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; ... (2017). Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds. BMC Genomics, 18(1), p. 565. BioMed Central 10.1186/s12864-017-3943-8

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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.

Item Type:

Journal Article (Original Article)

Division/Institute:

05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH)
05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH) > Institute of Genetics
05 Veterinary Medicine > Department of Clinical Veterinary Medicine (DKV) > Equine Clinic
05 Veterinary Medicine > Department of Clinical Veterinary Medicine (DKV)

UniBE Contributor:

Gerber, Vinzenz; Jagannathan, Vidya and Leeb, Tosso

Subjects:

500 Science > 590 Animals (Zoology)
600 Technology > 630 Agriculture
500 Science > 570 Life sciences; biology
600 Technology > 610 Medicine & health

ISSN:

1471-2164

Publisher:

BioMed Central

Language:

English

Submitter:

Tosso Leeb

Date Deposited:

06 Nov 2017 14:15

Last Modified:

12 Nov 2017 02:16

Publisher DOI:

10.1186/s12864-017-3943-8

PubMed ID:

28750625

Uncontrolled Keywords:

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

BORIS DOI:

10.7892/boris.104854

URI:

https://boris.unibe.ch/id/eprint/104854

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