NDLI: Imprinting detection by extending a regression-based QTL analysis method

Content Provider	Springer Nature Link
Author	Gorlova, Olga Y. Lei, Lei Zhu, Dakai Weng, Shih Feng Shete, Sanjay Zhang, Yiqun Li, Wei Dong Arlen Price, R. Amos, Christopher I.
Copyright Year	2007
Abstract	We present an extension of a regression-based quantitative-trait linkage analysis method to incorporate parent-of-origin effects. We separately regressed total, paternal, and maternal IBD sharing on traits’ squared sums and differences. We also developed a test for imprinting that indicates whether there is any difference between the paternal and maternal regression coefficients. Since this method treats the identity-by-descent information as the dependent variable that is conditioned on the trait, it can be readily applied to data from complex ascertainment processes. We performed a simulation study to examine the performance of the method. We found that when using empirical critical values, the method shows identical or higher power compared to existing methods for evaluation of parent-of-origin effect in linkage analysis of quantitative traits. Missing parental genotypes increase the type I error rate of the linkage test and decrease the power of the imprinting test. When the major gene has a low heritability, the power of the method decreases considerably, but the statistical tests still perform well. We also applied a permutation algorithm, which ensures the appropriate type I error rate for the test for imprinting. The method was applied to a data from a study of 6 body size related measures and 23 loci on chromosome 7 for 255 nuclear families. Multipoint identities-by-descent (IBD) were obtained using a modification of the SIMWALK 2 program. A parent-of-origin effect consistent with maternal imprinting was suggested at 99.67–111.26 Mb for body mass index, bioelectrical impedance analysis, waist circumference, and leptin concentration.
Starting Page	159
Ending Page	174
Page Count	16
File Format	PDF
ISSN	03406717
Journal	Human Genetics
Volume Number	122
Issue Number	2
e-ISSN	14321203
Language	English
Publisher	Springer-Verlag
Publisher Date	2007-06-12
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Metabolic Diseases Internal Medicine Molecular Medicine Human Genetics
Content Type	Text
Resource Type	Article
Subject	Genetics Genetics (clinical)

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