Including copy number variation in association studies to predict genotypic values
The objective of this study was to investigate, both empirically and deterministically, the ability to explain genetic variation resulting from a copy number polymorphism (CNP) by including the CNP, either by its genotype or by a continuous derivation thereof, alone or together with a nearby single nucleotide polymorphism (SNP) in the model. This continuous measure of a CNP genotype could be a raw hybridization measurement, or a predicted CNP genotype. Results from simulations showed that the linkage disequilibrium (LD) between an SNP and CNP was lower than LD between two SNPs, due to the higher mutation rate at the CNP loci. The model R2 values from analysing the simulated data were very similar to the R2 values predicted with the deterministic formulae. Under the assumption that x copies at a CNP locus lead to the effect of x times the effect of 1 copy, including a continuous measure of a CNP locus in the model together with the genotype of a nearby SNP increased power to explain variation at the CNP locus, even when the continuous measure explained only 15% of the variation at the CNP locus.
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| Format: | Article/Letter to editor biblioteca |
| Language: | English |
| Subjects: | cattle, disease, genetic risk, human genome, markers, microsatellite, mutation-rates, polymorphism, snps, wide linkage disequilibrium, |
| Online Access: | https://research.wur.nl/en/publications/including-copy-number-variation-in-association-studies-to-predict |
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dig-wur-nl-wurpubs-3977922025-01-22 Calus, M.P.L. Koning, de, D.J. Haley, C.S. Article/Letter to editor Genetics Research 92 (2010) 2 ISSN: 0016-6723 Including copy number variation in association studies to predict genotypic values 2010 The objective of this study was to investigate, both empirically and deterministically, the ability to explain genetic variation resulting from a copy number polymorphism (CNP) by including the CNP, either by its genotype or by a continuous derivation thereof, alone or together with a nearby single nucleotide polymorphism (SNP) in the model. This continuous measure of a CNP genotype could be a raw hybridization measurement, or a predicted CNP genotype. Results from simulations showed that the linkage disequilibrium (LD) between an SNP and CNP was lower than LD between two SNPs, due to the higher mutation rate at the CNP loci. The model R2 values from analysing the simulated data were very similar to the R2 values predicted with the deterministic formulae. Under the assumption that x copies at a CNP locus lead to the effect of x times the effect of 1 copy, including a continuous measure of a CNP locus in the model together with the genotype of a nearby SNP increased power to explain variation at the CNP locus, even when the continuous measure explained only 15% of the variation at the CNP locus. en application/pdf https://research.wur.nl/en/publications/including-copy-number-variation-in-association-studies-to-predict 10.1017/S0016672310000091 https://edepot.wur.nl/155717 cattle disease genetic risk human genome markers microsatellite mutation-rates polymorphism snps wide linkage disequilibrium Wageningen University & Research |
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cattle disease genetic risk human genome markers microsatellite mutation-rates polymorphism snps wide linkage disequilibrium cattle disease genetic risk human genome markers microsatellite mutation-rates polymorphism snps wide linkage disequilibrium |
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cattle disease genetic risk human genome markers microsatellite mutation-rates polymorphism snps wide linkage disequilibrium cattle disease genetic risk human genome markers microsatellite mutation-rates polymorphism snps wide linkage disequilibrium Calus, M.P.L. Koning, de, D.J. Haley, C.S. Including copy number variation in association studies to predict genotypic values |
| description |
The objective of this study was to investigate, both empirically and deterministically, the ability to explain genetic variation resulting from a copy number polymorphism (CNP) by including the CNP, either by its genotype or by a continuous derivation thereof, alone or together with a nearby single nucleotide polymorphism (SNP) in the model. This continuous measure of a CNP genotype could be a raw hybridization measurement, or a predicted CNP genotype. Results from simulations showed that the linkage disequilibrium (LD) between an SNP and CNP was lower than LD between two SNPs, due to the higher mutation rate at the CNP loci. The model R2 values from analysing the simulated data were very similar to the R2 values predicted with the deterministic formulae. Under the assumption that x copies at a CNP locus lead to the effect of x times the effect of 1 copy, including a continuous measure of a CNP locus in the model together with the genotype of a nearby SNP increased power to explain variation at the CNP locus, even when the continuous measure explained only 15% of the variation at the CNP locus. |
| format |
Article/Letter to editor |
| topic_facet |
cattle disease genetic risk human genome markers microsatellite mutation-rates polymorphism snps wide linkage disequilibrium |
| author |
Calus, M.P.L. Koning, de, D.J. Haley, C.S. |
| author_facet |
Calus, M.P.L. Koning, de, D.J. Haley, C.S. |
| author_sort |
Calus, M.P.L. |
| title |
Including copy number variation in association studies to predict genotypic values |
| title_short |
Including copy number variation in association studies to predict genotypic values |
| title_full |
Including copy number variation in association studies to predict genotypic values |
| title_fullStr |
Including copy number variation in association studies to predict genotypic values |
| title_full_unstemmed |
Including copy number variation in association studies to predict genotypic values |
| title_sort |
including copy number variation in association studies to predict genotypic values |
| url |
https://research.wur.nl/en/publications/including-copy-number-variation-in-association-studies-to-predict |
| work_keys_str_mv |
AT calusmpl includingcopynumbervariationinassociationstudiestopredictgenotypicvalues AT koningdedj includingcopynumbervariationinassociationstudiestopredictgenotypicvalues AT haleycs includingcopynumbervariationinassociationstudiestopredictgenotypicvalues |
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1822272924120252416 |