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 Status: Updated 27 November 2011;  ***Please consult the "Top Results Methods" for details on new ranking procedure***
Ranking based on HuGENet interim guidelines for the assessment of genetic association studies
# Gene Polymorphism Ethnicity OR (95% CI) P-value N minor (Grade) I2 (Grade) Bias Reason (Grade) Overall Grade Bayes Factor (log10)
1 MAPT/STH MAPT_H1H2Caucasian0.78 (0.75-0.80)3.54E-5220415 (A)n.a. (A) (A)A48.7
2 SNCA rs356220All1.30 (1.25-1.34)3.06E-4941898 (A)n.a. (A) (A)A45.8
3 GBA GBA_N370SAll3.37 (2.67-4.29)1.11E-241014 (A)n.a. (A) (A)A15.4
4 LRRK2 rs34778348Asian2.23 (1.89-2.63)2.97E-21750 (B)n.a. (A) (A)B15.4
5 PM20D1 rs11240572All0.74 (0.69-0.80)1.01E-148131 (A)n.a. (A) (A)A10.6
6 GAK rs1564282All1.29 (1.20-1.38)6.54E-1314408 (A)n.a. (A) (A)A10.1
7 MCCC1 rs11711441All0.84 (0.80-0.89)8.72E-128963 (A)n.a. (A) (A)A9.1
8 STK39 rs2102808All1.28 (1.19-1.38)1.54E-113973 (A)n.a. (A) (A)A8.8
9 BST1 rs4698412All0.87 (0.83-0.91)2.28E-1053380 (A)n.a. (A) (A)A7.7
10 GPNMB rs156429All0.89 (0.86-0.93)2.69E-1025216 (A)n.a. (A) (A)A7.6
11 SETD1A rs4889603All1.14 (1.09-1.19)4.68E-1026381 (A)n.a. (A) (A)A7.4
12 GWA_8p22 rs591323All0.89 (0.86-0.93)2.59E-0917072 (A)n.a. (A) (A)A6.7
13 SYT11/RAB25 chr1:154105678All1.67 (1.41-1.98)5.70E-09677 (B)n.a. (A) (A)A5.6
14 FAM47E rs6812193All0.89 (0.85-0.93)1.07E-0746695 (A)44 (B)Low OR (C)C5.1
15 HLA-DRB5 chr6:32588205All0.75 (0.68-0.84)2.90E-073565 (A)0 (A) (A)A4.7
16 CCDC62/HIP1R rs12817488All1.17 (1.09-1.25)2.99E-0614743 (A)35 (B) (A)B3.8
17 ACMSD/TMEM163 rs6710823All1.40 (1.2-1.63)1.61E-0511661 (A)48 (B) (A)B3.0
18 MED13 rs8081812All1.13 (1.07-1.2)6.09E-0514016 (A)8 (A)Low OR, Regr (C)C2.6

NEW: Only meta-analysis results with P-values <0.0001 are displayed in this table. Loci are ranked by statistical significance (P-value). For loci containing more than one polymorphism showing significant association with P <0.0001, only the polymorphism with the smallest P-value is displayed here. Please contact us to request a list of other at least nominally significant meta-analysis results.

All results are assessed for their epidemiological credibility using two methods:

1. The HuGENet interim criteria for the cumulative assessment of genetic associations: These criteria (Ioannidis et al, 2008a; Khoury et al, 2009) take into account amount of evidence (i.e. sample size, measured as "N minor"), consistency of replication (i.e. heterogeneity across studies, measured as "I2" [NB: this criterion does not apply [n.a.] to genome-wide significant findings [P < 5.0E-8]), and protection from bias ("Bias reason"). Overall epidemiological credibility is graded as "A" (=strong) if associations received three A grades, "B" (=moderate) if they received at least one B grade but no C grades, and "C" (=weak) if they received a C grade in any of the three assessment criteria.

2. Bayesian analyses: For this assessment we calculate Bayes factors (expressed here as log10-values) assuming an average non-null odds ratio of 1.15 using a spike and smear prior distribution of effects (as described in Ioannidis, 2008b) Generally, a logBF ≥5, which suggests that the data increase over 100,000-fold the odds of a given finding being true vs. not true, is considered as strong support in the context of genetic association studies (Stephens and Balding, 2009).

For more details see "Top Results Methods" and reference below.

References:
Ioannidis JP, Boffetta P, Little J, O'Brien TR, Uitterlinden AG, Vineis P, Balding DJ, Chokkalingam A, Dolan SM, Flanders WD, Higgins JP, McCarthy MI, McDermott DH, Page GP, Rebbeck TR, Seminara D, Khoury MJ (2008a) "Assessment of cumulative evidence on genetic associations: interim guidelines." Int J Epidemiol 37(1):120-32. Abstract

Ioannidis JP (2008b) "Effect of Formal Statistical Significance on the Credibility of Observational Associations." Am J Epidemiol 168:374-383. Abstract

Khoury MJ, Bertram L, Boffetta P, Butterworth AS, Chanock SJ, Dolan SM, Fortier I, Garcia-Closas M, Gwinn M, Higgins JP, Janssens AC, Ostell J, Owen RP, Pagon RA, Rebbeck TR, Rothman N, Bernstein JL, Burton PR, Campbell H, Chockalingam A, Furberg H, Little J, O'Brien TR, Seminara D, Vineis P, Winn DM, Yu W, Ioannidis JP (2009) "Genome-wide association studies, field synopses, and the development of the knowledge base on genetic variation and human diseases." Am J Epidemiol 170(3):269-79. Abstract

Stephens M, Balding DJ (2009) "Bayesian statistical methods for genetic association studies" Nat Rev Genet 10(10):681-90. Abstract

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