. 2011 May 20;12:71. doi: 10.1186/1471-2350-12-71

Table 4.

Population-based association analysis between SLC11A1 and VL

(A) Logistic regression test under additive model
Common Designation	Allele	Affected	Unaffected	OR	L95	U95	P

GT_n	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

GT_n	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

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].