Table 3.

Family-based association analysis between SLC11A1 and VL

(A) Additive model
Common Designation	Allele	Allele frequency	# Fam	S	E(S)	Var(S)	Z	P
GTn	2	0.15	68	60	70.38	28.4	-1.947	0.052
	3	0.85	68	176	165.62	28.4	1.947	0.052
274C/T	1	0.88	43	104	99.65	16.3	1.076	0.282
	2	0.12	43	36	40.35	16.3	-1.076	0.282
469 + 14G/C	1	0.11	20	17	21.50	9.7	-1.445	0.148
	2	0.89	20	61	56.50	9.7	1.445	0.148
823 C/T	1	0.92	46	127	121.97	20	1.127	0.260
	2	0.08	46	41	46.03	20	-1.127	0.260
1465-85G/A	1	0.31	92	117	119.63	42.9	-0.402	0.688
	2	0.69	92	229	226.37	42.9	0.402	0.688
1729 + 55del4 (TGTG)	1	0.05	19	18	21.50	9.57	-1.131	0.258
	2	0.95	19	54	50.50	9.57	1.131	0.258
1729 + 263del4 (CAAA)	1	0.74	88	216	203.33	41.2	1.974	0.048
	2	0.26	88	104	116.67	41.2	-1.974	0.048
(B) Genotype-wise model
Common Designation	Genotype	Genotype frequency	# Fam	S	E(S)	Var(S)	Z	P
GTn	2\2	0.025	9	8	6.69	2.9	0.759	0.447
	2\3	0.250	68	44	57.00	25.7	-2.565	0.010
	3\3	0.725	65	66	54.31	24.1	2.382	0.017
1729 + 263del4 (CAAA)	1\1	0.566	75	69	63.57	27.9	1.027	0.304
	1\2	0.347	87	78	76.19	33.9	0.311	0.755
	2\2	0.087	26	13	20.24	9.64	-2.332	0.019

FBAT analysis under (A) additive and (B) genotype-wise models of inheritance for associations between SLC11A1 polymorphisms and the primary family-based sample of VL from Bihar State, India. # Fam = number of families informative for the FBAT analysis; S and E(S) represent the observed and expected transmissions for that allele, Var(S) is the variance. A positive Z score indicates association with disease; a negative Z score indicates the non-associated or protective allele or genotype. Bold indicates 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. Results are shown for the 7 polymorphisms that were genotyped in the primary family-based sample. All passed HWE (P-value cut-off 0.05/7 = 0.07 for 7 markers genotyped) in unaffected family founders.