Table 2 Association results for the two replicated Buruli ulcer GWAS signals.

From: Genome-wide association study of Buruli ulcer in rural Benin highlights role of two LncRNAs and the autophagy pathway

     

Discovery

Replication

Combined sample

SNP

Chr

Positiona

Gene

M/mb

P valuec

P valuec,d

MAF Controls

MAF Cases

P valuec

Effect sizee

rs9814705*

3

145680345

ENSG00000240095.1

T/C

1.67 × 10−4

6.51 × 10−4

0.10

0.16

2.85 × 10−7

1.80 (1.43–2.27)

rs76647377

6

985196

LINC01622

G/A

1.78 × 10−6

3.26 × 10−3

0.05

0.02

9.85 × 10−8

0.41 (0.28–0.60)

  1. aGRCh37.p13.
  2. bAllele m is the minor allele and M is the major allele in the combined cohort.
  3. cDiscovery, replication and combined P values obtained when the logistic model (Buruli ulcer per se phenotype) is considered for rs9814705, and when the Cox model (taking age at onset into account) is considered for rs76647377. When considering mixed-models in the discovery sample, i.e. GEMMA for rs9814705 and coxme for rs76647377, discovery P values are 2.13 × 10−4 and 2.06 × 10−6, respectively.
  4. dOne-tailed test.
  5. eEffect size corresponds to odds ratios (95% confidence interval) when the logistic model (Buruli ulcer per se phenotype) is considered (rs9814705), and hazard ratios (95% confidence interval) when the Cox model (taking age at onset into account) is considered (rs76647377). Effect size is assessed under an additive model, using the minor allele as the reference.
  6. *rs9814705 was resequenced in the discovery sample.
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