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Chunk #18 — Pitfalls of the analysis — Pitfall 1: Validation and discovery sample overlap

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Pitfalls of predicting complex traits from SNPs.
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samples occurred in a recent study reporting a genetic predictor of autism56. SNPs putatively associated with autism in multiple biological pathways were selected based upon p-values from GWAS in the entire data set. Model selection was subsequently applied using cross-validation to narrow down the number of SNPs. The authors did follow up with an independent validation sample, and the prediction accuracy was reduced.