Genetic diversity of HLA system in two populations from Durango, Mexico: Durango City and rural Durango. Liliana González-Medina*, Héctor Delgado-Aguirre*, Rodrigo Barquera*‡, Stephen Clayton*, Carmen Adalid-Sáinz*, Esteban Arrieta-Bolaños*, Hanna Pacheco-Ubaldo, Diana Iraíz Hernández-Zaragoza, Néstor Escareño-Montiel, Javier Morán-Martínez, Alicia Bravo-Acevedo, Abraham Lona-Sánchez, Marisela del Rocío González-Martínez, Yolanda Jaramillo-Rodríguez, Antonio Salgado-Adame, Federico Juárez-de la Cruz, Joaquín Zúñiga‡, Edmond J. Yunis, Carolina Bekker-Méndez, Julio Granados. * These authors contributed equally to the present work. ‡ Addresses for correspondence: Rodrigo Barquera: [email protected]; Joaquín Zúñiga: [email protected]. Supplementary information Supplementary Table 1: HLA-A allelic frequencies from the state of Durango: Mexico Durango, Durango city (AFND-ID: 3516) and Mexico Durango Rural (AFND-ID: 3575). ..................................................................................................................................................... 2 Supplementary Table 2: HLA-B allelic frequencies from the state of Durango: Mexico Durango, Durango city (AFND-ID: 3516) and Mexico Durango Rural (AFND-ID: 3575). .................................................................................................................................................................. 3 Supplementary Table 3: HLA-DRB1 allelic frequencies from the state of Durango: Mexico Durango, Durango city (AFND-ID: 3516) and Mexico Durango Rural (AFND-ID: 3575). ..................................................................................................................................................... 4 Supplementary Table 4: HLA-DQB1 allelic frequencies from the state of Durango: Mexico Durango, Durango city (AFND-ID: 3516) and Mexico Durango Rural (AFND-ID: 3575). ..................................................................................................................................................... 5 Supplementary Table 5: HLA-A~B~DRB1~DQB1 haplotypes from the state of Durango. ......................................................................... 6 Supplementary Table 6: HLA-A~B~DRB1~DQB1 haplotypes from Mexico Durango, Durango city (AFND-ID: 3516). .................. 7 Supplementary Table 7: HLA-A~B~DRB1~DQB1 haplotypes from Mexico Durango Rural (AFND-ID: 3575). ................................... 8 Supplementary Table 8: Hardy-Weinberg equilibrium (HWE) parameters for the sample sets from Durango. ................................ 9 Supplementary Table 1: HLA-A allelic frequencies from the state of Durango: Mexico Durango, Durango city (AFND-ID: 3516) and Mexico Durango Rural (AFND-ID: 3575). Durango Durango city Durango Rural Allele (N=479) (N=153) A.F. (N=326) A.F. A*01 0.0965 0.0935 0.0979 A*02 0.2863 0.2419 0.3073 A*03 0.0415 0.0548 0.0352 A*11 0.0477 0.0742 0.0352 A*23 0.0218 0.0161 0.0245 A*24 0.1743 0.1871 0.1682 A*25 0.0052 0.0032 0.0061 A*26 0.0270 0.0323 0.0245 A*29 0.0394 0.0258 0.0459 A*30 0.0425 0.0419 0.0428 A*31 0.0622 0.0839 0.0520 A*32 0.0187 0.0226 0.0168 A*33 0.0176 0.0161 0.0183 A*34 0.0031 0.0032 0.0031 A*43 0.0010 0.0000 0.0015 A*66 0.0093 0.0000 0.0138 A*68 0.0996 0.1000 0.0994 A*69 0.0031 0.0000 0.0046 A*74 0.0010 0.0000 0.0015 A*80 0.0010 0.0000 0.0015 A.F.: Allelic frequency. N refers to the number of individuals analyzed. 2 Supplementary Table 2: HLA-B allelic frequencies from the state of Durango: Mexico Durango, Durango city (AFND-ID: 3516) and Mexico Durango Rural (AFND-ID: 3575). Durango Durango city Durango Rural Allele (N=479) (N=153) A.F. (N=326) A.F. B*07 0.0436 0.0452 0.0428 B*08 0.0571 0.0452 0.0627 B*13 0.0104 0.0129 0.0092 B*14:01 0.0083 0.0097 0.0076 B*14:02 0.0270 0.0323 0.0245 B*15:01 0.0425 0.0323 0.0474 B*15:02 0.0010 0.0000 0.0015 B*15:03 0.0062 0.0032 0.0076 B*15:05 0.0021 0.0000 0.0031 B*15:09 0.0041 0.0032 0.0046 B*15:10 0.0062 0.0000 0.0092 B*15:15 0.0031 0.0065 0.0015 B*15:16 0.0031 0.0000 0.0046 B*15:17 0.0062 0.0097 0.0046 B*15:56 0.0010 0.0000 0.0015 B*18 0.0373 0.0290 0.0413 B*27 0.0176 0.0290 0.0122 B*35 0.1701 0.2000 0.1560 B*37 0.0052 0.0000 0.0076 B*38 0.0104 0.0097 0.0107 B*39 0.0954 0.0774 0.1040 B*40:01 0.0083 0.0065 0.0092 B*40:02 0.0934 0.1065 0.0872 B*40:05 0.0197 0.0226 0.0183 B*40:08 0.0052 0.0032 0.0061 B*41 0.0166 0.0161 0.0168 B*42 0.0041 0.0097 0.0015 B*44 0.0820 0.0710 0.0872 B*45 0.0145 0.0065 0.0183 B*47 0.0041 0.0065 0.0031 B*48 0.0228 0.0452 0.0122 B*49 0.0249 0.0355 0.0199 B*50 0.0073 0.0065 0.0076 B*51 0.0477 0.0613 0.0413 B*52 0.0363 0.0290 0.0398 B*53 0.0124 0.0129 0.0122 B*55 0.0083 0.0000 0.0122 B*56 0.0010 0.0032 0.0000 B*57 0.0176 0.0032 0.0245 B*58 0.0093 0.0065 0.0107 B*78 0.0010 0.0000 0.0015 A.F.: Allelic frequency. N refers to the number of individuals analyzed. 3 Supplementary Table 3: HLA-DRB1 allelic frequencies from the state of Durango: Mexico Durango, Durango city (AFND-ID: 3516) and Mexico Durango Rural (AFND-ID: 3575). Durango Durango city Durango Rural Allele (N=479) (N=153) A.F. (N=326) A.F. DRB1*01 0.0539 0.0484 0.0566 DRB1*01:03 0.0073 0.0065 0.0076 DRB1*03:01 0.0757 0.0548 0.0856 DRB1*03:02 0.0021 0.0032 0.0015 DRB1*04 0.3019 0.3226 0.2920 DRB1*07 0.0654 0.0581 0.0688 DRB1*08 0.1027 0.1323 0.0887 DRB1*09 0.0093 0.0129 0.0076 DRB1*10 0.0114 0.0129 0.0107 DRB1*11 0.0975 0.0935 0.0994 DRB1*12 0.0062 0.0000 0.0092 DRB1*13 0.0788 0.0516 0.0917 DRB1*14 0.0923 0.0935 0.0917 DRB1*15 0.0529 0.0581 0.0505 DRB1*16 0.0425 0.0516 0.0382 A.F.: Allelic frequency. N refers to the number of individuals analyzed. 4 Supplementary Table 4: HLA-DQB1 allelic frequencies from the state of Durango: Mexico Durango, Durango city (AFND-ID: 3516) and Mexico Durango Rural (AFND-ID: 3575). Durango Durango city Durango Rural Allele (N=479) (N=153) A.F. (N=326) A.F. DQB1*02 0.1421 0.1194 0.1529 DQB1*03:01 0.2293 0.2129 0.2370 DQB1*03:02 0.2853 0.3129 0.2722 DQB1*03:03 0.0124 0.0097 0.0138 DQB1*04 0.1100 0.1419 0.0948 DQB1*05 0.0996 0.1032 0.0979 DQB1*06 0.1214 0.1000 0.1315 A.F.: Allelic frequency. N refers to the number of individuals analyzed. 5 Supplementary Table 5: HLA-A~B~DRB1~DQB1 haplotypes from the state of Durango. Haplotype n= (2N=958) H.F. Δ' t A*02~B*35~DRB1*04~DQB1*03:02 22 2.30 0.1884 3.5 A*01~B*08~DRB1*03:01~DQB1*02 21 2.20 0.7017 9.1 A*02~B*40:02~DRB1*04~DQB1*03:02 20 2.09 0.4287 5.9 A*68~B*39~DRB1*04~DQB1*03:02 18 1.88 0.8018 7.8 A*02~B*39~DRB1*04~DQB1*03:02 17 1.78 0.4861 5.9 A*29~B*44~DRB1*07~DQB1*02 14 1.46 0.5087 7.2 A*02~B*15:01~DRB1*04~DQB1*03:02 12 1.26 0.3693 4.2 A*02~B*35~DRB1*08~DQB1*04 12 1.26 0.1401 4.2 A*24~B*35~DRB1*04~DQB1*03:02 12 1.26 0.2219 5.1 A*24~B*35~DRB1*08~DQB1*04 11 1.15 -0.0154 -0.1 A*24~B*39~DRB1*04~DQB1*03:02 11 1.15 0.1212 1.7 A*24~B*39~DRB1*14~DQB1*03:01 11 1.15 0.3143 5.8 A*24~B*40:02~DRB1*04~DQB1*03:02 11 1.15 0.3100 5.4 A*24~B*40:02~DRB1*08~DQB1*04 11 1.15 0.1388 1.9 A*68~B*40:02~DRB1*04~DQB1*03:02 10 1.05 0.6798 5.3 H.F.: Haplotypic frequency. Δ’: Standardized linkage disequilibrium. t: validation statistic parameter; t values > 2 were taken as significant. N refers to the number of individuals analyzed. Native American most probable ancestry (MPA) haplotypes are shadowed in purple and European MPA haplotypes in green. Only haplotypes with H.F. ≥ 1.0% are included in this table. 6 Supplementary Table 6: HLA-A~B~DRB1~DQB1 haplotypes from Mexico Durango, Durango city (AFND-ID: 3516). Haplotype n= (2N=306) H.F. Δ' t A*02~B*40:02~DRB1*04~DQB1*03:02 9 2.90 0.7363 5.2 A*68~B*39~DRB1*04~DQB1*03:02 9 2.90 0.8550 5.7 A*24~B*35~DRB1*04~DQB1*03:02 6 2.26 -0.0337 -0.2 A*24~B*40:02~DRB1*08~DQB1*04 6 1.94 0.4226 4.2 A*02~B*35~DRB1*04~DQB1*03:02 5 1.61 0.0030 0.0 A*02~B*35~DRB1*08~DQB1*04 5 1.61 0.2061 2.9 A*02~B*48~DRB1*04~DQB1*03:02 5 1.61 0.4562 2.9 A*24~B*40:02~DRB1*04~DQB1*03:02 5 1.61 0.1540 1.3 A*02~B*44~DRB1*04~DQB1*03:02 4 1.29 0.3785 2.3 A*11~B*14:02~DRB1*01~DQB1*05 4 1.29 1.0000 4.1 A*24~B*35~DRB1*08~DQB1*04 4 1.29 0.0762 1.4 A*30~B*13~DRB1*07~DQB1*02 4 1.29 1.0000 4.1 A*68~B*48~DRB1*04~DQB1*03:02 4 1.29 0.7100 3.4 H.F.: Haplotypic frequency.