Estimated type I error probability for test of deviation from HWP of SNP₄, a SNP unassociated with secondary phenotype and primary disease (MAF = 40%), at 0.05 and 0.0001 significance levels in simulation studies^* using different approaches for HWP testing.

*Simulation studies were based on 1,000,000 replicates, each replicate with 2,000 cases in terms of primary disease and 2,000 controls frequency-matched on secondary phenotype. MAF: minor allele frequency. LRT_t: LRT approach, using presence and absence of secondary phenotype as cases and controls. mHWP_t: mHWP exact test, using presence and absence of secondary phenotype as cases and controls. LRT_d: LRT approach, using presence and absence of primary disease as cases and controls. mHWP_d: mHWP exact test, using presence and absence of primary disease as cases and controls. eLRT: extended LRT approach. emHWP: extended mHWP exact test. : prevalence of primary disease in general population. : prevalence of secondary phenotype in general population.* 本模拟研究基于100万次重复实验，每次重复实验包含2000例原发疾病病例与2000例对照，对照按照次级表型进行频率匹配。 MAF：次要等位基因频率（minor allele frequency） LRT_t：以次级表型的存在与否作为病例与对照分组依据的似然比检验（Likelihood Ratio Test，LRT）方法 mHWP_t：以次级表型的存在与否作为病例与对照分组依据的精确mHWP检验法 LRT_d：以原发疾病的存在与否作为病例与对照分组依据的似然比检验方法 mHWP_d：以原发疾病的存在与否作为病例与对照分组依据的精确mHWP检验法 eLRT：扩展似然比检验方法 emHWP：扩展精确mHWP检验方法 ：普通人群中原发疾病的患病率 ：普通人群中次级表型的患病率