A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation

被引：56

作者：

Bonfante, Betty ^{[1
]}

Faux, Pierre ^{[1
]}

Navarro, Nicolas ^{[2
,3
]}

Mendoza-Revilla, Javier ^{[4
,5
]}

Dubied, Morgane ^{[2
]}

Montillot, Charlotte ^{[6
]}

Wentworth, Emma ^{[7
]}

Poloni, Lauriane ^{[2
,3
]}

Varon-Gonzalez, Ceferino ^{[8
]}

Jones, Philip ^{[9
,10
]}

Xiong, Ziyi ^{[11
]}

Fuentes-Guajardo, Macarena ^{[12
]}

Palmal, Sagnik ^{[1
]}

Chacon-Duque, Juan Camilo ^{[13
]}

Hurtado, Malena ^{[4
]}

Villegas, Valeria ^{[4
]}

Granja, Vanessa ^{[4
]}

Jaramillo, Claudia ^{[14
]}

Arias, William ^{[14
]}

Barquera, Rodrigo ^{[15
,16
]}

Everardo-Martinez, Paola ^{[15
]}

Sanchez-Quinto, Mirsha ^{[17
]}

Gomez-Valdes, Jorge ^{[15
]}

Villamil-Ramirez, Hugo ^{[18
]}

de Cerqueira, Caio C. Silva ^{[19
]}

Hunemeier, Tabita ^{[20
]}

Ramallo, Virginia ^{[21
,22
]}

Liu, Fan ^{[11
,23
,24
]}

Weinber, Seth M. ^{[25
,26
,27
]}

Shaffer, John R. ^{[25
,26
]}

Stergiakouli, Evie ^{[28
,29
]}

Howe, Laurence J. ^{[28
]}

Hysi, Pirro G. ^{[30
]}

Spector, Timothy D. ^{[30
]}

Gonzalez-Jose, Rolando ^{[22
]}

Schuler-Faccini, Lavinia ^{[21
]}

Bortolini, Ria-Catira ^{[21
]}

Acuna-Alonzo, Victor ^{[15
]}

Canizales-Quinteros, Samuel ^{[18
]}

Gallo, Carla ^{[4
]}

Poletti, Giovanni ^{[4
]}

Bedoya, Gabriel ^{[14
]}

Rothhammer, Francisco ^{[31
]}

Thauvin-Robinet, Christel ^{[6
,32
]}

Faivre, Laurence ^{[6
,32
]}

Costedoat, Caroline ^{[1
]}

Balding, David ^{[9
,10
,33
,34
]}

Cox, Timothy ^{[35
,36
]}

Kayser, Manfred ^{[11
]}

Duplomb, Laurence ^{[6
]}

机构：

[1] Aix Marseille Univ, ADES, EFS, CNRS, F-13005 Marseille, France

[2] Univ Bourgogne Franche Comte, EPHE, Biogeosci, UMR 6282,CNRS, F-21078 Dijon, France

[3] PSL Univ, EPHE, F-75014 Paris, France

[4] Univ Peruana Cayetano Heredia, Fac Ciencias & Filosofia, Labs Invest & Desarrollo, Lima 31, Peru

[5] Inst Pasteur, Unit Human Evolutionary Genet, F-75015 Paris, France

[6] Univ Bourgogne Franche Comte, INSERM UMR Genet Anomalies Dev 1231, F-21000 Dijon, France

[7] Univ Connecticut Hlth, Dept Genet & Genome Sci, Farmington, CT 06030 USA

[8] Sorbonne Univ, Inst Systemat, Museum Natl Hist Nat,EPHE, UA,ISYEB,UMR 7205,CNRS,Evolut,Biodiversite,MNHN,U, F-75005 Paris, France

[9] UCL, Dept Genet Evolut & Environm, London WC1E 6BT, England

[10] UCL, UCL Genet Inst, London WC1E 6BT, England

[11] Erasmus MC Univ Med Ctr Rotterdam, Dept Genet Identificat, NL-3015 GD Rotterdam, Netherlands

[12] Univ Tarapaca, Fac Ciencias Salud, Dept Tecnol Med, Arica 1000000, Chile

[13] Nat Hist Museum, Dept Earth Sci, Div Vertebrates & Anthropol, London SW7 5BD, England

[14] Univ Antioquia, GENMOL Genet Mol, Medellin 5001000, Colombia

[15] Natl Sch Anthropol & Hist, Mol Genet Lab, Mexico City 14050, DF, Mexico

[16] Max Planck Inst Sci Human Hist MPI SHH, Dept Archaeogenet, D-07745 Jena, Germany

[17] UNAM Univ Nacl Autonoma Mexico, Fac Med, Forens Sci, Mexico City 06320, DF, Mexico

[18] UNAM Inst Nacl Med Genom, Fac Quim, Unidad Genom Poblac Aplicada Salud, Mexico City 4510, DF, Mexico

[19] Sci Police Sao Paulo State, BR-19900109 Ourinhos, SP, Brazil

[20] Univ Sao Paulo, Inst Biociencias, Dept Genet & Biol Evolut, BR-05508090 Sao Paulo, SP, Brazil

[21] Univ Fed Rio Grande do Sul, Dept Genet, BR-90040060 Porto Alegre, RS, Brazil

[22] Consejo Nacl Invest Cient & Tecn, Inst Patagon Ciencias Sociales & Humanas, Ctr Nacl Patagon, U9129ACD, Puerto Madryn, Argentina

[23] Chinese Acad Sci, Beijing Inst Genom, Key Lab Genom & Precis Med, Beijing 100864, Peoples R China

[24] Univ Chinese Acad Sci, Beijing 100864, Peoples R China

[25] Univ Pittsburgh, Dept Human Genet, Pittsburgh, PA 15260 USA

[26] Univ Pittsburgh, Ctr Craniofacial & Dent Genet, Dept Oral Biol, Pittsburgh, PA 15260 USA

[27] Univ Pittsburgh, Dept Anthropol, Pittsburgh, PA 15260 USA

[28] Univ Bristol, Med Res Council, Integrat Epidemiol Unit, Populat Hlth Sci, Bristol BS1 2LY, Avon, England

[29] Univ Bristol, Sch Oral & Dent Sci, Bristol BS1 2LY, Avon, England

[30] Kings Coll London, Dept Twin Res & Genet Epidemiol, London WC2R 2LS, England

[31] Univ Tarapaca, Inst Alta Invest, Arica 1000000, Chile

[32] CHU Dijon, Ctr Genet, Ctr Reference Malad Rares Anomalies Dev & Syndrom, FHU TRANSLAD, F-21000 Dijon, France

[33] Univ Melbourne, Sch BioSci & Math, Melbourne Integrat Genom, Melbourne, Vic 3052, Australia

[34] Univ Melbourne, Sch Stat, Melbourne Integrat Genom, Melbourne, Vic 3052, Australia

[35] Univ Missouri, Sch Dent, Dept Oral & Craniofacial Sci, Kansas City, MO 64108 USA

[36] Univ Missouri, Sch Med, Dept Pediat, Kansas City, MO 64108 USA

[37] Open Univ, Fac Sci Technol Engn & Math, Sch Math & Stat, Milton Keynes MK7 6AA, Bucks, England

[38] Fudan Univ, Minist Educ, Key Lab Contemporary Anthropol, Shanghai, Peoples R China

[39] Fudan Univ, Sch Life Sci, Collaborat Innovat Ctr Genet & Dev, Shanghai, Peoples R China

[40] Fudan Univ, Human Phenome Inst, Shanghai, Peoples R China

来源：

SCIENCE ADVANCES | 2021年 / 7卷 / 06期

基金：

中国国家自然科学基金; 英国生物技术与生命科学研究理事会;

关键词：

Morphology;

D O I：

10.1126/sciadv.abc6160

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

To characterize the genetic basis of facial features in Latin Americans, we performed a genome-wide association study (GWAS) of more than 6000 individuals using 59 landmark-based measurements from two-dimensional profile photographs and similar to 9,000,000 genotyped or imputed single-nucleotide polymorphisms. We detected significant association of 32 traits with at least 1 (and up to 6) of 32 different genomic regions, more than doubling the number of robustly associated face morphology loci reported until now (from 11 to 23). These GWAS hits are strongly enriched in regulatory sequences active specifically during craniofacial development. The associated region in 1p12 includes a tract of archaic adaptive introgression, with a Denisovan haplotype common in Native Americans affecting particularly lip thickness. Among the nine previously unidentified face morphology loci we identified is the VPS13B gene region, and we show that variants in this region also affect midfacial morphology in mice.

引用

页数：18

共 79 条

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← 1 2 3 4 5 6 7 8 →

共 79 条

[1] A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia [J].

Adhikari, Kaustubh ;

Mendoza-Revilla, Javier ;

Sohail, Anood ;

Fuentes-Guajardo, Macarena ;

Lampert, Jodie ;

Chacon-Duque, Juan Camilo ;

Hurtado, Malena ;

Villegas, Valeria ;

Granja, Vanessa ;

Acuna-Alonzo, Victor ;

Jaramillo, Claudia ;

Arias, William ;

Barquera Lozano, Rodrigo ;

Everardo, Paola ;

Gomez-Valdes, Jorge ;

Villamil-Ramirez, Hugo ;

Silva de Cerqueira, Caio C. ;

Hunemeier, Tabita ;

Ramallo, Virginia ;

Schuler-Faccini, Lavinia ;

Salzano, Francisco M. ;

Gonzalez-Jose, Rolando ;

Bortolini, Maria-Catira ;

Canizales-Quinteros, Samuel ;

Gallo, Carla ;

Poletti, Giovanni ;

Bedoya, Gabriel ;

Rothhammer, Francisco ;

Tobin, Desmond J. ;

Fumagalli, Matteo ;

Balding, David ;

Ruiz-Linares, Andres .

NATURE COMMUNICATIONS, 2019, 10 (1)

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Adhikari, Kaustubh ;

Fuentes-Guajardo, Macarena ;

Quinto-Sanchez, Mirsha ;

Mendoza-Revilla, Javier ;

Chacon-Duque, Juan Camilo ;

Acuna-Alonzo, Victor ;

Jaramillo, Claudia ;

Arias, William ;

Barquera Lozano, Rodrigo ;

Macin Perez, Gaston ;

Gomez-Valdes, Jorge ;

Villamil-Ramirez, Hugo ;

Hunemeier, Tabita ;

Ramallo, Virginia ;

Silva de Cerqueira, Caio C. ;

Hurtado, Malena ;

Villegas, Valeria ;

Granja, Vanessa ;

Gallo, Carla ;

Poletti, Giovanni ;

Schuler-Faccini, Lavinia ;

Salzano, Francisco M. ;

Bortolini, Maria-Catira ;

Canizales-Quinteros, Samuel ;

Cheeseman, Michael ;

Rosique, Javier ;

Bedoya, Gabriel ;

Rothhammer, Francisco ;

Headon, Denis ;

Gonzalez-Jose, Rolando ;

Balding, David ;

Ruiz-Linares, Andres .

NATURE COMMUNICATIONS, 2016, 7

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Fontanil, Tania ;

Cal, Santiago ;

Mendoza-Revilla, Javier ;

Fuentes-Guajardo, Macarena ;

Chacon-Duque, Juan-Camilo ;

Al-Saadi, Farah ;

Johansson, Jeanette A. ;

Quinto-Sanchez, Mirsha ;

Acuna-Alonzo, Victor ;

Jaramillo, Claudia ;

Arias, William ;

Barquera Lozano, Rodrigo ;

Macin Perez, Gaston ;

Gomez-Valdes, Jorge ;

Villamil-Ramirez, Hugo ;

Hunemeier, Tabita ;

Ramallo, Virginia ;

Silva de Cerqueira, Caio C. ;

Hurtado, Malena ;

Villegas, Valeria ;

Granja, Vanessa ;

Gallo, Carla ;

Poletti, Giovanni ;

Schuler-Faccini, Lavinia ;

Salzano, Francisco M. ;

Bortolini, Maria-Catira ;

Canizales-Quinteros, Samuel ;

Rothhammer, Francisco ;

Bedoya, Gabriel ;

Gonzalez-Jose, Rolando ;

Headon, Denis ;

Lopez-Otin, Carlos ;

Tobin, Desmond J. ;

Balding, David ;

Ruiz-Linares, Andres .

NATURE COMMUNICATIONS, 2016, 7

[4] A genome-wide association study identifies multiple loci for variation in human ear morphology [J].

Adhikari, Kaustubh ;

Reales, Guillermo ;

Smith, Andrew J. P. ;

Konka, Esra ;

Palmen, Jutta ;

Quinto-Sanchez, Mirsha ;

Acuna-Alonzo, Victor ;

Jaramillo, Claudia ;

Arias, William ;

Fuentes, Macarena ;

Pizarro, Maria ;

Barquera Lozano, Rodrigo ;

Macin Perez, Gaston ;

Gomez-Valdes, Jorge ;

Villamil-Ramirez, Hugo ;

Hunemeier, Tabita ;

Ramallo, Virginia ;

Silva de Cerqueira, Caio C. ;

Hurtado, Malena ;

Villegas, Valeria ;

Granja, Vanessa ;

Gallo, Carla ;

Poletti, Giovanni ;

Schuler-Faccini, Lavinia ;

Salzano, Francisco M. ;

Bortolini, Maria-Catira ;

Canizales-Quinteros, Samuel ;

Rothhammer, Francisco ;

Bedoya, Gabriel ;

Calderon, Rosario ;

Rosique, Javier ;

Cheeseman, Michael ;

Bhutta, Mahmood F. ;

Humphries, Steve E. ;

Gonzalez-Jose, Rolando ;

Headon, Denis ;

Balding, David ;

Ruiz-Linares, Andres .

NATURE COMMUNICATIONS, 2015, 6

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Alexander, David H. ;

Novembre, John ;

Lange, Kenneth .

GENOME RESEARCH, 2009, 19 (09) :1655-1664

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Altshuler, David M. ;

Durbin, Richard M. ;

Abecasis, Goncalo R. ;

Bentley, David R. ;

Chakravarti, Aravinda ;

Clark, Andrew G. ;

Donnelly, Peter ;

Eichler, Evan E. ;

Flicek, Paul ;

Gabriel, Stacey B. ;

Gibbs, Richard A. ;

Green, Eric D. ;

Hurles, Matthew E. ;

Knoppers, Bartha M. ;

Korbel, Jan O. ;

Lander, Eric S. ;

Lee, Charles ;

Lehrach, Hans ;

Mardis, Elaine R. ;

Marth, Gabor T. ;

McVean, Gil A. ;

Nickerson, Deborah A. ;

Wang, Jun ;

Wilson, Richard K. ;

Boerwinkle, Eric ;

Doddapaneni, Harsha ;

Han, Yi ;

Korchina, Viktoriya ;

Kovar, Christie ;

Lee, Sandra ;

Muzny, Donna ;

Reid, Jeffrey G. ;

Zhu, Yiming ;

Chang, Yuqi ;

Feng, Qiang ;

Fang, Xiaodong ;

Guo, Xiaosen ;

Jian, Min ;

Jiang, Hui ;

Jin, Xin ;

Lan, Tianming ;

Li, Guoqing ;

Li, Jingxiang ;

Li, Yingrui ;

Liu, Shengmao ;

Liu, Xiao ;

Lu, Yao ;

Ma, Xuedi ;

Tang, Meifang ;

Wang, Bo .

NATURE, 2015, 526 (7571) :68-+

[7] A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4 [J].

Beaty, Terri H. ;

Murray, Jeffrey C. ;

Marazita, Mary L. ;

Munger, Ronald G. ;

Ruczinski, Ingo ;

Hetmanski, Jacqueline B. ;

Liang, Kung Yee ;

Wu, Tao ;

Murray, Tanda ;

Fallin, M. Daniele ;

Redett, Richard A. ;

Raymond, Gerald ;

Schwender, Holger ;

Jin, Sheng-Chih ;

Cooper, Margaret E. ;

Dunnwald, Martine ;

Mansilla, Maria A. ;

Leslie, Elizabeth ;

Bullard, Stephen ;

Lidral, Andrew C. ;

Moreno, Lina M. ;

Menezes, Renato ;

Vieira, Alexandre R. ;

Petrin, Aline ;

Wilcox, Allen J. ;

Lie, Rolv T. ;

Jabs, Ethylin W. ;

Wu-Chou, Yah Huei ;

Chen, Philip K. ;

Wang, Hong ;

Ye, Xiaoqian ;

Huang, Shangzhi ;

Yeow, Vincent ;

Chong, Samuel S. ;

Jee, Sun Ha ;

Shi, Bing ;

Christensen, Kaare ;

Melbye, Mads ;

Doheny, Kimberly F. ;

Pugh, Elizabeth W. ;

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