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Chunk #23 — Pitfalls of the analysis — Pitfall 2: The validation sample

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Pitfalls of predicting complex traits from SNPs.
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Sometimes the validation population differs from the application (target) population in that it is much more genetically diverse. For example, the validation (and possibly discovery) population might include a diverse set of lines of animals or plants. A prediction equation may work well in this population but less well in an application population that is less diverse such as commercial strains of a crop62.