HLA Allele and Haplotype Frequencies in Three Urban Mexican Populations: Genetic Diversity for the Approach of Genomic Medicine
Abstract
1. Introduction
2. Materials and Methods
2.1. The Sample
2.2. HLA Typing
2.3. Statical Analysis and Data Visualization
3. Results
3.1. Allele Frequency
3.1.1. HLA-A
3.1.2. HLA-B
3.1.3. HLA-DRB1
3.1.4. HLA-DQB1
3.2. Haplotype Frequency
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Population | HLA-A | HLA-B | HLA-DRB1 | HLA-DQB1 | |
---|---|---|---|---|---|
MM | Obs. Het. | 0.8725 | 0.9383 | 0.9143 | 0.8327 |
Exp. Het. | 0.8714 | 0.9326 | 0.9329 | 0.8186 | |
p-value | 0.0127 * | 0.0069 * | 0.1043 | 0.6764 | |
Tlalpan | Obs. Het. | 0.8636 | 0.9364 | 0.9273 | 0.8546 |
Exp. Het. | 0.8712 | 0.9328 | 0.9324 | 0.8214 | |
p-value | 0.0411 * | 0.0221 * | 0.1350 | 0.4558 | |
Chihuahua | Obs. Het. | 0.9091 | 0.9546 | 0.9205 | 0.8296 |
Exp. Het. | 0.8753 | 0.9371 | 0.9494 | 0.8510 | |
p-value | 0.1074 | 0.0729 | 0.4980 | 0.5634 | |
Xalapa | Obs. Het. | 0.8691 | 0.9286 | 0.8571 | 0.7500 |
Exp. Het. | 0.8602 | 0.9146 | 0.8954 | 0.7457 | |
p-value | 0.9130 | 0.3824 | 0.0939 | 0.6401 |
Allele | MM | Tlalpan | Chihuahua | Xalapa | p-Value | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Tlalpan vs. | Chihuahua vs. Xalapa | ||||||||||
n | AF | n | AF | n | AF | n | AF | Chihuahua | Xalapa | ||
A*01:01 | 59 | 5.88 | 40 | 6.06 | 16 | 9.09 | 3 | 1.79 | 0.0300 | 0.0036 | |
A*02:01 | 265 | 26.39 | 171 | 25.91 | 48 | 27.27 | 46 | 27.38 | |||
A*02:02 | 20 | 1.99 | 16 | 2.42 | 1 | 0.57 | 3 | 1.79 | |||
A*03:01 | 48 | 4.78 | 29 | 4.39 | 10 | 5.68 | 9 | 5.36 | |||
A*11:01 | 27 | 2.69 | 18 | 2.73 | 6 | 3.41 | 3 | 1.79 | |||
A*23:01 | 30 | 2.99 | 18 | 2.73 | 6 | 3.41 | 6 | 3.57 | |||
A*24:02 | 165 | 16.43 | 113 | 17.12 | 28 | 15.91 | 24 | 14.29 | |||
A*26:01 | 33 | 3.29 | 19 | 2.88 | 9 | 5.11 | 5 | 2.98 | |||
A*29:01 | 29 | 2.89 | 18 | 2.73 | 8 | 4.55 | 3 | 1.79 | |||
A*30:01 | 34 | 3.39 | 26 | 3.94 | 4 | 2.27 | 4 | 2.38 | |||
A*31:01 | 65 | 6.47 | 34 | 5.15 | 15 | 8.52 | 16 | 9.52 | |||
A*32:01 | 17 | 1.69 | 9 | 1.36 | 4 | 2.27 | 4 | 2.38 | |||
A*33:01 | 19 | 1.89 | 13 | 1.97 | 3 | 1.7 | 3 | 1.79 | |||
A*36 | 18 | 1.79 | 10 | 1.52 | 4 | 2.27 | 4 | 2.38 | |||
A*68:01 | 129 | 12.85 | 91 | 13.79 | 8 | 4.55 | 30 | 17.86 | 0.0011 | 0.0002 | |
A*68:03 | 10 | 1.00 | 9 | 1.36 | 0 | 0.00 | 1 | 0.60 | |||
Others | 36 | 3.58 | 26 | 3.94 | 6 | 3.42 | 4 | 2.35 |
Allele | MM | Tlalpan | Chihuahua | Xalapa | p-Value | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Tlalpan vs. | Chihuahua vs. Xalapa | ||||||||||
n | AF | n | AF | n | AF | n | AF | Chihuahua | Xalapa | ||
B*07:02 | 47 | 4.68 | 23 | 3.48 | 16 | 9.09 | 8 | 4.76 | 0.0336 | ||
B*08:01 | 30 | 2.99 | 20 | 3.03 | 9 | 5.11 | 1 | 0.60 | 0.0200 | ||
B*13:01 | 12 | 1.20 | 9 | 1.36 | 2 | 1.14 | 1 | 0.60 | |||
B*14:01 | 24 | 2.39 | 12 | 1.82 | 9 | 5.11 | 3 | 1.79 | 0.0270 | ||
B*14:02 | 25 | 2.49 | 22 | 3.33 | 3 | 1.70 | 0 | 0.00 | |||
B*15:01 | 54 | 5.38 | 36 | 5.45 | 7 | 3.98 | 11 | 6.55 | |||
B*15:02 | 10 | 1.00 | 10 | 1.52 | 0 | 0.00 | 0 | 0.00 | |||
B*18:01 | 25 | 2.49 | 15 | 2.27 | 7 | 3.98 | 3 | 1.79 | |||
B*35:01 | 161 | 16.04 | 109 | 16.52 | 19 | 10.80 | 33 | 19.64 | 0.0324 | ||
B*35:02 | 43 | 4.28 | 28 | 4.24 | 5 | 2.84 | 10 | 5.95 | |||
B*38:01 | 11 | 1.10 | 3 | 0.45 | 6 | 3.41 | 2 | 1.19 | |||
B*39:01 | 131 | 13.05 | 86 | 13.03 | 20 | 11.36 | 25 | 14.88 | |||
B*39:02 | 23 | 2.29 | 21 | 3.18 | 1 | 0.57 | 1 | 0.60 | |||
B*39:06 | 16 | 1.59 | 14 | 2.12 | 1 | 0.57 | 1 | 0.60 | |||
B*40:01 | 22 | 2.19 | 15 | 2.27 | 5 | 2.84 | 2 | 1.19 | |||
B*40:02 | 65 | 6.47 | 41 | 6.21 | 7 | 3.98 | 17 | 10.12 | 0.0430 | ||
B*44:02 | 62 | 6.18 | 39 | 5.91 | 14 | 7.95 | 9 | 5.36 | |||
B*48:01 | 32 | 3.19 | 26 | 3.94 | 1 | 0.57 | 5 | 2.98 | 0.0274 | ||
B*49:01 | 13 | 1.29 | 9 | 1.36 | 1 | 0.57 | 3 | 1.79 | |||
B*50:01 | 11 | 1.10 | 8 | 1.21 | 3 | 1.70 | 0 | 0.00 | |||
B*51:01 | 65 | 6.47 | 36 | 5.45 | 21 | 11.93 | 8 | 4.76 | 0.0042 | 0.0279 | |
B*52:01 | 16 | 1.59 | 8 | 1.21 | 4 | 2.27 | 4 | 2.38 | |||
B*53:01 | 11 | 1.10 | 7 | 1.06 | 0 | 0.00 | 4 | 2.38 | |||
Others | 95 | 9.46 | 63 | 9.58 | 15 | 8.53 | 17 | 10.09 |
Allele | MM | Tlalpan | Chihuahua | Xalapa | p-Value | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Tlalpan vs. | Chihuahua vs. Xalapa | ||||||||||
n | AF | n | AF | n | AF | n | AF | Chihuahua | Xalapa | ||
DRB1*01:01 | 35 | 3.49 | 23 | 3.48 | 9 | 5.11 | 3 | 1.79 | |||
DRB1*01:02 | 29 | 2.89 | 22 | 3.33 | 6 | 3.41 | 1 | 0.60 | |||
DRB1*03:01 | 49 | 4.88 | 36 | 5.45 | 11 | 6.25 | 2 | 1.19 | 0.0133 | 0.0205 | |
DRB1*04:01 | 13 | 1.29 | 10 | 1.52 | 2 | 1.14 | 1 | 0.60 | |||
DRB1*04:02 | 16 | 1.59 | 10 | 1.52 | 2 | 1.14 | 4 | 2.38 | |||
DRB1*04:03 | 24 | 2.39 | 19 | 2.88 | 2 | 1.14 | 3 | 1.79 | |||
DRB1*04:04 | 66 | 6.57 | 38 | 5.76 | 13 | 7.39 | 15 | 8.93 | |||
DRB1*04:05 | 13 | 1.29 | 13 | 1.97 | 0 | 0.00 | 0 | 0.00 | |||
DRB1*04:07 | 174 | 17.33 | 110 | 16.67 | 18 | 10.23 | 46 | 27.38 | 0.0466 | 0.0022 | 0.0001 |
DRB1*04:11 | 17 | 1.69 | 8 | 1.21 | 2 | 1.14 | 7 | 4.17 | 0.0251 | ||
DRB1*07:01 | 74 | 7.37 | 53 | 8.03 | 15 | 8.52 | 6 | 3.57 | |||
DRB1*08:02 | 100 | 9.96 | 73 | 11.06 | 13 | 7.39 | 14 | 8.33 | |||
DRB1*10:01 | 13 | 1.29 | 9 | 1.36 | 3 | 1.70 | 1 | 0.60 | |||
DRB1*11:01 | 36 | 3.59 | 27 | 4.09 | 7 | 3.98 | 2 | 1.19 | |||
DRB1*11:04 | 13 | 1.29 | 6 | 0.91 | 3 | 1.70 | 4 | 2.38 | |||
DRB1*13:01 | 33 | 3.29 | 20 | 3.03 | 7 | 3.98 | 6 | 3.57 | |||
DRB1*13:02 | 10 | 1.00 | 7 | 1.06 | 1 | 0.57 | 2 | 1.19 | |||
DRB1*13:03 | 10 | 1.00 | 6 | 0.91 | 4 | 2.27 | 0 | 0.00 | |||
DRB1*14:01 | 15 | 1.49 | 3 | 0.45 | 9 | 5.11 | 3 | 1.79 | <0.0001 | ||
DRB1*14:02 | 49 | 4.88 | 29 | 4.39 | 9 | 5.11 | 11 | 6.55 | |||
DRB1*14:06 | 51 | 5.08 | 37 | 5.61 | 11 | 6.25 | 3 | 1.79 | 0.0424 | ||
DRB1*15:01 | 47 | 4.68 | 28 | 4.24 | 12 | 6.82 | 7 | 4.17 | |||
DRB1*15:02 | 11 | 1.10 | 9 | 1.36 | 0 | 0.00 | 2 | 1.19 | |||
DRB1*16:02 | 43 | 4.28 | 27 | 4.09 | 3 | 1.70 | 13 | 7.74 | |||
Others | 63 | 6.27 | 37 | 5.62 | 14 | 7.95 | 12 | 7.11 |
Allele | MM | Tlalpan | Chihuahua | Xalapa | p-Value | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Tlalpan vs. | Chihuahua vs. Xalapa | ||||||||||
n | AF | n | AF | n | AF | n | AF | Chihuahua | Xalapa | ||
DQB1*02:01 | 78 | 7.77 | 59 | 8.94 | 14 | 7.95 | 5 | 2.98 | 0.0088 | ||
DQB1*02:02 | 55 | 5.48 | 36 | 5.45 | 16 | 9.09 | 3 | 1.79 | 0.0426 | 0.0036 | |
DQB1*03:01 | 222 | 22.11 | 145 | 21.97 | 43 | 24.43 | 34 | 20.24 | |||
DQB1*03:02 | 316 | 31.47 | 202 | 30.61 | 40 | 22.73 | 74 | 44.05 | 0.0013 | <0.0001 | |
DQB1*04:02 | 118 | 11.75 | 82 | 12.42 | 14 | 7.95 | 22 | 13.10 | |||
DQB1*05:01 | 91 | 9.06 | 62 | 9.39 | 21 | 11.93 | 8 | 4.76 | 0.0279 | ||
DQB1*06:01 | 29 | 2.89 | 19 | 2.88 | 4 | 2.27 | 6 | 3.57 | |||
DQB1*06:02 | 36 | 3.59 | 22 | 3.33 | 10 | 5.68 | 4 | 2.38 | |||
DQB1*06:03 | 31 | 3.09 | 16 | 2.42 | 10 | 5.68 | 5 | 2.98 | 0.0491 | ||
Others | 28 | 2.79 | 17 | 2.59 | 4 | 2.29 | 7 | 4.15 |
Haplotype | n (2n = 1004) | HF | ∆′ |
---|---|---|---|
A*02:01-B*35:01-DRB1*08:02-DQB1*04:02 | 17 | 1.69 | 0.1889 |
A*68:01-B*39:01-DRB1*04:07-DQB1*03:02 | 17 | 1.69 | 0.2429 |
A*02:01-B*35:01-DRB1*04:07-DQB1*03:02 | 12 | 1.20 | 0.0242 |
A*01:01-B*08:01-DRB1*03:01-DQB1*02:01 | 11 | 1.10 | 0.7747 |
A*68:01-B*39:01-DRB1*08:02-DQB1*04:02 | 11 | 1.10 | 0.1596 |
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Del Angel-Pablo, A.D.; Juárez-Martín, A.I.; Pérez-Rubio, G.; Ambrocio-Ortiz, E.; López-Flores, L.A.; Camarena, A.E.; Falfán-Valencia, R. HLA Allele and Haplotype Frequencies in Three Urban Mexican Populations: Genetic Diversity for the Approach of Genomic Medicine. Diagnostics 2020, 10, 47. https://doi.org/10.3390/diagnostics10010047
Del Angel-Pablo AD, Juárez-Martín AI, Pérez-Rubio G, Ambrocio-Ortiz E, López-Flores LA, Camarena AE, Falfán-Valencia R. HLA Allele and Haplotype Frequencies in Three Urban Mexican Populations: Genetic Diversity for the Approach of Genomic Medicine. Diagnostics. 2020; 10(1):47. https://doi.org/10.3390/diagnostics10010047
Chicago/Turabian StyleDel Angel-Pablo, Alma D., Ana Itzel Juárez-Martín, Gloria Pérez-Rubio, Enrique Ambrocio-Ortiz, Luis A. López-Flores, Angel E. Camarena, and Ramcés Falfán-Valencia. 2020. "HLA Allele and Haplotype Frequencies in Three Urban Mexican Populations: Genetic Diversity for the Approach of Genomic Medicine" Diagnostics 10, no. 1: 47. https://doi.org/10.3390/diagnostics10010047
APA StyleDel Angel-Pablo, A. D., Juárez-Martín, A. I., Pérez-Rubio, G., Ambrocio-Ortiz, E., López-Flores, L. A., Camarena, A. E., & Falfán-Valencia, R. (2020). HLA Allele and Haplotype Frequencies in Three Urban Mexican Populations: Genetic Diversity for the Approach of Genomic Medicine. Diagnostics, 10(1), 47. https://doi.org/10.3390/diagnostics10010047