Including copy number variation in association studies to predict genotypic values

Genetics Research
M P L CalusC S Haley

Abstract

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 R(2) values from analysing the simulated data were very similar to the R(2) 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.

References

Nov 2, 2018·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Danilo Hottis LyraRoberto Fritsche-Neto
Nov 1, 2017·Plant Disease·Emmanouil A MarkakisEleftherios K Ligoxigakis

Citations

Nov 7, 1995·Proceedings of the National Academy of Sciences of the United States of America·M T Tusié-Luna, P C White
Nov 28, 2000·Annual Review of Genetics·L G Shaffer, James R Lupski
Jan 17, 2002·Proceedings of the National Academy of Sciences of the United States of America·Sudhir Kumar, Sankar Subramanian
Aug 26, 2003·Journal of Human Genetics·Jun Ohashi, Katsushi Tokunaga
Feb 19, 2004·Nature Reviews. Genetics·Leif Andersson, Michel Georges
Jul 27, 2004·Science·Jonathan SebatMichael Wigler
Dec 21, 2004·Briefings in Bioinformatics·Jakob C Mueller
Apr 1, 2005·Nature Genetics·Gert-Jan B van Ommen
Dec 6, 2005·Nature Genetics·David A HindsKelly A Frazer
Jun 30, 2006·Trends in Genetics : TIG·Bret A Payseur, Asher D Cutter
Jul 11, 2006·American Journal of Human Genetics·Devin P LockeEvan E Eichler
Mar 22, 2007·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Hildegard Kehrer-Sawatzki
Sep 6, 2007·Genome Research·Naomi R WrayPeter M Visscher
Apr 22, 2008·American Journal of Human Genetics·Bret A PayseurJames L Weber
Oct 8, 2008·BMC Genomics·Vincenza MaselliSandro Banfi
Oct 15, 2008·PloS One·Hans D DaetwylerJohn A Woolliams
Aug 4, 2009·Human Molecular Genetics·Luz D OrozcoAldons J Lusis
Sep 1, 2009·Annual Review of Genomics and Human Genetics·Feng ZhangJames R Lupski

Related Concepts

In Silico
DNA Copy Number Changes
Nucleic Acid Hybridization Procedure
Dysequilibrium Syndrome
Dicom Derivation
Linkage Disequilibrium
Locus
Single Nucleotide Polymorphism
Genetic Linkage
Genotype Determination

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