Jason H. Moore, Scott M. Williams's Epistasis: Methods and Protocols PDF

By Jason H. Moore, Scott M. Williams

ISBN-10: 1493921541

ISBN-13: 9781493921546

ISBN-10: 149392155X

ISBN-13: 9781493921553

This quantity provides a necessary and simply reproducible choice of validated and rising suggestions on glossy genetic analyses. Chapters specialise in statistical or facts mining analyses, genetic structure, the weight of a number of trying out, genetic variance, measuring epistasis, multifactor dimensionality relief, and ReliefF. Written within the hugely winning Methods in Molecular Biology sequence structure, chapters comprise introductions to their respective issues, lists of the mandatory fabrics and reagents, step by step, without difficulty reproducible laboratory protocols, and key pointers on troubleshooting and heading off recognized pitfalls.

Authoritative and functional, Epistasis: equipment and Protocols aids scientists in carrying on with to review elucidate epistasis within the context of recent facts availability.

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4. Many methods for incorporation of biological knowledge into epistasis analysis exist and continue to be developed. 30 Marylyn D. Ritchie References 1. Maher B (2008) Personal genomes: the case of the missing heritability. Nature 456:18–21. 1038/456018a 2. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TFC, McCarroll SA, Visscher PM (2009) Finding the missing heritability of complex diseases.

Individuals self-reported to be taking lipid-­ lowering medications were excluded. Sex, age, age squared, body mass index (BMI) were included as covariates in all analyses. The average values for age, age squared, and BMI were also used whenever multiple measurements were available. Plate number is also included as a covariate factor in the ARIC data due to its correlation with some of the lipid levels (known as “plate effect”). 4 Test of Statistical Interactions Statistical interactions between pairs of SNPs were tested on a quantitative trait.

PC analysis was conducted using EIGENSOFT [37] and the top ten PCs were included in the analysis as covariates to account for population stratification in ARIC and MESA samples. For FHS, a mixed model approach was first applied to account for familial relatedness and then pairwise interaction was tested on the residuals from the mixed models [22]. 5 Locus-Based Validation of Interactions We sought to validate (replicate) the interactions detected in the discovery study using data from FHS, MESA, and another AA sample from the ARIC study.

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Epistasis: Methods and Protocols by Jason H. Moore, Scott M. Williams

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