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

Table 4 Association results

SNP	Gene	${\hat{f}}_{0}$	n ₀	${\hat{f}}_{1}$	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

Testing for association between common SNPs $({\hat{f}}_{0} \geq 1 %)$ and T1D with Fisher's preliminary p-value at most e-5. In the table, ${\hat{f}}_{0}$ and ${\hat{f}}_{1}$ are the estimated minor allele frequencies using the EM algorithm in the controls and cases, respectively, and $n_{i} = ⌊960 \times {\hat{f}}_{i}⌋$ , 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.

ISSN: 1471-2164