Table 1 Number of independent SNPs for different thresholds

From: Analysis of the joint effect of SNPs to identify independent loci and allelic heterogeneity in schizophrenia GWAS data

Threshold p th

10−3

10−4

10−5

10−6

10−7

5 × 10−8

Number of markers below threshold before CRa

82,041

35,630

18,710

11,028

6533

5706

Number of markers below threshold after CRb

7038

1048

460

200

101

88

Number of markers below 5 × 10−8 after CRc

2504

186

134

92

90

88

Number of markers validated with German cohort as LD referenced

—

69

74

80

83

83

% Markers validated with German cohort as LD referencee

 

37%

55%

87%

92%

94%

  1. CR conditional regression, LD linkage disequilibrium, p Germ joint p values with German LD reference, p Norg joint p values with Norwegian LD reference
  2. aNumber of SNPs below the indicated threshold in the initial data set
  3. bNumber of markers that were selected using the stepwise procedure with the Norwegian LD reference sample
  4. cNumber of signals that passed the genome-wide significance threshold in the joint model
  5. dNumber of validated SNPs: a marker is deemed validated for joint effect if it passes the genome-wide significance level (5 × 10−8) after stepwise analysis with the Norwegian LD reference sample and after joint analysis with the German LD reference sample, and if −log10(pGerm)/−log10(pNorg) <2 (the joint p values estimated using the Norwegian sample as LD reference do not differ essentially from the joint p values estimated using the German LD reference)
  6. ePercentages of validated SNPs for different thresholds. For the threshold 10−3, the list of selected markers after the stepwise procedure could not be fitted with the German sample because of redundant signals
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