Interval Mapping

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What it is
Interval mapping (IM) is an extension of single-marker analysis. In single-marker analysis, only one marker is used in QTL mapping but effects are underestimated and the QTL position cannot be determined. Interval mapping provides a systematic way to scan the whole genome for evidence of QTL.

IM uses two observable flanking markers to construct an interval within which to search for QTL. A map function (either Haldane or Kosambi) is used to translate from recombination frequency to distance or vice visa. Then, a LOD score is calculated at each increment (walking step) in the interval. Finally, the LOD score profile is calculated for the whole genome. When a peak has exceeded the threshold value, we declare that a QTL have been found at that location.

When to use it
IM is a good general standard to use for all datasets.

Use it in combination with or as part of a process including
You may wish to start with a single-marker analysis and then run IM to further refine the analysis.

High-level process
Here's a quick overview of how to use WinQTLCart's IM implementation. The first few times you run this analysis, go with the WinQTLCart default values for the form's parameters. The defaults provide the best all-around parameter settings, especially for initial analysis sessions.

1.

Select the IM analysis method.

2.

Select the chromosome(s) and trait(s) you want to analyze.

3.

Select a threshold level to apply to the selected trait(s). Select either By manual input (the WinQTLCart default) or By permutations (to have WinQTLCart determine an optimum threshold). See Setting the threshold level for more information on the impact of each of these choices.

4.

Click OK to start the calculations for the threshold level.

5.

Following threshold calculation, set IM form parameters. Select a walk speed in cM. It's recommended you use the same walk speed for your entire dataset. Don't reset the walk speed between runs or your results will not be comparable.

6.   Click Start to begin the analysis.