Meta-analysis of haplotype-association studies: comparison of methods and empirical evaluation of the literature

BMC Genomic Data

Table 3 The results obtained using the methods described in this work on the 13 studies that reported complete data that suffice for the analysis to be replicated

ID/[reference]	Gene/Locus	Disease/Outcome	SNPs in haplotype	Number of studies	Significant results	Fixed effects			Random effects
						β = 0 (summary data)	β = 0 (IPD)	γ = 0 (IPD)	β = 0 (summary data)	β = 0 (IPD)
2/[98]	ITGAV	Rheumatoid Arthritis	3	3	Yes^$$	0.2506	0.2489	0.1564	0.3288	0.3851
5/[99]	CX3CR1	CAD	2	6	Yes^$	0.0834*	0.0677*	0.6263	0.0883*	0.1031*
16/[94]	CTLA4	Graves Disease	2	10	Yes	<0.0001	<0.0001	0.0371	<0.0001	<0.0001
17/[94]	CTLA4	Hashimoto Thyroiditis	2	5	Yes	0.0011	0.0010	<0.0001	0.0044	0.0072
20/[97]	CAPN10	T2DM	3	11	Yes^$$	0.1152	0.1036	0.6145	0.2243	0.1655
21/[93]	ADAM33	Asthma	5	3	No	0.6209	0.5508	0.4697	0.6134	0.5503
26/[78]	VDR	Osteoporosis	3	4	Yes^$$	0.1458	0.3051	<0.0001	0.1480	0.5781
27/[95]	ACE	Alzheimer's Disease	3	4	Yes	0.0193	0.0218	0.8906	0.0193	0.0223
30/[92]	FcgammaR	Celliac Disease	2	2	No	0.7331	0.7335	0.9502	0.7331	0.7336
32/[96]	G72/G30	Schizophrenia	2	2	Yes^$$	0.7790	0.7757	0.0001	0.5750	0.6719
33/[68]	VEGF	ALS	3	4	Yes^$	0.0437*	0.0414	0.0691	0.0716	0.0455*
39/[91]	TNFA	Prostate Cancer	5	2	No	0.2531	0.2515	0.6185	0.2867	0.2511
40/[90]	PTGS2	Prostate Cancer	4	2	No	0.3560	0.3550	0.2087	0.6573	0.4829

For either fixed or random effects methods, we list the p-values for the tests for the overall association (β = 0) using the summary data based methods and the IPD methods. The results for the IPD methods were obtained from the logistic regression method even though the multinomial logistic regression and the Poisson regression method yield nearly identical results. For the fixed effects IPD methods we also list the p-value of overall test for the heterogeneity (γ = 0).
(*): The significance of the multivariate Wald test (β = 0) contradicts univariate one (β_j= 0).
(^$): The initially claimed statistically significant results are contradicted by either the multivariate or univariate Wald tests (random effects).
(^$$): The initially claimed statistically significant results are contradicted by both the multivariate and univariate Wald tests (random effects).

ISSN: 2730-6844