Table 9 Association of HLA-A*02:01 and Bw4 with multiple sclerosis

A Locus level heterogeneity among tests of association between HLA-A and Bw4/Bw6-related polymorphisms in MS patients and controls
Locus	χ ²	d.f.	p-value	Significance^a
HLA-A~Bw4/Bw6	46.0751	24	4.34E−03	*
HLA-A~HLA-B position 80	43.2836	27	2.45E−02	*

B Association of HLA-A*02:01 and Bw4/Bw6-related polymorphism in MS patients and controls
Locus	Haplotype	Controls (N)	Cases (N)	OR	95% CI lower	95% CI upper	p-value	Significance^b
A~Bw4/Bw6	A*02:01~Bw4	123	79	0.62	0.45	0.85	1.69E−03	*
A~Bw4/Bw6	A*02:01~Bw6	100	85	0.85	0.62	1.17	3.11E−01	NS
A~HLA-B position 80	A*02:01~80I	45	34	0.76	0.47	1.23	2.42E−01	NS
A~HLA-B position 80	A*02:01~80T	83	45	0.53	0.35	0.78	7.55E−04	*

(A) Significant p-values are indicated with asterisks
d.f. degrees of freedom
Bw4: HLA-B alleles encoding either Threonine at codon 80 (80T) or Isoleucine at codon 80 (80I)
Bw6: HLA-B alleles encoding Asparagine at codon 80 (80N)
^a After correcting for two comparisons, significance was evaluated at the 2.5E−02 level
(B) p-values were not corrected for loci that displayed significant locus-level heterogeneity. p-values for loci that did not display significant locus-level heterogeneity were corrected for the number of analyzed categories
^b For each locus, the evaluation of significance was informed by the significance of locus-level heterogeneity as shown in Table 9A
The complete set of HLA-A~Bw4/Bw6 and A~HLA-B position 80 comparisons is included in Supplementary Table S5

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