The indigenous populations as the model by nature to understand human genomic-phenomics interactions
Boon-Peng Hoh, Thuhairah Abdul Rahman
The indigenous populations as the model by nature to understand human genomic-phenomics interactions
Background: The advancement of genomics has progressed in lightning speed over the past two decades. Numerous large-scale genome sequencing initiatives were announced, along with the rise of the holistic precision medicine approach. However, the field of genomic medicine has now come to a bottleneck since genomic-phenomic interactions are not fully comprehended due to the complexity of the human systems biology and environmental influence, hence the emergence of human phenomics.
Results: This review attempts to provide an overview of the potential advantages of investigating the human phenomics of indigenous populations and the challenges ahead.
Conclusion: We believe that the indigenous populations serve as an ideal model to excavate our understanding of genomic-environmental-phenomics interactions.
The advancement of genomic technology has progressed in a lightning speed. However, the understanding of genotype-phenotype interactions has come to a bottleneck owing to the complex interplays between the human biology and environment, hence posing hindrance to materialising precision medicine in a holistic manner. The newly emerging discipline on human phenomics may be the solution. We argue that the indigenous populations serve as an ideal model to excavate our understanding on genomic-environmental-phenomics interactions. This review provides an overview on the potential advantages of investigating the human phenomics in the indigenous populations, and the challenges ahead.
indigenous populations / Orang Asli / genomics / phenomics
[1] |
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A.,
CrossRef
Pubmed
Google scholar
|
[2] |
Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W.,
CrossRef
Pubmed
Google scholar
|
[3] |
International HapMap Consortium. (2003) The International HapMap Project. Nature, 426, 789–796
CrossRef
Pubmed
Google scholar
|
[4] |
Frazer, K. A., Ballinger, D. G., Cox, D. R., Hinds, D. A., Stuve, L. L., Gibbs, R. A., Belmont, J. W., Boudreau, A., Hardenbol, P., Leal, S. M.,
CrossRef
Pubmed
Google scholar
|
[5] |
The International HapMap 3 Consortium. (2010) Integrating common and rare genetic variation in diverse human populations. Nature., 467, 52–58
|
[6] |
Wellcome Trust Case Control Consortium. (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 447, 661–678
CrossRef
Pubmed
Google scholar
|
[7] |
Fujimoto, A., Nakagawa, H., Hosono, N., Nakano, K., Abe, T., Boroevich, K. A., Nagasaki, M., Yamaguchi, R., Shibuya, T., Kubo, M.,
CrossRef
Pubmed
Google scholar
|
[8] |
Ahn, S. M., Kim, T. H., Lee, S., Kim, D., Ghang, H., Kim, D. S., Kim, B. C., Kim, S. Y., Kim, W. Y., Kim, C.,
CrossRef
Pubmed
Google scholar
|
[9] |
Kim, J. I., Ju, Y. S., Park, H., Kim, S., Lee, S., Yi, J. H., Mudge, J., Miller, N. A., Hong, D., Bell, C. J.,
CrossRef
Pubmed
Google scholar
|
[10] |
The 1000 Genomes Project Consortium. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061–1073
|
[11] |
The 1000 Genomes Project Consortium. (2015) A global reference for human genetic variation. Nature, 526, 68–74
|
[12] |
The UK10K Consortium. (2015) The UK10K project identifies rare variants in health and disease. Nature, 526, 82–89
|
[13] |
Wu, D., Dou, J., Chai, X., Bellis, C., Wilm, A., Shih, C. C., Soon, W. W. J., Bertin, N., Lin, C. B., Khor, C. C.,
CrossRef
Pubmed
Google scholar
|
[14] |
The GenomeAsia 100K Consortium. (2019) The GenomeAsia 100K Project enables genetic discoveries across Asia. Nature, 576, 106–111
|
[15] |
Cao, Y., Li, L., Xu, M., Feng, Z., Sun, X., Lu, J., Xu, Y., Du, P., Wang, T., Hu, R.,
CrossRef
Pubmed
Google scholar
|
[16] |
Jeon, S., Bhak, Y., Choi, Y., Jeon, Y., Kim, S., Jang, J., Jang, J., Blazyte, A., Kim, C., Kim, Y.,
CrossRef
Pubmed
Google scholar
|
[17] |
Houle, D., Govindaraju, D. R. and Omholt, S. (2010) Phenomics: the next challenge. Nat. Rev. Genet., 11, 855–866
CrossRef
Pubmed
Google scholar
|
[18] |
Cano-Gamez, E. and Trynka, G. (2020) From GWAS to function: using functional genomics to identify the mechanisms underlying complex diseases. Front. Genet., 11, 424
CrossRef
Pubmed
Google scholar
|
[19] |
Manolio, T. A., Collins, F. S., Cox, N. J., Goldstein, D. B., Hindorff, L. A., Hunter, D. J., McCarthy, M. I., Ramos, E. M., Cardon, L. R., Chakravarti, A.,
CrossRef
Pubmed
Google scholar
|
[20] |
Altshuler, D., Daly, M. J. and Lander, E. S. (2008) Genetic mapping in human disease. Science, 322, 881–888
CrossRef
Pubmed
Google scholar
|
[21] |
Bustamante, C. D., De La Vega, F. M. and Burchard, E. G. (2011) Genomics for the world. Nature, 475, 163–165
CrossRef
Pubmed
Google scholar
|
[22] |
Ozaki, K., Ohnishi, Y., Iida, A., Sekine, A., Yamada, R., Tsunoda, T., Sato, H., Sato, H., Hori, M., Nakamura, Y.,
CrossRef
Pubmed
Google scholar
|
[23] |
Lango Allen, H., Estrada, K., Lettre, G., Berndt, S. I., Weedon, M. N., Rivadeneira, F., Willer, C. J., Jackson, A. U., Vedantam, S., Raychaudhuri, S.,
CrossRef
Pubmed
Google scholar
|
[24] |
Yang, J., Benyamin, B., McEvoy, B. P., Gordon, S., Henders, A. K., Nyholt, D. R., Madden, P. A., Heath, A. C., Martin, N. G., Montgomery, G. W.,
CrossRef
Pubmed
Google scholar
|
[25] |
Nikpay, M., Goel, A., Won, H.-H., Hall, L. M., Willenborg, C., Kanoni, S., Saleheen, D., Kyriakou, T., Nelson, C. P., Hopewell, J. C.,
CrossRef
Pubmed
Google scholar
|
[26] |
Doherty, A., Smith-Byrne, K., Ferreira, T., Holmes, M. V., Holmes, C., Pulit, S. L. and Lindgren, C. M. (2018) GWAS identifies 14 loci for device-measured physical activity and sleep duration. Nat. Commun., 9, 5257
CrossRef
Pubmed
Google scholar
|
[27] |
Band, G., Le, Q. S., Jostins, L., Pirinen, M., Kivinen, K., Jallow, M., Sisay-Joof, F., Bojang, K., Pinder, M., Sirugo, G.,
CrossRef
Pubmed
Google scholar
|
[28] |
Klarin, D., Lynch, J., Aragam, K., Chaffin, M., Assimes, T. L., Huang, J., Lee, K. M., Shao, Q., Huffman, J. E., Natarajan, P.,
CrossRef
Pubmed
Google scholar
|
[29] |
Zhang, K., Weder, A. B., Eskin, E. and O’Connor, D. T. (2010) Genome-wide case/control studies in hypertension: only the ‘tip of the iceberg’. J. Hypertens., 28, 1115–1123
CrossRef
Pubmed
Google scholar
|
[30] |
Wang, Y. and Wang, J.-G. (2019) Genome-wide association studies of hypertension and several other cardiovascular diseases. Pulse (Basel), 6, 169–186
CrossRef
Pubmed
Google scholar
|
[31] |
Freimer, N. and Sabatti, C. (2003) The human phenome project. Nat. Genet., 34, 15–21
CrossRef
Pubmed
Google scholar
|
[32] |
Dominiczak, A., Delles, C. and Padmanabhan, S. (2017) Genomics and precision medicine for clinicians and scientists in hypertension. Hypertension, 69, e10–e13
CrossRef
Pubmed
Google scholar
|
[33] |
Peck, R. W. (2018) Precision medicine is not just genomics: the right dose for every patient. Annu. Rev. Pharmacol. Toxicol., 58, 105–122
CrossRef
Pubmed
Google scholar
|
[34] |
Hoh, B. P., Abdul Rahman, T. and Yusoff, K. (2019) Natural selection and local adaptation of blood pressure regulation and their perspectives on precision medicine in hypertension. Hereditas, 156, 1
CrossRef
Pubmed
Google scholar
|
[35] |
Mills, K. T., Bundy, J. D., Kelly, T. N., Reed, J. E., Kearney, P. M., Reynolds, K., Chen, J. and He, J. (2016) Global disparities of hypertension prevalence and control: A systematic analysis of population-based studies from 90 countries. Circulation, 134, 441–450
CrossRef
Pubmed
Google scholar
|
[36] |
Manosroi, W. and Williams, G. H. (2019) Genetics of Human Primary Hypertension: Focus on Hormonal Mechanisms. Endocr. Rev., 40, 825–856
CrossRef
Pubmed
Google scholar
|
[37] |
Tocci, G., Ferrucci, A., Pontremoli, R., Ferri, C., Rosei, E. A., Morganti, A., Trimarco, B., Mancia, G., Borghi, C. and Volpe, M. (2015) Blood pressure levels and control in Italy: comprehensive analysis of clinical data from 2000‒2005 and 2005‒2011 hypertension surveys. J. Hum. Hypertens., 29, 696–701
CrossRef
Pubmed
Google scholar
|
[38] |
Korner, P. I. (2010) The phenotypic patterns of essential hypertension are the key to identifying “high blood pressure” genes. Physiol. Res., 59, 841–857
CrossRef
Pubmed
Google scholar
|
[39] |
Basting, T. and Lazartigues, E. (2017) DOCA-salt hypertension: an update. Curr Hypertens Rep., 19, 1–8
CrossRef
Google scholar
|
[40] |
Coffman, T. M. (2011) Under pressure: the search for the essential mechanisms of hypertension. Nat. Med., 17, 1402–1409
CrossRef
Pubmed
Google scholar
|
[41] |
Kato, N. (2012) Ethnic differences in genetic predisposition to hypertension. Hypertens. Res., 35, 574–581
CrossRef
Pubmed
Google scholar
|
[42] |
Thompson, E. E., Kuttab-Boulos, H., Witonsky, D., Yang, L., Roe, B. A. and Di Rienzo, A. (2004) CYP3A variation and the evolution of salt-sensitivity variants. Am. J. Hum. Genet., 75, 1059–1069
CrossRef
Pubmed
Google scholar
|
[43] |
Nakajima, T., Wooding, S., Sakagami, T., Emi, M., Tokunaga, K., Tamiya, G., Ishigami, T., Umemura, S., Munkhbat, B., Jin, F.,
CrossRef
Pubmed
Google scholar
|
[44] |
Young, J.H., Chang, Y.P.C., Kim, J.D.O., Chretien, J.P., Klag, M.J., Levine, M.A., Ruff, C.B., Wang, N.Y., Chakravarti, A. (2005) Differential susceptibility to hypertension is due to selection during the out-of-Africa expansion. PLoS Genet., 1, e82
|
[45] |
Verma, A., Lucas, A., Verma, S. S., Zhang, Y., Josyula, N., Khan, A., Hartzel, D. N., Lavage, D. R., Leader, J., Ritchie, M. D.,
CrossRef
Pubmed
Google scholar
|
[46] |
Safarova, M. S., Satterfield, B. A., Fan, X., Austin, E. E., Ye, Z., Bastarache, L., Zheng, N., Ritchie, M. D., Borthwick, K. M., Williams, M. S.,
CrossRef
Pubmed
Google scholar
|
[47] |
Denny, J. C., Bastarache, L., Ritchie, M. D., Carroll, R. J., Zink, R., Mosley, J. D., Field, J. R., Pulley, J. M., Ramirez, A. H., Bowton, E.,
CrossRef
Pubmed
Google scholar
|
[48] |
Diogo, D., Tian, C., Franklin, C. S., Alanne-Kinnunen, M., March, M., Spencer, C. C. A., Vangjeli, C., Weale, M. E., Mattsson, H., Kilpeläinen, E.,
CrossRef
Pubmed
Google scholar
|
[49] |
Zhao, X., Geng, X., Srinivasasainagendra, V., Chaudhary, N., Judd, S., Wadley, V., Gutiérrez, O. M., Wang, H., Lange, E. M., Lange, L. A.,
CrossRef
Pubmed
Google scholar
|
[50] |
Pendergrass, S. A., Buyske, S., Jeff, J. M., Frase, A., Dudek, S., Bradford, Y., Ambite, J. L., Avery, C. L., Buzkova, P., Deelman, E.,
CrossRef
Pubmed
Google scholar
|
[51] |
Mashimo, T., Voigt, B., Kuramoto, T. and Serikawa, T. (2005) Rat Phenome Project: the untapped potential of existing rat strains. J. Appl. Physiol., 98, 371–379
CrossRef
Pubmed
Google scholar
|
[52] |
Bogue, M. A., Grubb, S. C., Walton, D. O., Philip, V. M., Kolishovski, G., Stearns, T., Dunn, M. H., Skelly, D. A., Kadakkuzha, B., TeHennepe, G.,
CrossRef
Pubmed
Google scholar
|
[53] |
FitzGerald, G., Botstein, D., Califf, R., Collins, R., Peters, K., Van Bruggen, N. and Rader, D. (2018) The future of humans as model organisms. Science, 361, 552–553
CrossRef
Pubmed
Google scholar
|
[54] |
Yew, C. W., Lu, D., Deng, L., Wong, L. P., Ong, R. T., Lu, Y., Wang, X., Yunus, Y., Aghakhanian, F., Mokhtar, S. S.,
CrossRef
Pubmed
Google scholar
|
[55] |
Hill, C., Soares, P., Mormina, M., Macaulay, V., Meehan, W., Blackburn, J., Clarke, D., Raja, J. M., Ismail, P., Bulbeck, D.,
CrossRef
Pubmed
Google scholar
|
[56] |
Deng, L., Lou, H., Zhang, X., Thiruvahindrapuram, B., Lu, D., Marshall, C. R., Liu, C., Xie, B., Xu, W., Wong, L. P.,
CrossRef
Pubmed
Google scholar
|
[57] |
Endicott, K. (2016) Malaysia’s Original People: Past, Present and Future of the Orang Asli. Singapore: NUS Press
|
[58] |
Mokhsin, A., Mokhtar, S. S., Mohd Ismail, A., M Nor, F., Shaari, S. A., Nawawi, H., Yusoff, K., Abdul Rahman, T. and Hoh, B. P. (2018) Observational study of the status of coronary risk biomarkers among Negritos with metabolic syndrome in the east coast of Malaysia. BMJ Open, 8, e021580
CrossRef
Pubmed
Google scholar
|
[59] |
Aghakhanian, F., Wong, C., Tan, J. S. Y., Yeo, L. F., Ramadas, A., Edo, J., Hoh, B. P., Khalid, B. A. K. and Phipps, M. E. (2019) Metabolic syndrome and cardiometabolic risk factors among indigenous Malaysians. Public Health, 176, 106–113
CrossRef
Pubmed
Google scholar
|
[60] |
Tuan Abdul Aziz, T. A., Teh, L. K., Md Idris, M. H., Bannur, Z., Ashari, L. S., Ismail, A. I., Ahmad, A., Isa, K. M., Nor, F. M., Rahman, T. H.,
CrossRef
Pubmed
Google scholar
|
[61] |
Mills, M. C. and Rahal, C. (2019) A scientometric review of genome-wide association studies. Comm Biol., doi:10.1038/s42003-018-0261-x
CrossRef
Google scholar
|
[62] |
Garrison, N. A., Hudson, M., Ballantyne, L. L., Garba, I., Martinez, A., Taualii, M., Arbour, L., Caron, N. R. and Rainie, S. C. (2019) Genomic research through an indigenous lens: understanding the expectations. Annu. Rev. Genomics Hum. Genet., 20, 495–517
CrossRef
Pubmed
Google scholar
|
[63] |
Jinam, T. A., Phipps, M. E., Aghakhanian, F., Majumder, P. P., Datar, F., Stoneking, M., Sawai, H., Nishida, N., Tokunaga, K., Kawamura, S.,
CrossRef
Pubmed
Google scholar
|
[64] |
Scholes, C., Siddle, K., Ducourneau, A., Crivellaro, F., Järve, M., Rootsi, S., Bellatti, M., Tabbada, K., Mormina, M., Reidla, M.,
CrossRef
Pubmed
Google scholar
|
[65] |
Kusuma, P., Brucato, N., Cox, M. P., Letellier, T., Manan, A., Nuraini, C., Grangé, P., Sudoyo, H. and Ricaut, F. X. (2017) The last sea nomads of the Indonesian archipelago: genomic origins and dispersal. Eur. J. Hum. Genet., 25, 1004–1010
CrossRef
Pubmed
Google scholar
|
[66] |
Deng, L., Hoh, B. P., Lu, D., Fu, R., Phipps, M. E., Li, S., Nur-Shafawati, A. R., Hatin, W. I., Ismail, E., Mokhtar, S. S.,
CrossRef
Pubmed
Google scholar
|
[67] |
Aghakhanian, F., Yunus, Y., Naidu, R., Jinam, T., Manica, A., Hoh, B. P. and Phipps, M. E. (2015) Unravelling the genetic history of Negritos and indigenous populations of Southeast Asia. Genome Biol. Evol., 7, 1206–1215
CrossRef
Pubmed
Google scholar
|
[68] |
McEvoy, B. P., Lind, J. M., Wang, E. T., Moyzis, R. K., Visscher, P. M., van Holst Pellekaan, S. M. and Wilton, A. N. (2010) Whole-genome genetic diversity in a sample of Australians with deep Aboriginal ancestry. Am. J. Hum. Genet., 87, 297–305
CrossRef
Pubmed
Google scholar
|
[69] |
Tokunaga, K., Ohashi, J., Bannai, M. and Juji, T. (2001) Genetic link between Asians and native Americans: evidence from HLA genes and haplotypes. Hum. Immunol., 62, 1001–1008
CrossRef
Pubmed
Google scholar
|
[70] |
Zhou, S., Xie, P., Quoibion, A., Ambalavanan, A., Dionne-Laporte, A., Spiegelman, D., Bourassa, C. V., Xiong, L., Dion, P. A. and Rouleau, G. A. (2019) Genetic architecture and adaptations of Nunavik Inuit. Proc. Natl. Acad. Sci. USA, 116, 16012–16017
CrossRef
Pubmed
Google scholar
|
[71] |
Fumagalli, M., Moltke, I., Grarup, N., Racimo, F., Bjerregaard, P., Jørgensen, M. E., Korneliussen, T. S., Gerbault, P., Skotte, L., Linneberg, A.,
CrossRef
Pubmed
Google scholar
|
[72] |
Liu, X., Yunus, Y., Lu, D., Aghakhanian, F., Saw, W. Y., Deng, L., Ali, M., Wang, X., Nor, F. M., Rahman, T. A.,
CrossRef
Pubmed
Google scholar
|
[73] |
Ilardo, M. A., Moltke, I., Korneliussen, T. S., Cheng, J., Stern, A. J., Racimo, F., de Barros Damgaard, P., Sikora, M., Seguin-Orlando, A., Rasmussen, S.,
CrossRef
Pubmed
Google scholar
|
[74] |
Kapoor, A. K. and Kaur, J. (2012) Natural selection in a population group of Andaman and Nicobar Islands. J. Nat. Sci. Biol. Med., 3, 71–77
CrossRef
Pubmed
Google scholar
|
[75] |
Roberts-Thomson, R. A. and Roberts-Thomson, P. J. (1999) Rheumatic disease and the Australian aborigine. Ann. Rheum. Dis., 58, 266–270
CrossRef
Pubmed
Google scholar
|
[76] |
Leung, L. (2016) Diabetes mellitus and the Aboriginal diabetic initiative in Canada: An update review. J. Family Med. Prim. Care, 5, 259–265
CrossRef
Pubmed
Google scholar
|
[77] |
Wong, E. C. L. and Kapoor, A. (2017) Epidemiology of prostate and kidney cancer in the Aboriginal population of Canada: A systematic review. Can. Urol. Assoc. J., 11, E222–E232
CrossRef
Pubmed
Google scholar
|
[78] |
Thomas, V., Sng, K. H. and Yap, P. L. (1980) Seroepidemiology of Malaria in Orang Asli (Aborgines) Children in Kelantan, Malaysia. Geneva, available from: http://apps.who.int/iris/handle/10665/65793
|
[79] |
Baer, A. S. (1999) Health, disease, and survival : a biomedical and genetic analysis of the Orang Asli of Malaysia. 1st ed. Subang Jaya: Center for Orang Asli Concerns
|
[80] |
Kaur, G. (2009) Prevalence of clinical malaria among an Orang Asli community in Malaysia. Southeast Asian J Trop Med Public Health, 40, 665–673
Pubmed
|
[81] |
Muslim, A., Mohd Sofian, S., Shaari, S. A., Hoh, B. P. and Lim, Y. A. L. (2019) Prevalence, intensity and associated risk factors of soil transmitted helminth infections: A comparison between Negritos (indigenous) in inland jungle and those in resettlement at town peripheries. PLoS Negl. Trop. Dis., 13, e0007331
CrossRef
Pubmed
Google scholar
|
[82] |
Sahlan, N., Fadzilah, M. N., Muslim, A., Shaari, S. A., Abdul Rahman, T. and Hoh, B. P. (2019) Hepatitis B virus infection: Epidemiology and seroprevalence rate amongst Negrito tribe in Malaysia. Med. J. Malaysia, 74, 320–325
Pubmed
|
[83] |
Ishida, T., Yamamoto, K. and Omoto, K. (1988) A seroepidemiological survey of HTLV-1 in the Philippines. Int. J. Epidemiol., 17, 625–628
CrossRef
Pubmed
Google scholar
|
[84] |
Phipps, M. E., Chan, K. K. L., Naidu, R., Mohamad, N. W., Hoh, B.-P., Quek, K.-F., Ahmad, B., Harnida, S. M., Zain, A. Z. and Kadir, K. A. (2015) Cardio-metabolic health risks in indigenous populations of Southeast Asia and the influence of urbanization. BMC Public Health, 15, 47
CrossRef
Pubmed
Google scholar
|
[85] |
Rønn, P. F., Lucas, M., Laouan Sidi, E. A., Tvermosegaard, M., Andersen, G. S., Lauritzen, T., Toft, U., Carstensen, B., Christensen, D. L. and Jørgensen, M. E. (2017) The obesity-associated risk of cardiovascular disease and all-cause mortality is not lower in Inuit compared to Europeans: A cohort study of Greenlandic Inuit, Nunavik Inuit and Danes. Atherosclerosis, 265, 207–214
CrossRef
Pubmed
Google scholar
|
[86] |
Appel, E. V. R., Moltke, I., Jørgensen, M. E., Bjerregaard, P., Linneberg, A., Pedersen, O., Albrechtsen, A., Hansen, T. and Grarup, N. (2018) Genetic determinants of glycated hemoglobin levels in the Greenlandic Inuit population. Eur. J. Hum. Genet., 26, 868–875
CrossRef
Pubmed
Google scholar
|
[87] |
Lu, D. and Xu, S. (2013) Principal component analysis reveals the 1000 Genomes Project does not sufficiently cover the human genetic diversity in Asia. Front. Genet., 4, 127
CrossRef
Pubmed
Google scholar
|
[88] |
Wang, L., Olson, J. E., Bielinski, S. J., St Sauver, J. L., Fu, S., He, H., Cicek, M. S., Hathcock, M. A., Cerhan, J. R. and Liu, H. (2020) Impact of diverse data sources on computational phenotyping. Front. Genet., 11, 556
CrossRef
Pubmed
Google scholar
|
[89] |
Caron, N. R., Chongo, M., Hudson, M., Arbour, L., Wasserman, W. W., Robertson, S., Correard, S. and Wilcox, P. (2020) Indigenous Genomic Databases: pragmatic considerations and cultural contexts. Front. Public Health, 8, 111
CrossRef
Pubmed
Google scholar
|
/
〈 | 〉 |