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Table 4 Association results

From: A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms

SNP Gene f ^ 0 n 0 f ^ 1 n 1 Fisher's p-value EM p-value
rs3184504 SH2B3 0.52 499 0.41 394 1.9e-6 8.4e-7
rs7076103 IL2RA 0.19 178 0.10 93 4.5e-8 2.7e-7
rs2476601 PTPN22 0.09 86 0.16 151 8.1e-6 9.2e-6
  1. Testing for association between common SNPs ( f ^ 0 1 % ) and T1D with Fisher's preliminary p-value at most e-5. In the table, f ^ 0 and f ^ 1 are the estimated minor allele frequencies using the EM algorithm in the controls and cases, respectively, and n i = 960 × f ^ i , i = 0, 1. The Fisher's p-value is the preliminary p-value using the Fisher's exact test as in [8] and the EM p-value is the p-value calculated based on the likelihood ratio statistic in equation 8.