RT Journal Article
SR Electronic
T1 Developing a 670k genotyping array to tag ∼2M SNPs across 24 horse breeds
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 112979
DO 10.1101/112979
A1 Robert J. Schaefer
A1 Mikkel Schubert
A1 Ernest Bailey
A1 Danika L. Bannasch
A1 Eric Barrey
A1 Gila Kahila Bar-Gal
A1 Gottfried Brem
A1 Samantha A. Brooks
A1 Ottmar Distl
A1 Ruedi Fries
A1 Carrie J. Finno
A1 Vinzenz Gerber
A1 Bianca Haase
A1 Vidhya Jagannathan
A1 Ted Kalbfleisch
A1 Tosso Leeb
A1 Gabriella Lindgren
A1 Maria Susana Lopes
A1 Nuria Mach
A1 Artur da Câmara Machado
A1 James N. MacLeod
A1 Annette McCoy
A1 Julia Metzger
A1 Cecilia Penedo
A1 Sagi Polani
A1 Stefan Rieder
A1 Imke Tammen
A1 Jens Tetens
A1 Georg Thaller
A1 Andrea Verini-Supplizi
A1 Claire M. Wade
A1 Barbara Wallner
A1 Ludovic Orlando
A1 James R. Mickelson
A1 Molly E. McCue
YR 2017
UL http://biorxiv.org/content/early/2017/07/05/112979.abstract
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.SNPSingle Nucleotide PolymorphismMNEc2Mthe 2 million SNP array developed hereMNEc670kthe 670 thousand SNP array developed hereWGSwhole genome sequencingbpbase pairGATKgenome analysis tool kitQUALgeneric quality score output by GATK and SAMtoolsMORthe Morgan horse breedSTDthe Standardbred horse breedVQSLODvariant quality score log-oddsGbgiga-basesMHCmajor histocompatibility complexECAEquus caballus chromosomeVIPvery important probeMAFminor allele frequencyALTalternate alleleKDEkernel density estimationLDlinkage disequilibriumChrUn1Equus calballus unknown chromosome