Table 1

Results of family based tests of the association of psoriasis with RAPTOR and RUNX1 SNPs and three-locus haplotypes

Locus	Associated allele*		TDT				PDT				FBAT
Locus	Base	Freq	No.fam†	No. inf fam‡	T:NT§	p value¶	No.fam†	No. inf fam‡	D̄**	p value¶	No.fam†	No. inf fam‡	Z††	p value¶
Non-trio pedigrees: those families larger than a trio with at least two affected members.
The alleles and haplotypes tested are those reported to be associated with psoriasis (Helms et al*¹⁰ for RUNX1; Anne Bowcock, personal communication for RAPTOR). Allele frequency is based on all founders in the pedigrees.
†The number of families shown for each association test counts only those families with at least one typed and phenotypically informative unit. For the TDT this unit is a trio (an affected child and both parents), for the PDT it is a trio or a discordant sibpair (an affected and unaffected sib), and for the FBAT with the settings used here it is a trio, discordant sibpair, or a sibship with three or more affected sibs.
‡The number of informative families is the subset of the typed and phenotypically informative families that are genotypically informative for the allele being tested.
§T:NT is the ratio of transmissions to non-transmissions of the test allele from heterozygous parents to affected children in the TDT.
¶All p values are uncorrected for multiple testing.
**D̄ is a standardised measure of disequilibrium for the PDT (see Methods).
††Large sample test statistic for association, distributed as a standard normal.
A: All pedigrees
RUNX1
rs745318	T	0.442	467	351	233:218	0.51	503	372	0.009	0.53	515	307	0.13	0.89
rs734232	A	0.440	466	350	235:219	0.48	502	371	0.006	0.51	514	306	0.17	0.87
rs895691	A	0.444	466	350	233:219	0.54	502	371	0.010	0.55	514	307	0.07	0.95
Haplotype	TAA	0.435	466	350	236:218	0.43	502	371	0.009	0.48	514	364	0.17	0.87
RAPTOR
rs1564864	T	0.772	468	286	163:159	0.87	504	304	0.030	0.96	516	271	0.17	0.86
rs2019154	C	0.772	467	284	168:160	0.73	503	302	0.037	0.83	515	270	0.31	0.76
rs869190	G	0.773	468	284	165:159	0.78	505	303	0.039	0.86	517	269	0.31	0.76
Haplotype	TCG	0.771	467	285	164:157	0.76	503	301	0.041	0.84	515	315	0.35	0.79

B: Non-trio pedigrees
RUNX1
rs745318	T	0.452	181	143	90:89	1.00	217	164	−0.031	0.87	229	129	−0.40	0.69
rs734232	A	0.448	180	142	91:90	1.00	216	163	−0.033	0.90	228	129	−0.36	0.72
rs895691	A	0.452	181	143	88:89	1.00	217	164	−0.037	0.74	229	130	−0.53	0.59
Haplotype	TAA	0.442	181	143	92:90	0.94	217	164	−0.026	0.98	229	187	−0.36	0.72
RAPTOR
rs1564864	T	0.767	182	112	65:62	0.86	218	130	0.032	0.88	230	110	0.11	0.91
rs2019154	C	0.766	182	112	59:57	0.93	218	130	0.031	0.86	230	111	0.11	0.91
rs869190	G	0.768	181	110	59:57	0.93	218	129	0.037	0.88	230	108	0.17	0.87
Haplotype	TCG	0.765	182	112	62:59	0.86	218	130	0.036	0.91	230	149	0.23	0.82