Linkage disequilibrium analysis

E

Table 3 Analysis of linkage disequilibrium. LD values present SNPs in their close proximity on a chromosome (Costas 2011).

stimation of D and r2 measures of linkage disequilibrium (LD) was determined using Unphased. The results displayed four SNPs in LD among them. SNP rs4818 (a synonymous SNP) and rs4680 (Val158Met) in complete LD (D=1; r2=1). SNP rs737865, located within intron 1of the MB-COMT transcript, was found to be in strong LD (D=0.71; r2= 0.28) with rs6269, located within intron 2 in the promoter region of S-COMT and SNPs rs4633 (a synonymous SNP), located within exon 3 of the MB-COMT found in high LD with SNP rs4680 (Table 2). Perfect LD between SNPs allows definition of few common haplotypes and data to be used for further investigation (Costas 2011).

SNP_ID	rs737865	rs6269	rs4633	rs4818	rs4680
rs737865	-	0.28	0.18	0.29	0.18
rs6269	0.71	-	068	0.91	0.67
rs4633	0.68	0.99	-	0.64	0.95
rs4818	0.70	0.99	0.99	-	0.63
rs4680	0.69	0.99	0.99	1	-

r2 and D’ values are shown above and below the diagonal, respectively.

r2 and D’ values are shown above and below the diagonal, respectively.

r2 and D’ values are shown above and below the diagonal, respectively.

r2 and D’ values are shown above and below the diagonal, respectively.

Common haplotype analysis

Individual diplotype determination was performed with statistical program PHASE v2.1.1. Almost all the samples were included in the analysis for common haplotypes. Three samples were uncertain in the diplotype analysis therefore were excluded from haplotype study. Two samples from these three were low pain sensibility haplotypes, so were included in the analysis of the low pain sensibility haplotype carriers. Common different haplotypes such as low pain sensibility (LPS), average pain sensibility (APS) and high pain sensibility (HPS) were accounted for 95% of the haplotypes in the Spaniard samples. What results showed was an association of these haplotypes with cannabis use. LPS, G-C-G-G haplotype was found to be the most common in cannabis non-users. Therefore, carriers of high activity haplotype (LPS) were significantly less frequent in cannabis users (Table 3). Association analysis at the genotype level (Table 4) confirmed the results at the haplotype level which indicated the presence of LPS in cannabis non-users more frequently t

Table 3 Association between common haplotypes and cannabis use. Carriers of high activity haplotype (LPS) were most common in cannabis non-users than in cannabis users (Costas 2011).

han in cannabis users (Costas 2011).

Population	Haplotype frequency cannabis users ‘a’			Haplotype frequency cannabis non users ‘a’			P value
	LPS	APS	HPS	LPS	APS	HPS
Santiago	55 (42.3%)	62 (47.7%)	9 (6.9%)	303 (47.9%)	240 (38.0%)	68 (10.8%)	0.088
Valencia	68 (37.8%)	91 (50.6%)	17 (9.4%)	271 (49.4%)	228 (41.6%)	40 (7.3%)	0.027
Joint							9.5e-3

‘a’ - Haplotypes are defined as LPS, G-C-G-G; APS, A-T-C-A;

HPS, A-C-C-G, according to SNP order: rs6269—rs4633—rs4818—rs4680.

Population	Cannabis users		Cannabis non users		P value	OR (95% CI)
	LPS carriers	non LPS carriers	LPS carriers	Non LPS carriers
Santiago	39 (60%)	26 (40%)	223 (70.3%)	94 (29.7%)	0.102	0.63 (0.35-1.15)
Valencia	51 (56.7%)	39 (43.3%)	202 (73.4%)	73 (26.5%)	2.7e—3	0.47 (0.28-0.80)
Joint					9.0e—4	0.54 (0.37-0.78)

Table 4 Association analysis at the genotype level showed decrease in high activity haplotype in cannabis users (Costas 2011)