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

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 MachadoJames 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

Research output: Contribution to journalArticle

28 Citations (Scopus)

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.

Original languageEnglish (US)
Article number565
JournalBMC Genomics
Volume18
Issue number1
DOIs
StatePublished - Jul 27 2017

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Horses
Single Nucleotide Polymorphism
Genome
Genotype
Genomics

Keywords

  • Equine genomics
  • Linkage disequilibrium
  • SNP chip
  • SNP discovery
  • SNP informativeness
  • SNP validation
  • SNP-tagging
  • Variant recalibration
  • Whole genome sequence

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Schaefer, R. J., Schubert, M., Bailey, E., Bannasch, D. L., Barrey, E., Bar-Gal, G. K., ... McCue, M. E. (2017). Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds. BMC Genomics, 18(1), [565]. https://doi.org/10.1186/s12864-017-3943-8

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

In: BMC Genomics, Vol. 18, No. 1, 565, 27.07.2017.

Research output: Contribution to journalArticle

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 2017, 'Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds', BMC Genomics, vol. 18, no. 1, 565. https://doi.org/10.1186/s12864-017-3943-8
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. / Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds. In: BMC Genomics. 2017 ; Vol. 18, No. 1.
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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.

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