of Genetics, University of BernDepartment of Animal Breeding and Genetics, Swedish University of Agricultural SciencesBiotechnology Centre of Azores, University of AzoresUnité de Génétique Animale et Biologie Intégrative- UMR1313, INRA, Université Paris-SaclayBiotechnology Centre of Azores, University of AzoresMaxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of KentuckyDepartment of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-ChampaignInstitute for Animal Breeding and Genetics, University of Veterinary MedicineVeterinary Genetics Laboratory, University of California DavisThe Robert H. Smith Faculty of Agriculture, Food and Environment, The Koret School of Veterinary Medicine, The Hebrew UniversityAgroscope, Swiss National Stud FarmSchool of Life and Environmental Sciences, Faculty of Veterinary Science, University of SydneyInstitute of Animal Breeding and Husbandry, Christian-Albrechts-University KielInstitute of Animal Breeding and Husbandry, Christian-Albrechts-University KielDepartment of Veterinary Medicine - Sport Horse Research Centre, University of PerugiaSchool of Life and Environmental Sciences, Faculty of Veterinary Science, University of SydneyInstitute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine ViennaCentre for GeoGenetics, Natural History Museum of Denmark, University of CopenhagenDepartment of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of MinnesotaDepartment of Veterinary Population Medicine, College of Veterinary Medicine, University of MinnesotaAbstract 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.http://link.springer.com/article/10.1186/s12864-017-3943-8Equine genomicsWhole genome sequenceSNP-taggingSNP chipVariant recalibrationSNP discovery |