14. Principles of Marker-Based Analysis

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Updated notes

An extension of, and comments on, Example 13.

Recent references on marker-assisted introgressions (pages 407--413)

The Transmission/Disequilibrium Test (TDT)

(Posted 30 Jan 1998)

Background: While the TDT is presented in the book (pages 420-422) as an approach for detecting linkage of a major QTL to a very tightly-linked marker that controls for the effects of population stratification (see Example 17, Chapter 14), it is now appreciated that it often has more power than allele-sharing methods (such as ASP, etc., see Chapter 16, pp. 525- 533) for detecting linkage to tightly-linked markers.

Meta-analysis of linkage data

(Posted 23 April 1998)

Background: Suppose a number of independent studies have been performed to test for linkage. How can one combine the data from all these tests into a single analysis, especially if the experimental designs are quite different in the different experiments? The statistical field of meta-analysis discusses how to obtain an overall p value given the p values m independent tests. Specifically, let p(i) be the p-value for the i-th test. With m independent tests, -2 Sum Ln[p(i)] follows a chi-square distribution with 2m df (Fisher 1954, pg. 99, Statistical Methods for Research Workers, 12th ed). Recent papers using meta-analysis on linkage data are:

Workshop notes

Identifying And Incorporating Genetic Markers And Major Genes In Animal Breeding Programs by Brian Kinghorn and Julius van der Werf (pdf file). Notes from a course given in Belo Horizonte (Brazil) 31 May to 5 June 2000.


The Journal of Quantitative Trait Loci (JQTL),, an electronic journal sponsored by the Crop Science Society of America

WWW pages of interest

QTL meetings