Testing the correspondence between map positions of quantitative trait loci

Area of Science:

• Genetics
• Statistical Genetics
• Bioinformatics

Background:

• Quantitative trait locus (QTL) mapping studies are frequently replicated across different laboratories for similar traits.
• Comparing results from independent QTL mapping experiments is crucial for validating findings and understanding genetic architectures.

Purpose of the Study:

• To develop and validate a statistical method for assessing the concordance of QTLs between independent genome-wide scans.
• To test if the same QTLs are segregating in independent experimental crosses.

Main Methods:

• Development of a permutation test to compare test statistics from genome-wide QTL scans.
• Simulation studies to evaluate the test's performance, considering chromosome length and autocorrelation.
• Application of the test to three independent mouse body weight QTL mapping datasets.

Main Results:

• The permutation test demonstrated desired properties with equal chromosome lengths but showed bias with unequal lengths due to autocorrelation.
• Application to mouse body weight QTL data yielded non-significant results.
• The findings imply a lack of overall concordance between segregating QTLs in the analyzed mouse experiments.

Conclusions:

• The developed permutation test offers a method for comparing independent QTL mapping studies.
• The study highlights potential biases in the test when dealing with unequal chromosome lengths.
• Results suggest limited concordance of major QTLs for mouse body weight across the examined independent studies.