Literature DB >> 29459680

Genome-wide mapping of global-to-local genetic effects on human facial shape.

Peter Claes1,2,3, Jasmien Roosenboom4, Julie D White5, Tomek Swigut6, Dzemila Sero7,8, Jiarui Li7,8, Myoung Keun Lee4, Arslan Zaidi5, Brooke C Mattern5, Corey Liebowitz5, Laurel Pearson5, Tomás González5, Elizabeth J Leslie4, Jenna C Carlson9, Ekaterina Orlova10, Paul Suetens7,8, Dirk Vandermeulen7,8, Eleanor Feingold9,10, Mary L Marazita4,10, John R Shaffer10, Joanna Wysocka11,12, Mark D Shriver13, Seth M Weinberg14,15.   

Abstract

Genome-wide association scans of complex multipartite traits like the human face typically use preselected phenotypic measures. Here we report a data-driven approach to phenotyping facial shape at multiple levels of organization, allowing for an open-ended description of facial variation while preserving statistical power. In a sample of 2,329 persons of European ancestry, we identified 38 loci, 15 of which replicated in an independent European sample (n = 1,719). Four loci were completely new. For the others, additional support (n = 9) or pleiotropic effects (n = 2) were found in the literature, but the results reported here were further refined. All 15 replicated loci highlighted distinctive patterns of global-to-local genetic effects on facial shape and showed enrichment for active chromatin elements in human cranial neural crest cells, suggesting an early developmental origin of the facial variation captured. These results have implications for studies of facial genetics and other complex morphological traits.

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Mesh:

Year:  2018        PMID: 29459680      PMCID: PMC5937280          DOI: 10.1038/s41588-018-0057-4

Source DB:  PubMed          Journal:  Nat Genet        ISSN: 1061-4036            Impact factor:   38.330


  49 in total

1.  GREAT improves functional interpretation of cis-regulatory regions.

Authors:  Cory Y McLean; Dave Bristor; Michael Hiller; Shoa L Clarke; Bruce T Schaar; Craig B Lowe; Aaron M Wenger; Gill Bejerano
Journal:  Nat Biotechnol       Date:  2010-05-02       Impact factor: 54.908

2.  Genome-wide association study of three-dimensional facial morphology identifies a variant in PAX3 associated with nasion position.

Authors:  Lavinia Paternoster; Alexei I Zhurov; Arshed M Toma; John P Kemp; Beate St Pourcain; Nicholas J Timpson; George McMahon; Wendy McArdle; Susan M Ring; George Davey Smith; Stephen Richmond; David M Evans
Journal:  Am J Hum Genet       Date:  2012-02-16       Impact factor: 11.025

3.  A genome-wide association study identifies five loci influencing facial morphology in Europeans.

Authors:  Fan Liu; Fedde van der Lijn; Claudia Schurmann; Gu Zhu; M Mallar Chakravarty; Pirro G Hysi; Andreas Wollstein; Oscar Lao; Marleen de Bruijne; M Arfan Ikram; Aad van der Lugt; Fernando Rivadeneira; André G Uitterlinden; Albert Hofman; Wiro J Niessen; Georg Homuth; Greig de Zubicaray; Katie L McMahon; Paul M Thompson; Amro Daboul; Ralf Puls; Katrin Hegenscheid; Liisa Bevan; Zdenka Pausova; Sarah E Medland; Grant W Montgomery; Margaret J Wright; Carol Wicking; Stefan Boehringer; Timothy D Spector; Tomáš Paus; Nicholas G Martin; Reiner Biffar; Manfred Kayser
Journal:  PLoS Genet       Date:  2012-09-13       Impact factor: 5.917

Review 4.  Exploring the Underlying Genetics of Craniofacial Morphology through Various Sources of Knowledge.

Authors:  Jasmien Roosenboom; Greet Hens; Brooke C Mattern; Mark D Shriver; Peter Claes
Journal:  Biomed Res Int       Date:  2016-12-08       Impact factor: 3.411

5.  Genome-wide association study of facial morphology reveals novel associations with FREM1 and PARK2.

Authors:  Myoung Keun Lee; John R Shaffer; Elizabeth J Leslie; Ekaterina Orlova; Jenna C Carlson; Eleanor Feingold; Mary L Marazita; Seth M Weinberg
Journal:  PLoS One       Date:  2017-04-25       Impact factor: 3.240

6.  An integrated map of genetic variation from 1,092 human genomes.

Authors:  Goncalo R Abecasis; Adam Auton; Lisa D Brooks; Mark A DePristo; Richard M Durbin; Robert E Handsaker; Hyun Min Kang; Gabor T Marth; Gil A McVean
Journal:  Nature       Date:  2012-11-01       Impact factor: 49.962

7.  Modeling 3D facial shape from DNA.

Authors:  Peter Claes; Denise K Liberton; Katleen Daniels; Kerri Matthes Rosana; Ellen E Quillen; Laurel N Pearson; Brian McEvoy; Marc Bauchet; Arslan A Zaidi; Wei Yao; Hua Tang; Gregory S Barsh; Devin M Absher; David A Puts; Jorge Rocha; Sandra Beleza; Rinaldo W Pereira; Gareth Baynam; Paul Suetens; Dirk Vandermeulen; Jennifer K Wagner; James S Boster; Mark D Shriver
Journal:  PLoS Genet       Date:  2014-03-20       Impact factor: 5.917

8.  A genome-wide association scan implicates DCHS2, RUNX2, GLI3, PAX1 and EDAR in human facial variation.

Authors:  Kaustubh Adhikari; Macarena Fuentes-Guajardo; Mirsha Quinto-Sánchez; Javier Mendoza-Revilla; Juan Camilo Chacón-Duque; Victor Acuña-Alonzo; Claudia Jaramillo; William Arias; Rodrigo Barquera Lozano; Gastón Macín Pérez; Jorge Gómez-Valdés; Hugo Villamil-Ramírez; Tábita Hunemeier; Virginia Ramallo; Caio C Silva de Cerqueira; Malena Hurtado; Valeria Villegas; Vanessa Granja; Carla Gallo; Giovanni Poletti; Lavinia Schuler-Faccini; Francisco M Salzano; Maria-Cátira Bortolini; Samuel Canizales-Quinteros; Michael Cheeseman; Javier Rosique; Gabriel Bedoya; Francisco Rothhammer; Denis Headon; Rolando González-José; David Balding; Andrés Ruiz-Linares
Journal:  Nat Commun       Date:  2016-05-19       Impact factor: 14.919

9.  Genomewide Association Study of African Children Identifies Association of SCHIP1 and PDE8A with Facial Size and Shape.

Authors:  Joanne B Cole; Mange Manyama; Emmanuel Kimwaga; Joshua Mathayo; Jacinda R Larson; Denise K Liberton; Ken Lukowiak; Tracey M Ferrara; Sheri L Riccardi; Mao Li; Washington Mio; Michaela Prochazkova; Trevor Williams; Hong Li; Kenneth L Jones; Ophir D Klein; Stephanie A Santorico; Benedikt Hallgrimsson; Richard A Spritz
Journal:  PLoS Genet       Date:  2016-08-25       Impact factor: 5.917

10.  Genome-Wide Association Study Reveals Multiple Loci Influencing Normal Human Facial Morphology.

Authors:  John R Shaffer; Ekaterina Orlova; Myoung Keun Lee; Elizabeth J Leslie; Zachary D Raffensperger; Carrie L Heike; Michael L Cunningham; Jacqueline T Hecht; Chung How Kau; Nichole L Nidey; Lina M Moreno; George L Wehby; Jeffrey C Murray; Cecelia A Laurie; Cathy C Laurie; Joanne Cole; Tracey Ferrara; Stephanie Santorico; Ophir Klein; Washington Mio; Eleanor Feingold; Benedikt Hallgrimsson; Richard A Spritz; Mary L Marazita; Seth M Weinberg
Journal:  PLoS Genet       Date:  2016-08-25       Impact factor: 5.917

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  59 in total

1.  Wavelet Screening identifies regions highly enriched for differentially methylated loci for orofacial clefts.

Authors:  William R P Denault; Julia Romanowska; Øystein A Haaland; Robert Lyle; Jack A Taylor; Zongli Xu; Rolv T Lie; Håkon K Gjessing; Astanand Jugessur
Journal:  NAR Genom Bioinform       Date:  2021-05-03

2.  EDAR, LYPLAL1, PRDM16, PAX3, DKK1, TNFSF12, CACNA2D3, and SUPT3H gene variants influence facial morphology in a Eurasian population.

Authors:  Yi Li; Wenting Zhao; Dan Li; Xianming Tao; Ziyi Xiong; Jing Liu; Wei Zhang; Anquan Ji; Kun Tang; Fan Liu; Caixia Li
Journal:  Hum Genet       Date:  2019-04-25       Impact factor: 4.132

Review 3.  Genetic factors contributing to skeletal class III malocclusion: a systematic review and meta-analysis.

Authors:  Alexandra Dehesa-Santos; Paula Iber-Diaz; Alejandro Iglesias-Linares
Journal:  Clin Oral Investig       Date:  2021-02-07       Impact factor: 3.573

4.  Temporomandibular Joint Condyle-Disc Morphometric Sexual Dimorphisms Independent of Skull Scaling.

Authors:  Matthew C Coombs; Xin She; Truman R Brown; Elizabeth H Slate; Janice S Lee; Hai Yao
Journal:  J Oral Maxillofac Surg       Date:  2019-04-25       Impact factor: 1.895

Review 5.  FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research.

Authors:  Bridget D Samuels; Robert Aho; James F Brinkley; Alejandro Bugacov; Eleanor Feingold; Shannon Fisher; Ana S Gonzalez-Reiche; Joseph G Hacia; Benedikt Hallgrimsson; Karissa Hansen; Matthew P Harris; Thach-Vu Ho; Greg Holmes; Joan E Hooper; Ethylin Wang Jabs; Kenneth L Jones; Carl Kesselman; Ophir D Klein; Elizabeth J Leslie; Hong Li; Eric C Liao; Hannah Long; Na Lu; Richard L Maas; Mary L Marazita; Jaaved Mohammed; Sara Prescott; Robert Schuler; Licia Selleri; Richard A Spritz; Tomek Swigut; Harm van Bakel; Axel Visel; Ian Welsh; Cristina Williams; Trevor J Williams; Joanna Wysocka; Yuan Yuan; Yang Chai
Journal:  Development       Date:  2020-09-21       Impact factor: 6.868

6.  The Era of the Genome and Dental Medicine.

Authors:  K Divaris
Journal:  J Dent Res       Date:  2019-08       Impact factor: 6.116

Review 7.  Hunting for genes that shape human faces: Initial successes and challenges for the future.

Authors:  Seth M Weinberg; Jasmien Roosenboom; John R Shaffer; Mark D Shriver; Joanna Wysocka; Peter Claes
Journal:  Orthod Craniofac Res       Date:  2019-05       Impact factor: 1.826

8.  Differential DNA methylation of vocal and facial anatomy genes in modern humans.

Authors:  David Gokhman; Malka Nissim-Rafinia; Lily Agranat-Tamir; Genevieve Housman; Raquel García-Pérez; Esther Lizano; Olivia Cheronet; Swapan Mallick; Maria A Nieves-Colón; Heng Li; Songül Alpaslan-Roodenberg; Mario Novak; Hongcang Gu; Jason M Osinski; Manuel Ferrando-Bernal; Pere Gelabert; Iddi Lipende; Deus Mjungu; Ivanela Kondova; Ronald Bontrop; Ottmar Kullmer; Gerhard Weber; Tal Shahar; Mona Dvir-Ginzberg; Marina Faerman; Ellen E Quillen; Alexander Meissner; Yonatan Lahav; Leonid Kandel; Meir Liebergall; María E Prada; Julio M Vidal; Richard M Gronostajski; Anne C Stone; Benjamin Yakir; Carles Lalueza-Fox; Ron Pinhasi; David Reich; Tomas Marques-Bonet; Eran Meshorer; Liran Carmel
Journal:  Nat Commun       Date:  2020-03-04       Impact factor: 14.919

9.  The effect of automated landmark identification on morphometric analyses.

Authors:  Christopher J Percival; Jay Devine; Benjamin C Darwin; Wei Liu; Matthijs van Eede; R Mark Henkelman; Benedikt Hallgrimsson
Journal:  J Anat       Date:  2019-03-22       Impact factor: 2.610

10.  An exploration of adolescent facial shape changes with age via multilevel partial least squares regression.

Authors:  D J J Farnell; S Richmond; J Galloway; A I Zhurov; P Pirttiniemi; T Heikkinen; V Harila; H Matthews; P Claes
Journal:  Comput Methods Programs Biomed       Date:  2021-01-08       Impact factor: 5.428

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