1. A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response
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Adolfo Correa, Kotaro Ogawa, Yukinori Okada, Paul J. McLaren, Philip E. Stuart, Kenichi Yamamoto, Peter K. Gregersen, Saori Sakaue, David W Haas, Tõnu Esko, Michael H. Cho, Albert V. Smith, Wanson Choi, Sebastian Schönherr, Yii-Der Ida Chen, James T. Elder, Soumya Raychaudhuri, Maria Gutierrez-Arcelus, Lukas Forer, Kent D. Taylor, Yang Luo, Xiuqing Guo, Jerome I. Rotter, Stephen S. Rich, Nicholette D. Palmer, Mary Carrington, Masahiro Kanai, Christian Fuchsberger, Buhm Han, Andres Metspalu, Xinyi Li, Sekar Kathiresan, James G. Wilson, Jacques Fellay, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Abe, N., Abecasis, G., Aguet, F., Albert, C., Almasy, L., Alonso, A., Ament, S., Anderson, P., Anugu, P., Applebaum-Bowden, D., Ardlie, K., Dan Arking, X., Arnett, D.K., Ashley-Koch, A., Aslibekyan, S., Assimes, T., Auer, P., Avramopoulos, D., Ayas, N., Balasubramanian, A., Barnard, J., Barnes, K., Barr, R.G., Barron-Casella, E., Barwick, L., Beaty, T., Beck, G., Becker, D., Becker, L., Beer, R., Beitelshees, A., Benjamin, E., Benos, T., Bezerra, M., Bielak, L., Bis, J., Blackwell, T., Blangero, J., Boerwinkle, E., Bowden, D.W., Bowler, R., Brody, J., Broeckel, U., Broome, J., Brown, D., Bunting, K., Burchard, E., Bustamante, C., Buth, E., Cade, B., Cardwell, J., Carey, V., Carrier, J., Carty, C., Casaburi, R., Romero, JPC, Casella, J., Castaldi, P., Chaffin, M., Chang, C., Chang, Y.C., Chasman, D., Chavan, S., Chen, B.J., Chen, W.M., Choi, S.H., Chuang, L.M., Chung, M., Chung, R.H., Clish, C., Comhair, S., Conomos, M., Cornell, E., Crandall, C., Crapo, J., Cupples, L.A., Curran, J., Curtis, J., Custer, B., Damcott, C., Darbar, D., David, S., Davis, C., Daya, M., de Andrade, M., Fuentes, L.L., de Vries, P., DeBaun, M., Deka, R., DeMeo, D., Devine, S., Dinh, H., Doddapaneni, H., Duan, Q., Dugan-Perez, S., Duggirala, R., Durda, J.P., Dutcher, S.K., Eaton, C., Ekunwe, L., Boueiz, A.E., Ellinor, P., Emery, L., Erzurum, S., Farber, C., Farek, J., Fingerlin, T., Flickinger, M., Fornage, M., Franceschini, N., Frazar, C., Fu, M., Fullerton, S.M., Fulton, L., Gabriel, S., Gan, W., Gao, S., Gao, Y., Gass, M., Geiger, H., Gelb, B., Geraci, M., Germer, S., Gerszten, R., Ghosh, A., Gibbs, R., Gignoux, C., Gladwin, M., Glahn, D., Gogarten, S., Gong, D.W., Goring, H., Graw, S., Gray, K.J., Grine, D., Gross, C., Gu, C.C., Guan, Y., Gupta, N., Haas, D.M., Haessler, J., Hall, M., Han, Y., Hanly, P., Harris, D., Hawley, N.L., He, J., Heavner, B., Heckbert, S., Hernandez, R., Herrington, D., Hersh, C., Hidalgo, B., Hixson, J., Hobbs, B., Hokanson, J., Hong, E., Hoth, K., Hsiung, C.A., Hu, J., Hung, Y.J., Huston, H., Hwu, C.M., Irvin, M.R., Jackson, R., Jain, D., Jaquish, C., Johnsen, J., Johnson, A., Johnson, C., Johnston, R., Jones, K., Kang, H.M., Kaplan, R., Kardia, S., Kelly, S., Kenny, E., Kessler, M., Khan, A., Khan, Z., Kim, W., Kimoff, J., Kinney, G., Konkle, B., Kooperberg, C., Kramer, H., Lange, C., Lange, E., Lange, L., Laurie, C., LeBoff, M., Lee, J., Lee, S., Lee, W.J., LeFaive, J., Levine, D., Dan Levy, X., Lewis, J., Li, X., Li, Y., Lin, H., Lin, X., Liu, S., Liu, Y., Loos, RJF, Lubitz, S., Lunetta, K., Luo, J., Magalang, U., Mahaney, M., Make, B., Manichaikul, A., Manning, A., Manson, J., Martin, L., Marton, M., Mathai, S., Mathias, R., May, S., McArdle, P., McDonald, M.L., McFarland, S., McGarvey, S., McGoldrick, D., McHugh, C., McNeil, B., Mei, H., Meigs, J., Menon, V., Mestroni, L., Metcalf, G., Meyers, D.A., Mignot, E., Mikulla, J., Min, N., Minear, M., Minster, R.L., Mitchell, B.D., Moll, M., Momin, Z., Montasser, M.E., Montgomery, C., Muzny, D., Mychaleckyj, J.C., Nadkarni, G., Naik, R., Naseri, T., Natarajan, P., Nekhai, S., Nelson, S.C., Neltner, B., Nessner, C., Nickerson, D., Nkechinyere, O., North, K., O'Connell, J., O'Connor, T., Ochs-Balcom, H., Okwuonu, G., Pack, A., Paik, D.T., Pankow, J., Papanicolaou, G., Parker, C., Peloso, G., Peralta, J.M., Perez, M., Perry, J., Peters, U., Peyser, P., Phillips, L.S., Pleiness, J., Pollin, T., Post, W., Becker, J.P., Boorgula, M.P., Preuss, M., Psaty, B., Qasba, P., Qiao, D., Qin, Z., Rafaels, N., Raffield, L., Rajendran, M., Ramachandran, V.S., Rao, D.C., Rasmussen-Torvik, L., Ratan, A., Redline, S., Reed, R., Reeves, C., Regan, E., Reiner, A., Reupena, M.S., Rice, K., Robillard, R., Robine, N., Dan Roden, X., Roselli, C., Ruczinski, I., Runnels, A., Russell, P., Ruuska, S., Ryan, K., Sabino, E.C., Saleheen, D., Salimi, S., Salvi, S., Salzberg, S., Sandow, K., Sankaran, V.G., Santibanez, J., Schwander, K., Schwartz, D., Sciurba, F., Seidman, C., Seidman, J., Sériès, F., Sheehan, V., Sherman, S.L., Shetty, A., Sheu, W.H., Shoemaker, M.B., Silver, B., Silverman, E., Skomro, R., Smith, J., Smith, N., Smith, T., Smoller, S., Snively, B., Snyder, M., Sofer, T., Sotoodehnia, N., Stilp, A.M., Storm, G., Streeten, E., Su, J.L., Sung, Y.J., Sylvia, J., Szpiro, A., Taliun, D., Tang, H., Taub, M., Taylor, M., Taylor, S., Telen, M., Thornton, T.A., Threlkeld, M., Tinker, L., Tirschwell, D., Tishkoff, S., Tiwari, H., Tong, C., Tracy, R., Tsai, M., Vaidya, D., Van Den Berg, D., VandeHaar, P., Vrieze, S., Walker, T., Wallace, R., Walts, A., Wang, F.F., Wang, H., Wang, J., Watson, K., Watt, J., Weeks, D.E., Weinstock, J., Weir, B., Weiss, S.T., Weng, L.C., Wessel, J., Willer, C., Williams, K., Williams, L.K., Wilson, C., Wilson, J., Winterkorn, L., Wong, Q., Wu, J., Xu, H., Yanek, L., Yang, I., Yu, K., Zekavat, S.M., Zhang, Y., Zhao, S.X., Zhao, W., Zhu, X., Zody, M., Zoellner, S., and Consortium, NHLBI Trans-Omics for Precision Medicine (TOPMed)
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haplotypes ,Population genetics ,Alleles ,Amino Acids/genetics ,Gene Frequency/genetics ,Genetic Variation ,Genetics, Population ,HIV Infections/genetics ,HIV-1/genetics ,HLA Antigens/genetics ,Haplotypes/genetics ,Host-Pathogen Interactions/genetics ,Humans ,Linkage Disequilibrium/genetics ,Physical Chromosome Mapping ,Reference Standards ,Selection, Genetic ,Viral Load ,HIV Infections ,Immunogenetics ,Human leukocyte antigen ,Major histocompatibility complex ,Linkage Disequilibrium ,Article ,Gene Frequency ,HLA Antigens ,Genetics ,mhc ,Amino Acids ,Allele ,biology ,Haplotype ,association ,genetic-basis ,micropolymorphism ,polygenic risk scores ,Evolutionary biology ,Host-Pathogen Interactions ,alleles ,loci ,HIV-1 ,biology.protein ,amino-acid ,identification ,Viral load ,Imputation (genetics) - Abstract
A high-resolution reference panel based on whole-genome sequencing data enables accurate imputation of HLA alleles across diverse populations and fine-mapping of HLA association signals for HIV-1 host response., Fine-mapping to plausible causal variation may be more effective in multi-ancestry cohorts, particularly in the MHC, which has population-specific structure. To enable such studies, we constructed a large (n = 21,546) HLA reference panel spanning five global populations based on whole-genome sequences. Despite population-specific long-range haplotypes, we demonstrated accurate imputation at G-group resolution (94.2%, 93.7%, 97.8% and 93.7% in admixed African (AA), East Asian (EAS), European (EUR) and Latino (LAT) populations). Applying HLA imputation to genome-wide association study data for HIV-1 viral load in three populations (EUR, AA and LAT), we obviated effects of previously reported associations from population-specific HIV studies and discovered a novel association at position 156 in HLA-B. We pinpointed the MHC association to three amino acid positions (97, 67 and 156) marking three consecutive pockets (C, B and D) within the HLA-B peptide-binding groove, explaining 12.9% of trait variance.