Data from: Accurate genomic predictions for chronic wasting disease in U.S. white-tailed deer
Data files
Mar 04, 2020 version files 657.40 MB
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807WTD_DRYAD.csv
402.23 MB
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807WTD_DRYAD.dsf
32.97 MB
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807WTD_MarkerMap.csv
3.36 MB
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AF1_EMMAX_P-P_WithX_MT_FullDosage_CWDBinary_NoCovariates.png
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AF1_EMMAXBinary_NoCovariatesFullDosage_WithX_MT_.xlsx
27.94 MB
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AF10_K3_CenteredCWDScores_NoCovariates_FullDosComp_WithX_WithMT.csv
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AF11_K3_CenteredCWDScores_SexAgeGenRegion_FullDosComp_WithX_WithMT.csv
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AF12_K5_CenteredCWDScores_NoCovariates_FullDosComp_WithX_WithMT.csv
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AF13_K5_CenteredCWDScores_SexAgeGenRegion_FullDosComp_WithX_WithMT.csv
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AF14_K3_CenteredBinary_NoCovariates_NoDosComp_WithX_MT.csv
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AF15_K3_CenteredBinary_SexAgeGenRegion_NoDosComp_WithX_MT.csv
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AF16_K5_CenteredBinary_NoCovariates_NoDosComp_WithX_MT.csv
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AF17_K5_CenteredBinary_SexAgeGenRegion_NoDosComp_WithX_MT.csv
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AF18_K3_CenteredCWDScores_NoCovariates_NoDosComp_WithX_MT.csv
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AF19_K3_CenteredCWDScores_SexAgeGenRegion_NoDosComp_WithX_MT.csv
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AF2_EMMAX_P-P_WithX_MT_FullDosage_CWDBinary_SexAgeGenRegion.png
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AF2_EMMAXBinary_SexAgeGenRegionFullDosage_WithX_MT_.xlsx
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AF20_K5_CenteredCWDScores_NoCovariates_NoDosComp_WithX_MT.csv
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AF21_K5_CenteredCWDScores_SexAgeGenRegion_NoDosComp_WithX_MT.csv
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AF22_K3_CenteredBinary_NoCovariates_NoX_NoMT.csv
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AF23_K3_CenteredBinary_SexAgeGenRegion_NoX_NoMT.csv
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AF24_K5_CenteredBinary_NoCovariates_NoX_NoMT.csv
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AF25_K5_CenteredBinary_SexAgeGenRegion_NoX_NoMT.csv
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AF26_K3_CenteredCWDScores_NoCovariates_NoX_NoMT.csv
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AF27_K3_CenteredCWDScores_SexAgeGenRegion_NoX_NoMT.csv
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AF28_K5_CenteredCWDScores_NoCovariates_NoX_NoMT.csv
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AF29_K5_CenteredCWDScores_SexAgeGenRegion_NoX_NoMT.csv
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AF3_EMMAX_P-P_WithX_MT_FullDosage_CWDBinary_SexAgeGenRegionCWDTissueScores.png
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AF3_EMMAXBinary_SexAgeGenRegionCWDTissueScores_FullDosageWithX_MT_.xlsx
45.63 MB
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AF30DocumentationFor_affy_choose_snps.docx
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AF31_IBSDistanceDuplicatesControlsTwins.csv
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AF32_Seabury_DeerTAMU_20190712_QC_SNPTable.xlsx
32.55 MB
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AF4_EMMAX_P-P_WithX_MT_FullDosageCWDScores_NoCovariates.png
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AF4_EMMAXCWDScores_NoCovariatesFullDosage_WithX_MT.xlsx
27.65 MB
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AF5_EMMAX_P-P_WithX_MT_FullDosageCWDScores_SexAgeGenRegion.png
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AF5_EMMAXCWDScores_SexAgeGenRegionFullDosage_WithX_MT.xlsx
41.95 MB
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AF6_K3_CenteredBinary_NoCovariates_FullDosComp_WithX_WithMT.csv
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AF7_K3_CenteredBinary_SexAgeGenRegion_FullDosComp_WithX_WithMT.csv
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AF8_K5_CenteredBinary_NoCovariates_FullDosComp_WithX_WithMT.csv
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AF9_K5_CenteredBinary_SexAgeGenRegion_FullDosComp_WithX_WithMT.csv
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affy_choose_snps.py
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ReadMe_v2.txt
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Supplemental_Seabury.zip
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VarianceComponents807WTD.txt
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Abstract
The geographic expansion of chronic wasting disease (CWD) in U.S. white-tailed deer (Odocoileus virginianus) has been largely unabated by best management practices, diagnostic surveillance, and depopulation of positive herds. Using a custom Affymetrix Axiom® single nucleotide polymorphism (SNP) array, we demonstrate that both differential susceptibility to CWD, and natural variation in disease progression, are moderately to highly heritable ( among farmed U.S. white-tailed deer, and that loci other than PRNP are involved. Genome-wide association analyses using 123,987 quality filtered SNPs for a geographically diverse cohort of 807 farmed U.S. white-tailed deer (n = 284 CWD positive; n = 523 CWD non-detect) confirmed the prion gene (PRNP; G96S) as a large-effect risk locus (P-value < 6.3E-11), as evidenced by the estimated proportion of phenotypic variance explained (PVE ≥ 0.05), but also demonstrated that more phenotypic variance was collectively explained by loci other than PRNP. Genomic best linear unbiased prediction (GBLUP; n = 123,987 SNPs) with k-fold cross validation (k = 3; k = 5) and random sampling (n = 50 iterations) for the same cohort of 807 farmed U.S. white-tailed deer produced mean genomic prediction accuracies ≥ 0.81; thereby providing the necessary foundation for exploring a genomically-estimated CWD eradication program.
The geographic expansion of chronic wasting disease (CWD) in U.S. white-tailed deer has been largely unabated by best management practices, diagnostic surveillance, and depopulation of positive herds. Using a custom SNP array, we show that differential susceptibility to CWD is heritable, and that loci other than PRNP are involved. Genomic prediction with k-fold cross validation for a geographically diverse cohort of farmed U.S. white-tailed deer produced prediction accuracies ≥ 0.81.