{"paper":{"title":"Evaluating HWE and Association in Genome Wide Association Studies: A Unified Procedure","license":"http://creativecommons.org/licenses/by-sa/4.0/","headline":"","cross_cats":["stat.AP"],"primary_cat":"stat.ME","authors_text":"Hajo Holzmann, Stefan B\\\"ohringer","submitted_at":"2026-06-29T13:53:31Z","abstract_excerpt":"In genome wide association studies (GWASs) based on a case-control design, single nucleotide polymorphisms (SNPs) are typically evaluated for an association test and a Hardy-Weinberg equilibrium (HWE) goodness-of-fit test. SNPs are then excluded from analysis based on a HWE cutoff to avoid false positives. In order to avoid cutoffs based on arbitrary threshold values, we propose a conditional genotype--based test that conditions the Pearson $\\chi^2$-statistic in the 3x2 contingency table on the $\\chi^2$-statistic for HWE in the control group, and develop the relevant asymptotic distribution th"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2606.30311","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2606.30311/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}