Association tests based on the principal-component analysis

BMC Proceedings

Table 1 The results of the PC score based and haplotype-based tests using Replicate 48

					Association test via logistic regression^c H₀: Global β = 0		AIC
	LD block (SNP)	No. SNPs	No. PC score^a	No. haplotype^b	PC score	Haplotype	PC score	Haplotype
Blocks not associated with RA	1 (47~51)	5	1	3 (3)	0.4602	0.9947	2252.880 ^d	2254.346
	2 (79~82)	4	1	3 (8)	1.4472	3.3423	2251.893	2254.004
	3 (356~361)	6	3	5 (16)	0.8239	3.3700	2256.517	2257.973
	4 (387~390)	4	2	4 (9)	2.7136	3.3676	2252.627	2256.012
Blocks associated with RA	5 (128~130)	3	1	3 (6)	15.0769	18.1052	2238.264	2239.058
	6 (140~144)	5	3	4 (14)	17.4702	5.5822	2239.870	2253.928
	7 (149~151)	3	2	3 (5)	10.1205	11.6309	2245.220	2245.644
	8 (162~163)	2	2	2 (4)	40.4704	40.3278	2214.870	2215.014

^aWe consider the haplotypes that have frequencies greater than 0.05, and PC score whose sum of variations explains more than 70% of the total variations.
^bNumber in parentheses is the number of estimated haplotypes. Haplotypes with frequencies less than 0.05 were pooled together and included in the model as one group.
^cWe test all β = 0 using the likelihood ratio test.
^dBold indicates the smallest AIC value.

ISSN: 1753-6561