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

Bonfante, Betty; Faux, Pierre; Navarro, Nicolas; Mendoza-Revilla, Javier; Dubied, Morgane; Montillot, Charlotte; Wentworth, Emma; Poloni, Lauriane; Varón-González, Ceferino; Jones, Philip; Xiong, Ziyi; Fuentes-Guajardo, Macarena; Palmal, Sagnik; Chacón-Duque, Juan Camilo; Hurtado, Malena; Villegas, Valeria; Granja, Vanessa; Jaramillo, Claudia; Arias, William; Barquera, Rodrigo; Everardo-Martínez, Paola; Sánchez-Quinto, Mirsha; Gómez-Valdés, Jorge; Villamil-Ramírez, Hugo; Silva de Cerqueira, Caio C.; Hünemeier, Tábita; Ramallo, Virginia; Liu, Fan; Weinberg, Seth M.; Shaffer, John R.; Stergiakouli, Evie; Howe, Laurence J.; Hysi, Pirro G.; Spector, Timothy D.; Gonzalez-José, Rolando; Schüler-Faccini, Lavinia; Bortolini, Maria-Cátira; Acuña-Alonzo, Victor; Canizales-Quinteros, Samuel; Gallo, Carla; Poletti, Giovanni; Bedoya, Gabriel; Rothhammer, Francisco; Thauvin-Robinet, Christel; Faivre, Laurence; Costedoat, Caroline; Balding, David; Cox, Timothy; Kayser, Manfred; Duplomb, Laurence; Yalcin, Binnaz; Cotney, Justin; Adhikari, Kaustubh and Ruiz-Linares, Andrés (2021). A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation. Science Advances, 7(6), article no. eabc6160.

DOI: https://doi.org/10.1126/sciadv.abc6160

Abstract

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 ~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.