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Table 4 Population-based association analysis between SLC11A1 and VL

From: No evidence for association between SLC11A1and visceral leishmaniasis in India

(A) Logistic regression test under additive model

Common Designation

Allele

Affected

Unaffected

OR

L95

U95

P

GTn

2

355/1473

353/1533

1.05

0.89

1.23

0.585

-237C/T

2

135/1747

122/1862

1.18

0.91

1.52

0.205

274C/T

2

258/1624

286/1698

1.06

0.88

1.27

0.529

469 + 14G/C

1

266/1582

274/1632

1.00

0.83

1.19

0.987

1465-85G/A

1

605/1263

646/1308

1.03

0.90

1.18

0.664

D543N G/A

2

145/1735

112/1526

0.88

0.68

1.14

0.313

1729 + 55del4 (TGTG)

1

110/1488

112/1608

1.06

0.81

1.39

0.669

1729 + 263del4 (CAAA)

2

437/1123

515/1233

0.93

0.80

1.08

0.364

(B) Genotypic-wise logistic regression analysis (2df)

Common Designation

Genotypes

Cases

Controls

OR

P

  

GTn

2/2

40

27

1

-

  
 

2/3

275

299

0.62

0.070

  
 

3/3

599

617

0.66

0.098

  

1729 + 263del4 (CAAA)

2/2

67

79

1

-

  
 

1/2

303

357

0.91

0.346

  
 

1/1

410

438

0.90

0.583

  
  1. Logistic regression analyses under (A) an additive model and (B) using a genotypic (2 df) test for the replication sample of VL cases and controls from Bihar State, India OR = odds ratio (for minor allele relative to major allele in part A); L95 and U95 are lower and upper 95% confidence intervals. In (A) allele counts are shown for mino/major allele for affected and unaffected individuals. There were no significant associations at nominal P ≤ 0.05. The corrected P-value required to achieve significance taking account of multiple but not independent markers is P ≤ 0.017. Data are shown for all markers that were in HWE (P-value cut-off 0.05/9 = 0.006 for 9 markers genotyped) in the control sample. Marker 823C/T failed HWE quality control. Markers D543N G/A (0.1% cases versus 17% controls) and 1729 + 263del4 (CAAA) (17% cases versus 10.7% controls) showed differential missingness between cases and controls, which can be a concern for its potential to generate false positive results [34].