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 (βj = 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:10.1186/1471-2156-12-8

Open Data