Genetic determinants of immune-response to a polysaccharide vaccine for typhoid

The HUGO Journal

Official Journal of the Human Genome Organisation

Table 6 Details of 8 SNPs in 7 Genes that showed significant cross-validated association with antibody response, and of other assayed SNPs in those genes that showed significant association in both half-samples

Gene	Chromosome no.	Total no. of SNPs assayed^a	No. of “significant” SNPs	Details of “significant” SNPs			r In half-sample 1 (n = 492)^d	r In half-sample 2 (n = 492)^d	P-value using PLINK in the total sample^e (n = 984)
Gene	Chromosome no.	Total no. of SNPs assayed^a	No. of “significant” SNPs	rs #	nt Position	SNP location within gene (mRNA transcript no. in NCBI database)	r In half-sample 1 (n = 492)^d	r In half-sample 2 (n = 492)^d	P-value using PLINK in the total sample^e (n = 984)
IL1RL1	2	13	3	4142132^b	102303914	Intron 1 (NM_016232.4)	0.96	0.94	0.011
				1997466^b	102317899	Intron 1 (NM_016232.4)	0.91	0.94	0.016
				10208293 ^c	102332742	Intron 10 (NM_016232.4)	0.95	0.91	0.002
CTLA4	2	1	1	231779 ^c	204442732	Intron 1 (NM_005214.3)	−0.99	−0.93	0.028
CD86	3	17	1	17203439 ^c	123278196	Intron 1 (NM_175862.3)	0.95	0.97	0.016
TLR1	4	24	2	55815313^b	38481645	Intron 2 (NM_003263.3)	0.95	0.94	0.022
TLR1	4	24	2	5743572 ^c	38481786	Intron 2 (NM_003263.3)	0.98	0.93	0.050
DEFB1	8	33	7	2978873 ^c	6717373	Intron 1 (NM_005218.3)	0.98	0.98	0.016
				2977780^b	6717513	Intron 1 (NM_005218.3)	0.95	0.95	0.018
				2980928^b	6717829	Intron 1 (NM_005218.3)	0.95	0.95	0.018
				2978872^b	6718140	Intron 1 (NM_005218.3)	0.93	0.98	0.008
				2951854^b	6718836	Intron 1 (NM_005218.3)	0.92	0.94	0.028
				2980923^b	6720467	Intron 1 (NM_005218.3)	0.95	0.93	0.015
				2977772 ^c	6720606	Intron 1 (NM_005218.3)	0.91	0.94	0.013
MAPK8	10	7	1	10857564 ^c	49282578	Intron 1 (NM_002750.2)	−0.95	−0.96	0.030
IL17D	13	6	1	1888001 ^c	20183906	Intron 2 (NM_138284.1)	0.94	0.91	0.018

^aIncluding assayed SNPs in 2 kb regions upstream and downstream of the gene
^bAssociation significant in both Half-samples (was not included in the initial analysis of 469 SNPs)
^cAssociation found to be significant in Half-Sample 1 and cross-validated in Half-Sample 2 (i.e., included in the initial analysis of 469 SNPs)
^dP-values corresponding to these correlation coefficients are all <0.005, and with FDR < 0.05
^eEssentially each P-value corresponds to a test of equality of mean values of logAR among individuals belonging to the three genotypes at the locus under consideration