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 pvalues 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 pvalue 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). 

Bagos BMC Genetics 2011 12:8 doi:10.1186/14712156128 