Table 5.

Step-wise Conditional Analysis of PD-Associated Variants

Allele	Round 1: Not Conditioned		Round 2: Conditioned on rs3129882		Round 3: Conditioned on rs3129882 and C∗03:04		Round 4: Conditioned on rs3129882, C∗03:04, and rs9268515
	OR	p	OR	p	OR	p	OR	p
rs3129882_G	1.30	9 × 10−11	-	-	1.28	1 × 10−09	1.22	2 × 10−6
rs9268515_C	0.75	8 × 10−8	0.81	3 × 10−4	0.84	2 × 10−3	-	-
rs2395163_C	0.77	2 × 10−7	0.86	5 × 10−3	0.88	0.02	1.00	0.97
DQA1∗03:01	0.77	1 × 10−6	0.84	3 × 10−3	0.87	0.01	0.97	0.77
DQB1∗03:02	0.74	7 × 10−6	0.82	3 × 10−3	0.86	0.03	0.92	0.33
C∗03:04	0.72	8 × 10−6	0.75	2 × 10−4	-	-	0.78	2 × 10−3
rs41269955/rs77539933	0.81	2 × 10−5	0.88	0.02	0.90	0.05	0.97	0.67
DRB1∗04:04	0.65	4 × 10−5	0.71	1 × 10−3	0.75	8 × 10−3	0.78	0.03
DQB1∗06:02	1.26	4 × 10−5	1.08	0.24	1.07	0.26	1.06	0.37
DRB4∗01	0.83	4 × 10−5	0.93	0.17	0.95	0.30	1.03	0.63
DRB5∗01	1.25	5 × 10−5	1.07	0.30	1.06	0.35	1.05	0.49
DRB1∗15:01	1.26	6 × 10−5	1.07	0.29	1.07	0.33	1.05	0.46
rs660895_G	0.82	9 × 10−5	0.88	0.02	0.91	0.07	1.02	0.74
C∗07:02	1.23	2 × 10−4	1.13	0.03	1.11	0.08	1.13	0.04
B∗07:02	1.23	3 × 10−4	1.13	0.04	1.11	0.08	1.12	0.05
DQA1∗01:02	1.17	1 × 10−3	1.04	0.49	1.06	0.30	1.03	0.59
B∗40:01	0.76	2 × 10−3	0.79	9 × 10−3	1.12	0.46	1.09	0.58

Five SNPs and 12 HLA variants that were individually associated with PD were included in the analysis (round 1). The marker with the strongest effect (in this case, lowest p value, rs3129882) was selected as a covariate for successive analyses, and association tests were repeated (round 2) with conditioning on rs3129882. The strongest effect in round 2 was associated with C^∗03:04. Round 3 tested remaining markers conditioned on rs3129882 and C^∗03:04. Round 4, with rs3129882, C^∗03:04, and rs9268515 in the model, identified DRB1^∗04:04. No marker survived being adjusted for rs3129882, C^∗03:04, rs9268515, and DRB1^∗04:04.