Comparison of the Accuracy of Epistasis and Haplotype Models for Genomic Prediction of Seven Human Phenotypes
The accuracy of predicting seven human phenotypes of 3657–7564 individuals using global epistasis effects was evaluated and compared to the accuracy of haplotype genomic prediction using 380,705 SNPs and 10-fold cross-validation studies. The seven human phenotypes were the normality transformed high...
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| Format: | Article |
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MDPI AG
2023-10-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/13/10/1478 |
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| author | Zuoxiang Liang Dzianis Prakapenka Yang Da |
| author_facet | Zuoxiang Liang Dzianis Prakapenka Yang Da |
| author_sort | Zuoxiang Liang |
| collection | DOAJ |
| description | The accuracy of predicting seven human phenotypes of 3657–7564 individuals using global epistasis effects was evaluated and compared to the accuracy of haplotype genomic prediction using 380,705 SNPs and 10-fold cross-validation studies. The seven human phenotypes were the normality transformed high density lipoproteins (HDL), low density lipoproteins (LDL), total cholesterol (TC), triglycerides (TG), weight (WT), and the original phenotypic observations of height (HTo) and body mass index (BMIo). Fourth-order epistasis effects virtually had no contribution to the phenotypic variances, and third-order epistasis effects did not affect the prediction accuracy. Without haplotype effects in the prediction model, pairwise epistasis effects improved the prediction accuracy over the SNP models for six traits, with accuracy increases of 2.41%, 3.85%, 0.70%, 0.97%, 0.62% and 0.93% for HDL, LDL, TC, HTo, WT and BMIo respectively. However, none of the epistasis models had higher prediction accuracy than the haplotype models we previously reported. The epistasis model for TG decreased the prediction accuracy by 2.35% relative to the accuracy of the SNP model. The integrated models with epistasis and haplotype effects had slightly higher prediction accuracy than the haplotype models for two traits, HDL and BMIo. These two traits were the only traits where additive × dominance effects increased the prediction accuracy. These results indicated that haplotype effects containing local high-order epistasis effects had a tendency to be more important than global pairwise epistasis effects for the seven human phenotypes, and that the genetic mechanism of HDL and BMIo was more complex than that of the other traits. |
| first_indexed | 2024-03-10T21:24:14Z |
| format | Article |
| id | doaj.art-2c5378fb196145a8a62d9d8c7c0bbb8d |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-10T21:24:14Z |
| publishDate | 2023-10-01 |
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| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-2c5378fb196145a8a62d9d8c7c0bbb8d2023-11-19T15:49:49ZengMDPI AGBiomolecules2218-273X2023-10-011310147810.3390/biom13101478Comparison of the Accuracy of Epistasis and Haplotype Models for Genomic Prediction of Seven Human PhenotypesZuoxiang Liang0Dzianis Prakapenka1Yang Da2Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USADepartment of Animal Science, University of Minnesota, Saint Paul, MN 55108, USADepartment of Animal Science, University of Minnesota, Saint Paul, MN 55108, USAThe accuracy of predicting seven human phenotypes of 3657–7564 individuals using global epistasis effects was evaluated and compared to the accuracy of haplotype genomic prediction using 380,705 SNPs and 10-fold cross-validation studies. The seven human phenotypes were the normality transformed high density lipoproteins (HDL), low density lipoproteins (LDL), total cholesterol (TC), triglycerides (TG), weight (WT), and the original phenotypic observations of height (HTo) and body mass index (BMIo). Fourth-order epistasis effects virtually had no contribution to the phenotypic variances, and third-order epistasis effects did not affect the prediction accuracy. Without haplotype effects in the prediction model, pairwise epistasis effects improved the prediction accuracy over the SNP models for six traits, with accuracy increases of 2.41%, 3.85%, 0.70%, 0.97%, 0.62% and 0.93% for HDL, LDL, TC, HTo, WT and BMIo respectively. However, none of the epistasis models had higher prediction accuracy than the haplotype models we previously reported. The epistasis model for TG decreased the prediction accuracy by 2.35% relative to the accuracy of the SNP model. The integrated models with epistasis and haplotype effects had slightly higher prediction accuracy than the haplotype models for two traits, HDL and BMIo. These two traits were the only traits where additive × dominance effects increased the prediction accuracy. These results indicated that haplotype effects containing local high-order epistasis effects had a tendency to be more important than global pairwise epistasis effects for the seven human phenotypes, and that the genetic mechanism of HDL and BMIo was more complex than that of the other traits.https://www.mdpi.com/2218-273X/13/10/1478genomic predictionepistasishaplotypeprediction accuracySNPhuman phenotype |
| spellingShingle | Zuoxiang Liang Dzianis Prakapenka Yang Da Comparison of the Accuracy of Epistasis and Haplotype Models for Genomic Prediction of Seven Human Phenotypes Biomolecules genomic prediction epistasis haplotype prediction accuracy SNP human phenotype |
| title | Comparison of the Accuracy of Epistasis and Haplotype Models for Genomic Prediction of Seven Human Phenotypes |
| title_full | Comparison of the Accuracy of Epistasis and Haplotype Models for Genomic Prediction of Seven Human Phenotypes |
| title_fullStr | Comparison of the Accuracy of Epistasis and Haplotype Models for Genomic Prediction of Seven Human Phenotypes |
| title_full_unstemmed | Comparison of the Accuracy of Epistasis and Haplotype Models for Genomic Prediction of Seven Human Phenotypes |
| title_short | Comparison of the Accuracy of Epistasis and Haplotype Models for Genomic Prediction of Seven Human Phenotypes |
| title_sort | comparison of the accuracy of epistasis and haplotype models for genomic prediction of seven human phenotypes |
| topic | genomic prediction epistasis haplotype prediction accuracy SNP human phenotype |
| url | https://www.mdpi.com/2218-273X/13/10/1478 |
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