Supplementary Table I. Full Table of Univariate Associations of for HLA Class I and II

Supplementary Table I. Full table of univariate associations of for HLA Class I and II loci with IgG antibody to protective antigen (AbPA) response in European -Americans

Mean Change Frequency (SE) p-value q-value† HLA-A A*01 0.167 / 0.307 0.023 (0.025) 0.3695 0.8390 A*02 0.310 / 0.530 -0.026 (0.021) 0.2325 0.8255 A*03 0.144 / 0.268 -0.019 (0.029) 0.4996 0.8897 A*11 0.059 / 0.116 0.036 (0.047) 0.4387 0.8897 A*23 0.014 / 0.028 -0.023 (0.115) 0.8432 0.9546 A*24 0.084 / 0.156 0.064 (0.035) 0.0642 0.4772 A*25 0.022 / 0.044 0.021 (0.070) 0.7621 0.9492 A*26 0.021 / 0.040 -0.029 (0.074) 0.6984 0.9492 A*29 0.033 / 0.064 0.023 (0.055) 0.6721 0.9492 A*30 0.023 / 0.047 -0.085 (0.047) 0.0672 0.4772 A*31 0.032 / 0.064 -0.033 (0.057) 0.5681 0.8964 A*32 0.033 / 0.064 -0.010 (0.062) 0.8682 0.9546 A*68 0.040 / 0.076 0.014 (0.045) 0.7535 0.9492 HLA-B-C Haplotypes B*27-Cw*01 0.032 0.056 (0.062) 0.3660 0.8390 B*56-Cw*01 0.021 -0.028 (0.114) 0.8063 0.9546 B*27-Cw*02 0.046 -0.072 (0.065) 0.2692 0.8390 B*15-Cw*03 0.098 0.015 (0.054) 0.7845 0.9546 B*40-Cw*03 0.114 0.006 (0.041) 0.8847 0.9546 B*55-Cw*03 0.024 -0.021 (0.114) 0.8533 0.9546 B*35-Cw*04 0.160 -0.062 (0.037) 0.0951 0.4822 B*44-Cw*04 0.032 0.069 (0.102) 0.4981 0.8897 B*44-Cw*05 0.160 -0.013 (0.036) 0.7141 0.9492 B*13-Cw*06 0.044 0.097 (0.056) 0.0823 0.4822 B*37-Cw*06 0.022 0.004 (0.066) 0.9514 0.9787 B*57-Cw*06 0.062 -0.016 (0.044) 0.7201 0.9492 B*07-Cw*07 0.258 -0.026 (0.029) 0.3693 0.839 B*08-Cw*07 0.213 0.019 (0.032) 0.5439 0.8897 B*18-Cw*07 0.032 0.166 (0.079) 0.0356 0.4213 B*39-Cw*07 0.021 0.073 (0.094) 0.4366 0.8897 B*49-Cw*07 0.039 0.025 (0.066) 0.7037 0.9492 B*14-Cw*08 0.072 -0.016 (0.05) 0.7491 0.9492 B*18-Cw*12 0.030 0.181 (0.107) 0.0896 0.4822 B*38-Cw*12 0.023 -0.016 (0.069) 0.8143 0.9546 B*39-Cw*12 0.021 -0.005 (0.077) 0.9510 0.9787 B*51-Cw*15 0.045 -0.134 (0.071) 0.0584 0.4772 B*44-Cw*16 0.060 -0.027 (0.042) 0.5125 0.8897 B*41-Cw*17 0.021 -0.082 (0.129) 0.5249 0.8897 HLA-DRB1-DQA1-DQB1 Haplotypes *0101-*0101-*0501 0.164 -0.075 (0.035) 0.0325 0.4213 *0102-*0101-*0501 0.032 -0.171 (0.067) 0.0104 0.2472 *0103-*0101-*0501 0.025 -0.178 (0.100) 0.0757 0.4822 *0301-*0501-*0201 0.213 -0.015 (0.031) 0.6265 0.9492 *0401-*0301-*0302 0.068 0.076 (0.056) 0.1755 0.6948 *0401-*0303-*0301 0.083 -0.017 (0.042) 0.6882 0.9492 *0404-*0301-*0302 0.068 -0.009 (0.055) 0.875 0.9546 *0407-*0303-*0301 0.020 0.121 (0.098) 0.2162 0.8081 *0701-*0201-*0202 0.175 0.062 (0.033) 0.0590 0.4772 *0701-*0201-*0303 0.062 0.030 (0.051) 0.5514 0.8897 *0801-*0401-*0402 0.048 0.050 (0.057) 0.3767 0.839 *0901-*0302-*0303 0.020 -0.073 (0.078) 0.3459 0.839 *1101-*0505-*0301 0.111 0.034 (0.047) 0.4646 0.8897 *1104-*0505-*0301 0.041 -0.008 (0.069) 0.9066 0.9607 *1201-*0505-*0301 0.042 0.054 (0.089) 0.5475 0.8897 *1301-*0103-*0603 0.102 0.057 (0.037) 0.1266 0.5619 *1302-*0102-*0604 0.070 0.054 (0.06) 0.3699 0.839 *1302-*0102-*0609 0.020 -0.004 (0.093) 0.9649 0.9787 *1401-*0104-*0503 0.037 0.148 (0.069) 0.0321 0.4213 *1501-*0102-*0602 0.232 -0.116 (0.029) 0.0001 0.0046 HLA-DPB1 *0101 0.041 / 0.082 0.044 (0.050) 0.3781 0.839 *0201 0.140 / 0.259 0.089 (0.028) 0.0016 0.0575 *0301 0.097 / 0.184 0.010 (0.032) 0.7454 0.9492 *0401 0.429 / 0.662 -0.017 (0.019) 0.374 0.839 *0402 0.122 / 0.231 -0.030 (0.031) 0.3321 0.839 *0501 0.020 / 0.039 -0.074 (0.055) 0.1761 0.6948 *0601 0.015 / 0.030 0.082 (0.081) 0.3102 0.839 *0901 0.011 / 0.021 -0.017 (0.124) 0.8874 0.9546 *1001 0.016 / 0.032 0.035 (0.083) 0.6732 0.9492 *1101 0.025 / 0.049 -0.047 (0.060) 0.4342 0.8897 *1301 0.013 / 0.025 -0.091 (0.089) 0.3106 0.839 *1401 0.009 / 0.019 -0.164 (0.100) 0.1021 0.4831 *1501 0.013 / 0.027 -0.053 (0.086) 0.5376 0.8897 *1701 0.013 / 0.027 0.000 (0.063) 0.9999 0.9999

Mean change denotes the estimated regression coefficient representing the mean change in log10[AbPA] under an additive genetic model based on a multivariable longitudinal model fit to measurements at 4, 8, 26, and 30 weeks. (SE) Standard error. All models adjusted for sex, age group, study site, route of administration, time between vaccination and blood draw, and cumulative number of AVA doses (See Methods). Individual haplotype/allele effects shown if there were 15 or more carriers of the particular allele/haplotype. Frequency (for alleles) represents the allele frequency out of 2N chromosomes followed by the carriage frequency out of N individuals. For haplotypes, frequency denotes carriage frequency out of N chromosomes. †q-value based on False Discovery Correction for the total number of alleles/haplotypes tested. Supplementary Table II. Full table of univariate associations of for HLA Class I and II loci with IgG antibody to protective antigen (AbPA) response in African-Americans

Frequency Mean Change (SE) p-value q-value† HLA-A A*01 0.047 / 0.095 -0.134 (0.097) 0.1672 0.6550 A*02 0.239 / 0.418 -0.030 (0.054) 0.5792 0.8231 A*03 0.092 / 0.179 -0.030 (0.073) 0.6794 0.9171 A*23 0.134 / 0.249 -0.004 (0.051) 0.9303 0.9661 A*30 0.117 / 0.229 0.067 (0.062) 0.2847 0.7155 A*33 0.045 / 0.090 0.095 (0.087) 0.2737 0.7155 A*68 0.092 / 0.184 0.001 (0.075) 0.9889 0.9889 A*74 0.055 / 0.109 0.013 (0.102) 0.8981 0.9661 HLA-B-C Haplotypes B*15-Cw*02 0.111 -0.056 (0.097) 0.5663 0.8231 B*53-Cw*04 0.137 0.170 (0.081) 0.0359 0.4844 B*07-Cw*07 0.168 0.056 (0.053) 0.2915 0.7155 B*14-Cw*08 0.079 0.027 (0.111) 0.8079 0.9661 B*45-Cw*16 0.116 -0.058 (0.080) 0.4690 0.8019 B*42-Cw*17 0.126 -0.155 (0.114) 0.1759 0.6550 HLA-DRB1-DQA1-DQB1 Haplotypes *0102-*0101-*0501 0.101 -0.188 (0.108) 0.0828 0.5110 *0301-*0501-*0201 0.131 0.126 (0.073) 0.0856 0.5110 *0701-*0201-*0202 0.141 0.082 (0.063) 0.1941 0.6550 *0302-*0401-*0402 0.121 -0.009 (0.085) 0.9122 0.9661 *1503-*0102-*0602 0.176 -0.018 (0.056) 0.7409 0.9526 HLA-DPB1 *0101 0.262 / 0.455 -0.077 (0.046) 0.0946 0.5110 *0201 0.149 / 0.262 0.124 (0.050) 0.0123 0.3324 *0301 0.064 / 0.129 -0.053 (0.085) 0.5301 0.8231 *0401 0.116 / 0.228 0.054 (0.076) 0.4752 0.8019 *0402 0.121 / 0.213 0.007 (0.053) 0.8995 0.9661 *1301 0.047 / 0.094 -0.093 (0.121) 0.4428 0.8019 *1701 0.067 / 0.134 0.070 (0.091) 0.4389 0.8019 *1801 0.067 / 0.124 0.052 (0.068) 0.4466 0.8019

Mean change denotes the estimated regression coefficient representing the mean change in log10[AbPA] under an additive genetic model based on a multivariable longitudinal model fit to measurements at 4, 8, 26, and 30 weeks. (SE) Standard error. All models adjusted for sex, age group, study site, route of administration, time between vaccination and blood draw, and cumulative number of AVA doses (See Methods). Individual haplotype/allele effects shown if there were 15 or more carriers of the particular allele/haplotype. Frequency (for alleles) represents the allele frequency out of 2N chromosomes followed by the carriage frequency out of N individuals. For haplotypes, frequency denotes carriage frequency out of N chromosomes. †q-value based on False Discovery Correction for the total number of alleles/haplotypes tested.