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Yuan M, Goovaerts S, Vanneste M, Matthews H, Hoskens H, Richmond S, Klein OD, Spritz RA, Hallgrimsson B, Walsh S, Shriver MD, Shaffer JR, Weinberg SM, Peeters H, Claes P. Mapping genes for human face shape: exploration of univariate phenotyping strategies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597731. [PMID: 38895298 PMCID: PMC11185724 DOI: 10.1101/2024.06.06.597731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Human facial shape, while strongly heritable, involves both genetic and structural complexity, necessitating precise phenotyping for accurate assessment. Common phenotyping strategies include simplifying 3D facial features into univariate traits such as anthropometric measurements (e.g., inter-landmark distances), unsupervised dimensionality reductions (e.g., principal component analysis (PCA) and auto-encoder (AE) approaches), and assessing resemblance to particular facial gestalts (e.g., syndromic facial archetypes). This study provides a comparative assessment of these strategies in genome-wide association studies (GWASs) of 3D facial shape. Specifically, we investigated inter-landmark distances, PCA and AE-derived latent dimensions, and facial resemblance to random, extreme, and syndromic gestalts within a GWAS of 8,426 individuals of recent European ancestry. Inter-landmark distances exhibit the highest SNP-based heritability as estimated via LD score regression, followed by AE dimensions. Conversely, resemblance scores to extreme and syndromic facial gestalts display the lowest heritability, in line with expectations. Notably, the aggregation of multiple GWASs on facial resemblance to random gestalts reveals the highest number of independent genetic loci. This novel, easy-to-implement phenotyping approach holds significant promise for capturing genetically relevant morphological traits derived from complex biomedical imaging datasets, and its applications extend beyond faces. Nevertheless, these different phenotyping strategies capture different genetic influences on craniofacial shape. Thus, it remains valuable to explore these strategies individually and in combination to gain a more comprehensive understanding of the genetic factors underlying craniofacial shape and related traits. Author Summary Advancements linking variation in the human genome to phenotypes have rapidly evolved in recent decades and have revealed that most human traits are influenced by genetic variants to at least some degree. While many traits, such as stature, are straightforward to acquire and investigate, the multivariate and multipartite nature of facial shape makes quantification more challenging. In this study, we compared the impact of different facial phenotyping approaches on gene mapping outcomes. Our findings suggest that the choice of facial phenotyping method has an impact on apparent trait heritability and the ability to detect genetic association signals. These results offer valuable insights into the importance of phenotyping in genetic investigations, especially when dealing with highly complex morphological traits.
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Wisetchat S, Stevens KA, Frost SR. Facial modeling and measurement based upon homologous topographical features. PLoS One 2024; 19:e0304561. [PMID: 38820264 PMCID: PMC11142440 DOI: 10.1371/journal.pone.0304561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 05/13/2024] [Indexed: 06/02/2024] Open
Abstract
Measurement of human faces is fundamental to many applications from recognition to genetic phenotyping. While anthropometric landmarks provide a conventional set of homologous measurement points, digital scans are increasingly used for facial measurement, despite the difficulties in establishing their homology. We introduce an alternative basis for facial measurement, which 1) provides a richer information density than discrete point measurements, 2) derives its homology from shared facial topography (ridges, folds, etc.), and 3) quantifies local morphological variation following the conventions and practices of anatomical description. A parametric model that permits matching a broad range of facial variation by the adjustment of 71 parameters is demonstrated by modeling a sample of 80 adult human faces. The surface of the parametric model can be adjusted to match each photogrammetric surface mesh generally to within 1 mm, demonstrating a novel and efficient means for facial shape encoding. We examine how well this scheme quantifies facial shape and variation with respect to geographic ancestry and sex. We compare this analysis with a more conventional, landmark-based geometric morphometric (GMM) study with 43 landmarks placed on the same set of scans. Our multivariate statistical analysis using the 71 attribute values separates geographic ancestry groups and sexes with a high degree of reliability, and these results are broadly similar to those from GMM, but with some key differences that we discuss. This approach is compared with conventional, non-parametric methods for the quantification of facial shape, including generality, information density, and the separation of size and shape. Potential uses for phenotypic and dysmorphology studies are also discussed.
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Affiliation(s)
- Sawitree Wisetchat
- Department of Anthropology, University of Oregon, Eugene, Oregon, United States of America
| | - Kent A. Stevens
- Department of Computer and Information Science, University of Oregon, Eugene, Oregon, United States of America
| | - Stephen R. Frost
- Department of Anthropology, University of Oregon, Eugene, Oregon, United States of America
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Qiao H, Tan J, Yan J, Sun C, Yin X, Li Z, Wu J, Guan H, Wen S, Zhang M, Xu S, Jin L. A comprehensive evaluation of the phenotype-first and data-driven approaches in analyzing facial morphological traits. iScience 2024; 27:109325. [PMID: 38487017 PMCID: PMC10937830 DOI: 10.1016/j.isci.2024.109325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/17/2024] [Accepted: 02/20/2024] [Indexed: 03/17/2024] Open
Abstract
The phenotype-first approach (PFA) and data-driven approach (DDA) have both greatly facilitated anthropological studies and the mapping of trait-associated genes. However, the pros and cons of the two approaches are poorly understood. Here, we systematically evaluated the two approaches and analyzed 14,838 facial traits in 2,379 Han Chinese individuals. Interestingly, the PFA explained more facial variation than the DDA in the top 100 and 1,000 except in the top 10 phenotypes. Accordingly, the ratio of heterogeneous traits extracted from the PFA was much greater, while more homogenous traits were found using the DDA for different sex, age, and BMI groups. Notably, our results demonstrated that the sex factor accounted for 30% of phenotypic variation in all traits extracted. Furthermore, we linked DDA phenotypes to PFA phenotypes with explicit biological explanations. These findings provide new insights into the analysis of multidimensional phenotypes and expand the understanding of phenotyping approaches.
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Affiliation(s)
- Hui Qiao
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Sciences, Fudan University, Shanghai 200438, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201203, China
| | - Jingze Tan
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Sciences, Fudan University, Shanghai 200438, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201203, China
| | - Jun Yan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201203, China
| | - Chang Sun
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201203, China
| | - Xing Yin
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201203, China
| | - Zijun Li
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201203, China
| | - Jiazi Wu
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201203, China
| | - Haijuan Guan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201203, China
| | - Shaoqing Wen
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Menghan Zhang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201203, China
- Institute of Modern Languages and Linguistics, Fudan University, Shanghai 200433, China
- Research Institute of Intelligent Complex Systems, Fudan University, Shanghai 200433, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Sciences, Fudan University, Shanghai 200438, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Sciences, Fudan University, Shanghai 200438, China
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Singh H, Shipra, Gupta M, Gupta N, Gupta G, Pandita AK, Sharma R, Pandita S, Singh V, Garg B, Rai E, Sharma S. SOX9 gene shows association with adolescent idiopathic scoliosis predisposition in Northwest Indians. Eur J Med Res 2024; 29:66. [PMID: 38245767 PMCID: PMC10799485 DOI: 10.1186/s40001-024-01635-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 01/02/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Adolescent idiopathic scoliosis (AIS) is a common structural deformity of the spine affecting adolescent individuals globally. The disorder is polygenic and is accompanied by the association of various genetic loci. Genetic studies in Chinese and Japanese populations have shown the association of genetic variants of SOX9 with AIS curve severity. However, no genetic study evaluating the association of SRY-Box Transcription Factor 9 (SOX9) variants with AIS predisposition has been conducted in any Indian population. Thus, we aimed to investigate the association of the genetic variants of the SOX9 along with 0.88 Mb upstream region with AIS susceptibility in the population of Northwest India. METHODS In total, 113 AIS cases and 500 non-AIS controls were recruited from the population of Northwest India in the study and screened for 155 genetic variants across the SOX9 gene and 0.88 Mb upstream region of the gene using Global Screening Array-24 v3.0 chip (Illumina). The statistical significance of the Bonferroni threshold was set at 0.000322. RESULT The results showed the association of 11 newly identified variants; rs9302936, rs7210997, rs77736349, rs12940821, rs9302937, rs77447012, rs8071904, rs74898711, rs9900249, rs2430514, and rs1042667 with the AIS susceptibility in the studied population. Only one variant, rs2430514, was inversely associated with AIS in the population, while the ten variants were associated with the AIS risk. Moreover, 47 variants clustered in the gene desert region of the SOX9 gene were associated at a p-value ≤ 0.05. CONCLUSION The present study is the first to demonstrate the association of SOX9 enhancer locus variants with AIS in any South Asian Indian population. The results are interesting as rs1042667, a 3' untranslated region (UTR) variant in the exon 3 and upstream variants of the SOX9 gene, were associated with AIS susceptibility in the Northwest Indian population. This provides evidence that the variants in the enhancer region of SOX9 might regulate its gene expression, thus leading to AIS pathology and might act as an important gene for AIS susceptibility.
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Affiliation(s)
- Hemender Singh
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Shipra
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Manish Gupta
- Department of Orthopaedics, All India Institute of Medical Sciences, New Delhi, India
| | - Nital Gupta
- District Hospital Poonch, Poonch, Jammu and Kashmir, India
| | - Geetanjali Gupta
- Department of Radiology, Shri Mata Vaishno Devi Narayana Superspeciality Hospital, Katra, Jammu and Kashmir, India
| | - Ajay K Pandita
- Accidental Hospital, Chowki Choura, Jammu, Jammu and Kashmir, India
| | - Rajesh Sharma
- Government Medical College, Jammu, Jammu and Kashmir, India
| | - Sarla Pandita
- Chest Disease Hospital, Bakshi Nagar, Jammu, Jammu and Kashmir, India
| | - Vinod Singh
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Bhavuk Garg
- Department of Orthopaedics, All India Institute of Medical Sciences, New Delhi, India
| | - Ekta Rai
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India.
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
| | - Swarkar Sharma
- Human Genetics Research Lab, Centre for Molecular Biology, Central University of Jammu, Jammu, India.
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Li Y, Xiong Z, Zhang M, Hysi PG, Qian Y, Adhikari K, Weng J, Wu S, Du S, Gonzalez-Jose R, Schuler-Faccini L, Bortolini MC, Acuna-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Wang J, Tan J, Yuan Z, Jin L, Uitterlinden AG, Ghanbari M, Ikram MA, Nijsten T, Zhu X, Lei Z, Jia P, Ruiz-Linares A, Spector TD, Wang S, Kayser M, Liu F. Combined genome-wide association study of 136 quantitative ear morphology traits in multiple populations reveal 8 novel loci. PLoS Genet 2023; 19:e1010786. [PMID: 37459304 PMCID: PMC10351707 DOI: 10.1371/journal.pgen.1010786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 05/16/2023] [Indexed: 07/20/2023] Open
Abstract
Human ear morphology, a complex anatomical structure represented by a multidimensional set of correlated and heritable phenotypes, has a poorly understood genetic architecture. In this study, we quantitatively assessed 136 ear morphology traits using deep learning analysis of digital face images in 14,921 individuals from five different cohorts in Europe, Asia, and Latin America. Through GWAS meta-analysis and C-GWASs, a recently introduced method to effectively combine GWASs of many traits, we identified 16 genetic loci involved in various ear phenotypes, eight of which have not been previously associated with human ear features. Our findings suggest that ear morphology shares genetic determinants with other surface ectoderm-derived traits such as facial variation, mono eyebrow, and male pattern baldness. Our results enhance the genetic understanding of human ear morphology and shed light on the shared genetic contributors of different surface ectoderm-derived phenotypes. Additionally, gene editing experiments in mice have demonstrated that knocking out the newly ear-associated gene (Intu) and a previously ear-associated gene (Tbx15) causes deviating mouse ear morphology.
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Affiliation(s)
- Yi Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China
| | - Ziyi Xiong
- Department of Genetic Identification, Erasmus MC, University Medical Center, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center, the Netherlands
| | - Manfei Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, China
| | - Pirro G. Hysi
- Department of Twin Research and Genetic Epidemiology, King’s College London, United Kingdom
| | - Yu Qian
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China
- Beijing No.8 High School, Beijing, China
| | - Kaustubh Adhikari
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, United Kingdom
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, United Kingdom
| | - Jun Weng
- Center for Biometrics and Security Research & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, China
| | - Sijie Wu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
| | - Siyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- University of Chinese Academy of Sciences, China
| | - Rolando Gonzalez-Jose
- Instituto Patagonico de Ciencias Sociales y Humanas, Centro Nacional Patagonico, CONICET, Argentina
| | | | | | - Victor Acuna-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Quimica, UNAM-Instituto Nacional de Medicina Genomica, Mexico
| | - Carla Gallo
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Peru
| | - Giovanni Poletti
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Peru
| | - Gabriel Bedoya
- GENMOL (Genetica Molecular), Universidad de Antioquia, Medellin, Colombia
| | | | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
| | - Jingze Tan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
| | - Ziyu Yuan
- Fudan-Taizhou Institute of Health Sciences, China
| | - Li Jin
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
- Fudan-Taizhou Institute of Health Sciences, China
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center, the Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, University Medical Center, the Netherlands
| | - M. Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center, the Netherlands
| | - Tamar Nijsten
- Department of Dermatology, Erasmus MC, University Medical Center, the Netherlands
| | - Xiangyu Zhu
- Center for Biometrics and Security Research & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, China
| | - Zhen Lei
- Center for Biometrics and Security Research & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, China
| | - Peilin Jia
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China
| | - Andres Ruiz-Linares
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, United Kingdom
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
- Aix-Marseille Universite, CNRS, EFS, ADES, France
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, United Kingdom
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, China
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center, the Netherlands
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China
- Department of Genetic Identification, Erasmus MC, University Medical Center, the Netherlands
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Li Q, Chen J, Faux P, Delgado ME, Bonfante B, Fuentes-Guajardo M, Mendoza-Revilla J, Chacón-Duque JC, Hurtado M, Villegas V, Granja V, Jaramillo C, Arias W, Barquera R, Everardo-Martínez P, Sánchez-Quinto M, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Hünemeier T, Ramallo V, Wu S, Du S, Giardina A, Paria SS, Khokan MR, Gonzalez-José R, Schüler-Faccini L, Bortolini MC, Acuña-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Rojas W, Rothhammer F, Navarro N, Wang S, Adhikari K, Ruiz-Linares A. Automatic landmarking identifies new loci associated with face morphology and implicates Neanderthal introgression in human nasal shape. Commun Biol 2023; 6:481. [PMID: 37156940 PMCID: PMC10167347 DOI: 10.1038/s42003-023-04838-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/12/2023] [Indexed: 05/10/2023] Open
Abstract
We report a genome-wide association study of facial features in >6000 Latin Americans based on automatic landmarking of 2D portraits and testing for association with inter-landmark distances. We detected significant associations (P-value <5 × 10-8) at 42 genome regions, nine of which have been previously reported. In follow-up analyses, 26 of the 33 novel regions replicate in East Asians, Europeans, or Africans, and one mouse homologous region influences craniofacial morphology in mice. The novel region in 1q32.3 shows introgression from Neanderthals and we find that the introgressed tract increases nasal height (consistent with the differentiation between Neanderthals and modern humans). Novel regions include candidate genes and genome regulatory elements previously implicated in craniofacial development, and show preferential transcription in cranial neural crest cells. The automated approach used here should simplify the collection of large study samples from across the world, facilitating a cosmopolitan characterization of the genetics of facial features.
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Affiliation(s)
- Qing Li
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, 200438, China
| | - Jieyi Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, 200438, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Pierre Faux
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille, 13005, France
| | - Miguel Eduardo Delgado
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, 200438, China
- División Antropología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, República Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET, Buenos Aires, República Argentina
| | - Betty Bonfante
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille, 13005, France
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, 1000000, Chile
| | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
- Unit of Human Evolutionary Genetics, Institut Pasteur, Paris, 75015, France
| | - J Camilo Chacón-Duque
- Division of Vertebrates and Anthropology, Department of Earth Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, Mexico, 6600, Mexico
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, 07745, Germany
| | - Paola Everardo-Martínez
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, Mexico, 6600, Mexico
| | - Mirsha Sánchez-Quinto
- Forensic Science, Faculty of Medicine, UNAM (Universidad Nacional Autónoma de México), Mexico City, 06320, Mexico
| | - Jorge Gómez-Valdés
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, Mexico, 6600, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, 4510, Mexico
| | | | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508-090, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90040-060, Brazil
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn, U9129ACD, Argentina
| | - Sijie Wu
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, 200438, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Siyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Andrea Giardina
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, United Kingdom
| | - Soumya Subhra Paria
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, United Kingdom
| | - Mahfuzur Rahman Khokan
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, United Kingdom
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn, U9129ACD, Argentina
| | - Lavinia Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90040-060, Brazil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90040-060, Brazil
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, Mexico, 6600, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, 4510, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Winston Rojas
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Arica, 1000000, Chile
| | - Nicolas Navarro
- Biogéosciences, UMR 6282 CNRS, Université de Bourgogne, Dijon, 21000, France
- EPHE, PSL University, Paris, 75014, France
| | - Sijia Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, 200438, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, United Kingdom.
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, 200438, China.
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille, 13005, France.
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
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7
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Advancement in Human Face Prediction Using DNA. Genes (Basel) 2023; 14:genes14010136. [PMID: 36672878 PMCID: PMC9858985 DOI: 10.3390/genes14010136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 01/05/2023] Open
Abstract
The rapid improvements in identifying the genetic factors contributing to facial morphology have enabled the early identification of craniofacial syndromes. Similarly, this technology can be vital in forensic cases involving human identification from biological traces or human remains, especially when reference samples are not available in the deoxyribose nucleic acid (DNA) database. This review summarizes the currently used methods for predicting human phenotypes such as age, ancestry, pigmentation, and facial features based on genetic variations. To identify the facial features affected by DNA, various two-dimensional (2D)- and three-dimensional (3D)-scanning techniques and analysis tools are reviewed. A comparison between the scanning technologies is also presented in this review. Face-landmarking techniques and face-phenotyping algorithms are discussed in chronological order. Then, the latest approaches in genetic to 3D face shape analysis are emphasized. A systematic review of the current markers that passed the threshold of a genome-wide association (GWAS) of single nucleotide polymorphism (SNP)-face traits from the GWAS Catalog is also provided using the preferred reporting items for systematic reviews and meta-analyses (PRISMA), approach. Finally, the current challenges in forensic DNA phenotyping are analyzed and discussed.
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8
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Xiong Z, Gao X, Chen Y, Feng Z, Pan S, Lu H, Uitterlinden AG, Nijsten T, Ikram A, Rivadeneira F, Ghanbari M, Wang Y, Kayser M, Liu F. Combining genome-wide association studies highlight novel loci involved in human facial variation. Nat Commun 2022; 13:7832. [PMID: 36539420 PMCID: PMC9767941 DOI: 10.1038/s41467-022-35328-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Standard genome-wide association studies (GWASs) rely on analyzing a single trait at a time. However, many human phenotypes are complex and composed by multiple correlated traits. Here we introduce C-GWAS, a method for combining GWAS summary statistics of multiple potentially correlated traits. Extensive computer simulations demonstrated increased statistical power of C-GWAS compared to the minimal p-values of multiple single-trait GWASs (MinGWAS) and the current state-of-the-art method for combining single-trait GWASs (MTAG). Applying C-GWAS to a meta-analysis dataset of 78 single trait facial GWASs from 10,115 Europeans identified 56 study-wide suggestively significant loci with multi-trait effects on facial morphology of which 17 are novel loci. Using data from additional 13,622 European and Asian samples, 46 (82%) loci, including 9 (53%) novel loci, were replicated at nominal significance with consistent allele effects. Functional analyses further strengthen the reliability of our C-GWAS findings. Our study introduces the C-GWAS method and makes it available as computationally efficient open-source R package for widespread future use. Our work also provides insights into the genetic architecture of human facial appearance.
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Affiliation(s)
- Ziyi Xiong
- grid.5645.2000000040459992XDepartment of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands ,grid.5645.2000000040459992XDepartment of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Xingjian Gao
- grid.9227.e0000000119573309CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China ,grid.440259.e0000 0001 0115 7868National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing, Jiangsu China
| | - Yan Chen
- grid.5645.2000000040459992XDepartment of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands ,grid.9227.e0000000119573309CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zhanying Feng
- grid.9227.e0000000119573309CEMS, NCMIS, HCMS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
| | - Siyu Pan
- grid.9227.e0000000119573309CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Haojie Lu
- grid.5645.2000000040459992XDepartment of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands ,grid.5645.2000000040459992XDepartment of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Andre G. Uitterlinden
- grid.5645.2000000040459992XDepartment of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands ,grid.5645.2000000040459992XDepartment of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Tamar Nijsten
- grid.5645.2000000040459992XDepartment of Dermatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Arfan Ikram
- grid.5645.2000000040459992XDepartment of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Fernando Rivadeneira
- grid.5645.2000000040459992XDepartment of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands ,grid.5645.2000000040459992XDepartment of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands ,grid.5645.2000000040459992XDepartment of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Mohsen Ghanbari
- grid.5645.2000000040459992XDepartment of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Yong Wang
- grid.9227.e0000000119573309CEMS, NCMIS, HCMS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
| | - Manfred Kayser
- grid.5645.2000000040459992XDepartment of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Fan Liu
- grid.5645.2000000040459992XDepartment of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands ,grid.9227.e0000000119573309CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
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9
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Dediu D, Jennings EM, Van't Ent D, Moisik SR, Di Pisa G, Schulze J, de Geus EJC, den Braber A, Dolan CV, Boomsma DI. The heritability of vocal tract structures estimated from structural MRI in a large cohort of Dutch twins. Hum Genet 2022; 141:1905-1923. [PMID: 35831475 PMCID: PMC9672028 DOI: 10.1007/s00439-022-02469-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/18/2022] [Indexed: 11/04/2022]
Abstract
While language is expressed in multiple modalities, including sign, writing, or whistles, speech is arguably the most common. The human vocal tract is capable of producing the bewildering diversity of the 7000 or so currently spoken languages, but relatively little is known about its genetic bases, especially in what concerns normal variation. Here, we capitalize on five cohorts totaling 632 Dutch twins with structural magnetic resonance imaging (MRI) data. Two raters placed clearly defined (semi)landmarks on each MRI scan, from which we derived 146 measures capturing the dimensions and shape of various vocal tract structures, but also aspects of the head and face. We used Genetic Covariance Structure Modeling to estimate the additive genetic, common environmental or non-additive genetic, and unique environmental components, while controlling for various confounds and for any systematic differences between the two raters. We found high heritability, h2, for aspects of the skull and face, the mandible, the anteroposterior (horizontal) dimension of the vocal tract, and the position of the hyoid bone. These findings extend the existing literature, and open new perspectives for understanding the complex interplay between genetics, environment, and culture that shape our vocal tracts, and which may help explain cross-linguistic differences in phonetics and phonology.
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Affiliation(s)
- Dan Dediu
- Department of Catalan Philology and General Linguistics, University of Barcelona, Barcelona, Spain.
- Universitat de Barcelona Institute of Complex Systems (UBICS), Barcelona, Spain.
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain.
| | - Emily M Jennings
- Faculty of Linguistics, Philology and Phonetics, University of Oxford, Oxford, UK
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Dennis Van't Ent
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Scott R Moisik
- Linguistics and Multilingual Studies, Nanyang Technological University, Singapore, Singapore
| | - Grazia Di Pisa
- Department of Linguistics, Universität Konstanz, Constance, Germany
| | | | - Eco J C de Geus
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Anouk den Braber
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Neurology, Alzheimer Center, Neuroscience Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Conor V Dolan
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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10
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Gou Z, Zhou Y, Jia H, Yang Z, Zhang Q, Yan X. Prenatal diagnosis and mRNA profiles of fetal tetralogy of Fallot. BMC Pregnancy Childbirth 2022; 22:853. [PMID: 36402964 PMCID: PMC9675103 DOI: 10.1186/s12884-022-05190-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/07/2022] [Indexed: 11/21/2022] Open
Abstract
Tetralogy of fallot (TOF) in the fetus is a typical congential heart disease that occurs during the early embryonic period, being characterized by the abnormal development of conus arteriosus. The early diagnosis and prevention of fetal TOF is very important and there is a great need for exploring the pathogenesis of it in clinic. In this study, there were three cases being detected with TOF by fetal echocardiogram and confirmed by autopsy. We characterize the difference of expression of lncRNAs and mRNAs through sequencing analysis of 3 pairs of myocardial tissues of fetal TOF and those of age-matched controls. Compared with normal group, there were 94 differentially expressed lncRNAs and 83 mRNA transcripts in TOF (P < 0.05). Correlation analysis between lncRNA and mRNA further showed that differentially expressed lncRNA can be linked to mRNAs, suggesting the potential regulator role of lncRNA in mRNA expression. Our data serve as a fundamental resource for understanding the disease etiology of TOF.
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Affiliation(s)
- Zhongshan Gou
- grid.89957.3a0000 0000 9255 8984Cardiovascular Disease Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Jiangsu 215008 Suzhou, P.R. China
| | - Yan Zhou
- grid.452799.4Department of Ultrasonography, The Fourth Affiliated Hospital of Anhui Medical University, 23000 Hefei, Anhui P.R. China
| | - Hongjing Jia
- grid.89957.3a0000 0000 9255 8984Department of Ultrasonography, The Affiliated Suzhou Hospital of Nanjing Medical University, 215008 Suzhou, Jiangsu P.R. China
| | - Zhong Yang
- grid.89957.3a0000 0000 9255 8984Department of Ultrasonography, The Affiliated Suzhou Hospital of Nanjing Medical University, 215008 Suzhou, Jiangsu P.R. China
| | - Qian Zhang
- grid.89957.3a0000 0000 9255 8984Department of Pharmacology, The Affiliated Suzhou Hospital of Nanjing Medical University, Jiangsu 215008 Suzhou, P.R. China
| | - Xinxin Yan
- grid.89957.3a0000 0000 9255 8984Department of Pharmacology, The Affiliated Suzhou Hospital of Nanjing Medical University, Jiangsu 215008 Suzhou, P.R. China
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11
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Naqvi S, Hoskens H, Wilke F, Weinberg SM, Shaffer JR, Walsh S, Shriver MD, Wysocka J, Claes P. Decoding the Human Face: Progress and Challenges in Understanding the Genetics of Craniofacial Morphology. Annu Rev Genomics Hum Genet 2022; 23:383-412. [PMID: 35483406 PMCID: PMC9482780 DOI: 10.1146/annurev-genom-120121-102607] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Variations in the form of the human face, which plays a role in our individual identities and societal interactions, have fascinated scientists and artists alike. Here, we review our current understanding of the genetics underlying variation in craniofacial morphology and disease-associated dysmorphology, synthesizing decades of progress on Mendelian syndromes in addition to more recent results from genome-wide association studies of human facial shape and disease risk. We also discuss the various approaches used to phenotype and quantify facial shape, which are of particular importance due to the complex, multipartite nature of the craniofacial form. We close by discussing how experimental studies have contributed and will further contribute to our understanding of human genetic variation and then proposing future directions and applications for the field.
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Affiliation(s)
- Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA; ,
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Hanne Hoskens
- Center for Processing Speech and Images, Department of Electrical Engineering, KU Leuven, Leuven, Belgium; ,
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Franziska Wilke
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana, USA; ,
| | - Seth M Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; ,
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Anthropology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John R Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; ,
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Susan Walsh
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana, USA; ,
| | - Mark D Shriver
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, USA;
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA; ,
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Peter Claes
- Center for Processing Speech and Images, Department of Electrical Engineering, KU Leuven, Leuven, Belgium; ,
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
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12
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Cha MY, Hong YJ, Choi JE, Kwon TS, Kim IJ, Hong KW. Classification of early age facial growth pattern and identification of the genetic basis in two Korean populations. Sci Rep 2022; 12:13828. [PMID: 35970861 PMCID: PMC9378761 DOI: 10.1038/s41598-022-18127-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 08/05/2022] [Indexed: 11/11/2022] Open
Abstract
Childhood to adolescence is an accelerated growth period, and genetic features can influence differences of individual growth patterns. In this study, we examined the genetic basis of early age facial growth (EAFG) patterns. Facial shape phenotypes were defined using facial landmark distances, identifying five growth patterns: continued-decrease, decrease-to-increase, constant, increase-to-decrease, and continued-increase. We conducted genome-wide association studies (GWAS) for 10 horizontal and 11 vertical phenotypes. The most significant association for horizontal phenotypes was rs610831 (TRIM29; β = 0.92, p-value = 1.9 × 10−9) and for vertical phenotypes was rs6898746 (ZSWIM6; β = 0.1103, p-value = 2.5 × 10−8). It is highly correlated with genes already reported for facial growth. This study is the first to classify and characterize facial growth patterns and related genetic polymorphisms.
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Affiliation(s)
- Mi-Yeon Cha
- Theragen Bio Co., Ltd., 240 Pangyoyeok-ro, Seongnam-si, Gyeonggi-do, 13493, Republic of Korea
| | - Yu-Jin Hong
- Center for Imaging Media Research, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Ja-Eun Choi
- Theragen Bio Co., Ltd., 240 Pangyoyeok-ro, Seongnam-si, Gyeonggi-do, 13493, Republic of Korea
| | - Tae-Song Kwon
- Human ICT CO., Ltd., 111, Dogok-ro, Gangnam-gu, Seoul, 06253, Republic of Korea
| | - Ig-Jae Kim
- Center for Imaging Media Research, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Kyung-Won Hong
- Theragen Bio Co., Ltd., 240 Pangyoyeok-ro, Seongnam-si, Gyeonggi-do, 13493, Republic of Korea.
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13
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Wang P, Sun X, Miao Q, Mi H, Cao M, Zhao S, Wang Y, Shu Y, Li W, Xu H, Bai D, Zhang Y. Novel genetic associations with five aesthetic facial traits: A genome-wide association study in the Chinese population. Front Genet 2022; 13:967684. [PMID: 36035146 PMCID: PMC9411802 DOI: 10.3389/fgene.2022.967684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 06/27/2022] [Indexed: 11/17/2022] Open
Abstract
Background: The aesthetic facial traits are closely related to life quality and strongly influenced by genetic factors, but the genetic predispositions in the Chinese population remain poorly understood. Methods: A genome-wide association studies (GWAS) and subsequent validations were performed in 26,806 Chinese on five facial traits: widow’s peak, unibrow, double eyelid, earlobe attachment, and freckles. Functional annotation was performed based on the expression quantitative trait loci (eQTL) variants, genome-wide polygenic scores (GPSs) were developed to represent the combined polygenic effects, and single nucleotide polymorphism (SNP) heritability was presented to evaluate the contributions of the variants. Results: In total, 21 genetic associations were identified, of which ten were novel: GMDS-AS1 (rs4959669, p = 1.29 × 10−49) and SPRED2 (rs13423753, p = 2.99 × 10−14) for widow’s peak, a previously unreported trait; FARSB (rs36015125, p = 1.96 × 10−21) for unibrow; KIF26B (rs7549180, p = 2.41 × 10−15), CASC2 (rs79852633, p = 4.78 × 10−11), RPGRIP1L (rs6499632, p = 9.15 × 10−11), and PAX1 (rs147581439, p = 3.07 × 10−8) for double eyelid; ZFHX3 (rs74030209, p = 9.77 × 10−14) and LINC01107 (rs10211400, p = 6.25 × 10−10) for earlobe attachment; and SPATA33 (rs35415928, p = 1.08 × 10−8) for freckles. Functionally, seven identified SNPs tag the missense variants and six may function as eQTLs. The combined polygenic effect of the associations was represented by GPSs and contributions of the variants were evaluated using SNP heritability. Conclusion: These identifications may facilitate a better understanding of the genetic basis of features in the Chinese population and hopefully inspire further genetic research on facial development.
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Affiliation(s)
- Peiqi Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xinghan Sun
- Genomic & Phenomic Data Center, Chengdu 23Mofang Biotechnology Co., Ltd, Chengdu, China
- Department of Biobank, Chengdu 23Mofang Biotechnology Co., Ltd, Chengdu, China
| | - Qiang Miao
- Department of Laboratory Medicine/Research Center of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Mi
- Department of Biobank, Chengdu 23Mofang Biotechnology Co., Ltd, Chengdu, China
| | - Minyuan Cao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Shan Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yiyi Wang
- Department of Dermatology, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Shu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Li
- Department of Dermatology, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Heng Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- Department of Laboratory Medicine/Research Center of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Ding Bai
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Ding Bai, ; Yan Zhang,
| | - Yan Zhang
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- State Key Laboratory of Biotherapy, Department of Thoracic Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Ding Bai, ; Yan Zhang,
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14
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Zhang M, Wu S, Du S, Qian W, Chen J, Qiao L, Yang Y, Tan J, Yuan Z, Peng Q, Liu Y, Navarro N, Tang K, Ruiz-Linares A, Wang J, Claes P, Jin L, Li J, Wang S. Genetic variants underlying differences in facial morphology in East Asian and European populations. Nat Genet 2022; 54:403-411. [PMID: 35393595 DOI: 10.1038/s41588-022-01038-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 01/19/2022] [Accepted: 02/25/2022] [Indexed: 11/09/2022]
Abstract
Facial morphology-a conspicuous feature of human appearance-is highly heritable. Previous studies on the genetic basis of facial morphology were performed mainly in European-ancestry cohorts (EUR). Applying a data-driven phenotyping and multivariate genome-wide scanning protocol to a large collection of three-dimensional facial images of individuals with East Asian ancestry (EAS), we identified 244 variants in 166 loci (62 new) associated with typical-range facial variation. A newly proposed polygenic shape analysis indicates that the effects of the variants on facial shape in EAS can be generalized to EUR. Based on this, we further identified 13 variants related to differences between facial shape in EUR and EAS populations. Evolutionary analyses suggest that the difference in nose shape between EUR and EAS populations is caused by a directional selection, due mainly to a local adaptation in Europeans. Our results illustrate the underlying genetic basis for facial differences across populations.
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Affiliation(s)
- Manfei Zhang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China.,CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Computer Science, Fudan University, Shanghai, China
| | - Sijie Wu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China.,CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Siyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wei Qian
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China.,CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Computer Science, Fudan University, Shanghai, China
| | - Jieyi Chen
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Lu Qiao
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yajun Yang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Jingze Tan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Ziyu Yuan
- Fudan-Taizhou Institute of Health Sciences, Taizhou, China
| | - Qianqian Peng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu Liu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Nicolas Navarro
- Biogéosciences, UMR 6282 CNRS-EPHE, Université Bourgogne Franche-Comté, Dijon, France.,Ecole Pratique des Hautes Etudes, PSL University, Paris, France
| | - Kun Tang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Andrés Ruiz-Linares
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China.,Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Aix-Marseille Université, CNRS, EFS, ADES, Marseille, France.,Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, UK
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China.,Fudan-Taizhou Institute of Health Sciences, Taizhou, China
| | - Peter Claes
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.,Medical Imaging Research Center, UZ Leuven, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China. .,CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,Fudan-Taizhou Institute of Health Sciences, Taizhou, China.
| | - Jiarui Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium. .,Medical Imaging Research Center, UZ Leuven, Leuven, Belgium.
| | - Sijia Wang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China. .,CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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15
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Dabas P, Jain S, Khajuria H, Nayak BP. Forensic DNA phenotyping: Inferring phenotypic traits from crime scene DNA. J Forensic Leg Med 2022; 88:102351. [DOI: 10.1016/j.jflm.2022.102351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 03/01/2022] [Accepted: 04/04/2022] [Indexed: 10/18/2022]
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16
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Qian W, Zhang M, Wan K, Xie Y, Du S, Li J, Mu X, Qiu J, Xue X, Zhuang X, Wu Y, Liu F, Wang S. Genetic evidence for facial variation being a composite phenotype of cranial variation and facial soft tissue thickness. J Genet Genomics 2022; 49:934-942. [DOI: 10.1016/j.jgg.2022.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 02/17/2022] [Accepted: 02/20/2022] [Indexed: 10/18/2022]
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17
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Knol MJ, Pawlak MA, Lamballais S, Terzikhan N, Hofer E, Xiong Z, Klaver CCW, Pirpamer L, Vernooij MW, Ikram MA, Schmidt R, Kayser M, Evans TE, Adams HHH. Genetic architecture of orbital telorism. Hum Mol Genet 2021; 31:1531-1543. [PMID: 34791242 PMCID: PMC9071440 DOI: 10.1093/hmg/ddab334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 11/19/2022] Open
Abstract
The interocular distance, or orbital telorism, is a distinctive craniofacial trait that also serves as a clinically informative measure. While its extremes, hypo- and hypertelorism, have been linked to monogenic disorders and are often syndromic, little is known about the genetic determinants of interocular distance within the general population. We derived orbital telorism measures from cranial magnetic resonance imaging by calculating the distance between the eyeballs’ centre of gravity, which showed a good reproducibility with an intraclass correlation coefficient of 0.991 (95% confidence interval 0.985–0.994). Heritability estimates were 76% (standard error = 12%) with a family-based method (N = 364) and 39% (standard error = 2.4%) with a single nucleotide polymorphism-based method (N = 34 130) and were unaffected by adjustment for height (model II) and intracranial volume (model III) or head width (model IV). Genome-wide association studies in 34 130 European individuals identified 56 significantly associated genomic loci (P < 5 × 10−8) across four different models of which 46 were novel for facial morphology, and overall these findings replicated in an independent sample (N = 10 115) with telorism-related horizontal facial distance measures. Genes located nearby these 56 identified genetic loci were 4.9-fold enriched for Mendelian hypotelorism and hypertelorism genes, underlining their biological relevance. This study provides novel insights into the genetic architecture underlying interocular distance in particular, and the face in general, and explores its potential for applications in a clinical setting.
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Affiliation(s)
- Maria J Knol
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - Mikolaj A Pawlak
- Department of Neurology and Cerebrovascular Disorders, Poznan University of Medical Sciences, Poznan, Poland.,Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - Sander Lamballais
- Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - Natalie Terzikhan
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - Edith Hofer
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University Graz, Auenbruggerplatz 22, 8036 Graz, Austria.,Institute of Medical Informatics, Statistics and Documentation, Medical University Graz, Auenbruggerplatz 22, 8036 Graz, Austria
| | - Ziyi Xiong
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands.,Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - Caroline C W Klaver
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands.,Department of Ophthalmology, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - Lukas Pirpamer
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University Graz, Auenbruggerplatz 22, 8036 Graz, Austria
| | - Meike W Vernooij
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands.,Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - Reinhold Schmidt
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University Graz, Auenbruggerplatz 22, 8036 Graz, Austria
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - Tavia E Evans
- Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands.,Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - Hieab H H Adams
- Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands.,Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
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18
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Su Z, Liang B, Shi F, Gelfond J, Šegalo S, Wang J, Jia P, Hao X. Deep learning-based facial image analysis in medical research: a systematic review protocol. BMJ Open 2021; 11:e047549. [PMID: 34764164 PMCID: PMC8587597 DOI: 10.1136/bmjopen-2020-047549] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 08/18/2021] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION Deep learning techniques are gaining momentum in medical research. Evidence shows that deep learning has advantages over humans in image identification and classification, such as facial image analysis in detecting people's medical conditions. While positive findings are available, little is known about the state-of-the-art of deep learning-based facial image analysis in the medical context. For the consideration of patients' welfare and the development of the practice, a timely understanding of the challenges and opportunities faced by research on deep-learning-based facial image analysis is needed. To address this gap, we aim to conduct a systematic review to identify the characteristics and effects of deep learning-based facial image analysis in medical research. Insights gained from this systematic review will provide a much-needed understanding of the characteristics, challenges, as well as opportunities in deep learning-based facial image analysis applied in the contexts of disease detection, diagnosis and prognosis. METHODS Databases including PubMed, PsycINFO, CINAHL, IEEEXplore and Scopus will be searched for relevant studies published in English in September, 2021. Titles, abstracts and full-text articles will be screened to identify eligible articles. A manual search of the reference lists of the included articles will also be conducted. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses framework was adopted to guide the systematic review process. Two reviewers will independently examine the citations and select studies for inclusion. Discrepancies will be resolved by group discussions till a consensus is reached. Data will be extracted based on the research objective and selection criteria adopted in this study. ETHICS AND DISSEMINATION As the study is a protocol for a systematic review, ethical approval is not required. The study findings will be disseminated via peer-reviewed publications and conference presentations. PROSPERO REGISTRATION NUMBER CRD42020196473.
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Affiliation(s)
- Zhaohui Su
- Center on Smart and Connected Health Technologies, Mays Cancer Center, School of Nursing, UT Health San Antonio, San Antonio, Texas, USA
| | - Bin Liang
- Department of Radiation Oncology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Feng Shi
- Department of Research and Development, Shanghai United Imaging Intelligence Co., Ltd, Shanghai, China
| | - J Gelfond
- Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, UK
| | - Sabina Šegalo
- Department of Microbiology, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Jing Wang
- College of Nursing, Florida State University, Tallahassee, Florida, USA
| | - Peng Jia
- Department of Land Surveying and Geo-Informatics, University of Twente, Enschede, Netherlands
- International Initiative on Spatial Lifecourse Epidemiology (ISLE), Enschede, UK
| | - Xiaoning Hao
- Division of Health Security Research, National Health Commission of the People's Republic of China, Beijing, Beijing, China
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19
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Potter JHT, Davies KTJ, Yohe LR, Sanchez MKR, Rengifo EM, Struebig M, Warren K, Tsagkogeorga G, Lim BK, dos Reis M, Dávalos LM, Rossiter SJ. Dietary Diversification and Specialization in Neotropical Bats Facilitated by Early Molecular Evolution. Mol Biol Evol 2021; 38:3864-3883. [PMID: 34426843 PMCID: PMC8382914 DOI: 10.1093/molbev/msab028] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Dietary adaptation is a major feature of phenotypic and ecological diversification, yet the genetic basis of dietary shifts is poorly understood. Among mammals, Neotropical leaf-nosed bats (family Phyllostomidae) show unmatched diversity in diet; from a putative insectivorous ancestor, phyllostomids have radiated to specialize on diverse food sources including blood, nectar, and fruit. To assess whether dietary diversification in this group was accompanied by molecular adaptations for changing metabolic demands, we sequenced 89 transcriptomes across 58 species and combined these with published data to compare ∼13,000 protein coding genes across 66 species. We tested for positive selection on focal lineages, including those inferred to have undergone dietary shifts. Unexpectedly, we found a broad signature of positive selection in the ancestral phyllostomid branch, spanning genes implicated in the metabolism of all major macronutrients, yet few positively selected genes at the inferred switch to plantivory. Branches corresponding to blood- and nectar-based diets showed selection in loci underpinning nitrogenous waste excretion and glycolysis, respectively. Intriguingly, patterns of selection in metabolism genes were mirrored by those in loci implicated in craniofacial remodeling, a trait previously linked to phyllostomid dietary specialization. Finally, we show that the null model of the widely-used branch-site test is likely to be misspecified, with the implication that the test is too conservative and probably under-reports true cases of positive selection. Our findings point to a complex picture of adaptive radiation, in which the evolution of new dietary specializations has been facilitated by early adaptations combined with the generation of new genetic variation.
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Affiliation(s)
- Joshua H T Potter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Kalina T J Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Laurel R Yohe
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Department of Earth and Planetary Science, Yale University, 210 Whitney Ave, New Haven, CT, USA
| | - Miluska K R Sanchez
- Escuela Profesional de Ciencias Biológicas, Universidad Nacional de Piura, Piura, Peru
| | - Edgardo M Rengifo
- Escola Superior de Agricultura ‘Luiz de Queiroz,’ Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil
- Centro de Investigación Biodiversidad Sostenible (BioS), Lima, Peru
| | - Monika Struebig
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Kim Warren
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Mario dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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20
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Liu C, Lee MK, Naqvi S, Hoskens H, Liu D, White JD, Indencleef K, Matthews H, Eller RJ, Li J, Mohammed J, Swigut T, Richmond S, Manyama M, Hallgrímsson B, Spritz RA, Feingold E, Marazita ML, Wysocka J, Walsh S, Shriver MD, Claes P, Weinberg SM, Shaffer JR. Genome scans of facial features in East Africans and cross-population comparisons reveal novel associations. PLoS Genet 2021; 17:e1009695. [PMID: 34411106 PMCID: PMC8375984 DOI: 10.1371/journal.pgen.1009695] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 07/02/2021] [Indexed: 12/16/2022] Open
Abstract
Facial morphology is highly variable, both within and among human populations, and a sizable portion of this variation is attributable to genetics. Previous genome scans have revealed more than 100 genetic loci associated with different aspects of normal-range facial variation. Most of these loci have been detected in Europeans, with few studies focusing on other ancestral groups. Consequently, the degree to which facial traits share a common genetic basis across diverse sets of humans remains largely unknown. We therefore investigated the genetic basis of facial morphology in an East African cohort. We applied an open-ended data-driven phenotyping approach to a sample of 2,595 3D facial images collected on Tanzanian children. This approach segments the face into hierarchically arranged, multivariate features that capture the shape variation after adjusting for age, sex, height, weight, facial size and population stratification. Genome scans of these multivariate shape phenotypes revealed significant (p < 2.5 × 10−8) signals at 20 loci, which were enriched for active chromatin elements in human cranial neural crest cells and embryonic craniofacial tissue, consistent with an early developmental origin of the facial variation. Two of these associations were in highly conserved regions showing craniofacial-specific enhancer activity during embryological development (5q31.1 and 12q21.31). Six of the 20 loci surpassed a stricter threshold accounting for multiple phenotypes with study-wide significance (p < 6.25 × 10−10). Cross-population comparisons indicated 10 association signals were shared with Europeans (seven sharing the same associated SNP), and facilitated fine-mapping of causal variants at previously reported loci. Taken together, these results may point to both shared and population-specific components to the genetic architecture of facial variation. Genetic factors play an important role in shaping human facial features. Over the last decade, studies have identified numerous genes associated with various facial traits. The vast majority of these studies have focused on European or Asian populations, while African populations have been underrepresented. Increasing the diversity of these analyses can reveal novel associations and cross-population analyses can help deepen our understanding of known genetic associations. We therefore performed a genome scan of 3D facial features in African children from Tanzania and then compared our results to Europeans. We found 20 regions of the genome associated with facial shape in Tanzanian children, 10 of which were also present in Europeans, indicating evidence for a partly shared genetic basis for human facial shape across populations. In addition, about half of the genetic associations observed in Tanzanians were not present in Europeans, and some of the shared signals differed between populations in the specific genetic variants associated or specific facial traits affected. These results shed light on the shared and population-specific genetic contributors to normal-range facial variation.
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Affiliation(s)
- Chenxing Liu
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Myoung Keun Lee
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Hanne Hoskens
- Medical Imaging Research Center, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Dongjing Liu
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Julie D. White
- Department of Anthropology, Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Karlijne Indencleef
- Medical Imaging Research Center, Katholieke Universiteit Leuven, Leuven, Belgium
- Processing Speech & Images, Department of Electrical Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Harold Matthews
- Medical Imaging Research Center, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Ryan J. Eller
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Jiarui Li
- Medical Imaging Research Center, Katholieke Universiteit Leuven, Leuven, Belgium
- Processing Speech & Images, Department of Electrical Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jaaved Mohammed
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Stephen Richmond
- Applied Clinical Research and Public Health, School of Dentistry, Cardiff University, Cardiff, United Kingdom
| | - Mange Manyama
- Anatomy in Radiology, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Benedikt Hallgrímsson
- Department of Anatomy and Cell Biology, Alberta Children´s Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Richard A. Spritz
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mary L. Marazita
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Mark D. Shriver
- Department of Anthropology, Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Peter Claes
- Medical Imaging Research Center, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
- Processing Speech & Images, Department of Electrical Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Seth M. Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Anthropology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (SMW); (JRS)
| | - John R. Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (SMW); (JRS)
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21
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Liu D, Ban HJ, El Sergani AM, Lee MK, Hecht JT, Wehby GL, Moreno LM, Feingold E, Marazita ML, Cha S, Szabo-Rogers HL, Weinberg SM, Shaffer JR. PRICKLE1 × FOCAD Interaction Revealed by Genome-Wide vQTL Analysis of Human Facial Traits. Front Genet 2021; 12:674642. [PMID: 34434215 PMCID: PMC8381734 DOI: 10.3389/fgene.2021.674642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022] Open
Abstract
The human face is a highly complex and variable structure resulting from the intricate coordination of numerous genetic and non-genetic factors. Hundreds of genomic loci impacting quantitative facial features have been identified. While these associations have been shown to influence morphology by altering the mean size and shape of facial measures, their effect on trait variance remains unclear. We conducted a genome-wide association analysis for the variance of 20 quantitative facial measurements in 2,447 European individuals and identified several suggestive variance quantitative trait loci (vQTLs). These vQTLs guided us to conduct an efficient search for gene-by-gene (G × G) interactions, which uncovered an interaction between PRICKLE1 and FOCAD affecting cranial base width. We replicated this G × G interaction signal at the locus level in an additional 5,128 Korean individuals. We used the hypomorphic Prickle1 Beetlejuice (Prickle1 Bj ) mouse line to directly test the function of Prickle1 on the cranial base and observed wider cranial bases in Prickle1 Bj/Bj . Importantly, we observed that the Prickle1 and Focadhesin proteins co-localize in murine cranial base chondrocytes, and this co-localization is abnormal in the Prickle1 Bj/Bj mutants. Taken together, our findings uncovered a novel G × G interaction effect in humans with strong support from both epidemiological and molecular studies. These results highlight the potential of studying measures of phenotypic variability in gene mapping studies of facial morphology.
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Affiliation(s)
- Dongjing Liu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Hyo-Jeong Ban
- Future Medicine Division, Korea Institute of Oriental Medicine, Daejeon, South Korea
| | - Ahmed M. El Sergani
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical Center, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - George L. Wehby
- Department of Health Management and Policy, The University of Iowa, Iowa City, IA, United States
| | - Lina M. Moreno
- Department of Orthodontics, The University of Iowa, Iowa City, IA, United States
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Psychiatry, Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Seongwon Cha
- Future Medicine Division, Korea Institute of Oriental Medicine, Daejeon, South Korea
| | - Heather L. Szabo-Rogers
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Developmental Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Regenerative Medicine at the McGowan Institute, University of Pittsburgh, Pittsburgh, PA, United States
- Center for Craniofacial Regeneration, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - John R. Shaffer
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
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22
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Hoskens H, Liu D, Naqvi S, Lee MK, Eller RJ, Indencleef K, White JD, Li J, Larmuseau MHD, Hens G, Wysocka J, Walsh S, Richmond S, Shriver MD, Shaffer JR, Peeters H, Weinberg SM, Claes P. 3D facial phenotyping by biometric sibling matching used in contemporary genomic methodologies. PLoS Genet 2021; 17:e1009528. [PMID: 33983923 PMCID: PMC8118281 DOI: 10.1371/journal.pgen.1009528] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/01/2021] [Indexed: 12/12/2022] Open
Abstract
The analysis of contemporary genomic data typically operates on one-dimensional phenotypic measurements (e.g. standing height). Here we report on a data-driven, family-informed strategy to facial phenotyping that searches for biologically relevant traits and reduces multivariate 3D facial shape variability into amendable univariate measurements, while preserving its structurally complex nature. We performed a biometric identification of siblings in a sample of 424 children, defining 1,048 sib-shared facial traits. Subsequent quantification and analyses in an independent European cohort (n = 8,246) demonstrated significant heritability for a subset of traits (0.17-0.53) and highlighted 218 genome-wide significant loci (38 also study-wide) associated with facial variation shared by siblings. These loci showed preferential enrichment for active chromatin marks in cranial neural crest cells and embryonic craniofacial tissues and several regions harbor putative craniofacial genes, thereby enhancing our knowledge on the genetic architecture of normal-range facial variation.
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Affiliation(s)
- Hanne Hoskens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
| | - Dongjing Liu
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Myoung Keun Lee
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ryan J. Eller
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Karlijne Indencleef
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Department of Otorhinolaryngology, KU Leuven, Leuven, Belgium
| | - Julie D. White
- Department of Anthropology, The Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Jiarui Li
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Maarten H. D. Larmuseau
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Department of Biology, Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven, Belgium
- Histories vzw, Mechelen, Belgium
| | - Greet Hens
- Department of Otorhinolaryngology, KU Leuven, Leuven, Belgium
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Stephen Richmond
- Applied Clinical Research and Public Health, School of Dentistry, Cardiff University, Cardiff, United Kingdom
| | - Mark D. Shriver
- Department of Anthropology, The Pennsylvania State University, State College, Pennsylvania, United States of America
| | - John R. Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Hilde Peeters
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Seth M. Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Anthropology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
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23
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Curtis SW, Chang D, Lee MK, Shaffer JR, Indencleef K, Epstein MP, Cutler DJ, Murray JC, Feingold E, Beaty TH, Claes P, Weinberg SM, Marazita ML, Carlson JC, Leslie EJ. The PAX1 locus at 20p11 is a potential genetic modifier for bilateral cleft lip. HGG ADVANCES 2021; 2:100025. [PMID: 33817668 PMCID: PMC8018676 DOI: 10.1016/j.xhgg.2021.100025] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Nonsyndromic orofacial clefts (OFCs) are a common birth defect and are phenotypically heterogenous in the structure affected by the cleft - cleft lip (CL) and cleft lip and palate (CLP) - as well as other features, such as the severity of the cleft. Here, we focus on bilateral and unilateral clefts as one dimension of OFC severity, because the genetic architecture of these subtypes is not well understood. We tested for subtype-specific genetic associations in 44 bilateral CL (BCL) cases, 434 unilateral CL (UCL) cases, 530 bilateral CLP cases (BCLP), 1123 unilateral CLP (UCLP) cases, and unrelated controls (N = 1626), using a mixed-model approach. While no novel loci were found, the genetic architecture of UCL was distinct compared to BCL, with 44.03% of suggestive loci having different effects between the two subtypes. To further understand the subtype-specific genetic risk factors, we performed a genome-wide scan for modifiers and found a significant modifier locus on 20p11 (p=7.53×10-9), 300kb downstream of PAX1, that associated with higher odds of BCL vs. UCL, and replicated in an independent cohort (p=0.0018) with no effect in BCLP (p>0.05). We further found that this locus was associated with normal human nasal shape. Taken together, these results suggest bilateral and unilateral clefts may have different genetic architectures. Moreover, our results suggest BCL, the rarest form of OFC, may be genetically distinct from the other OFC subtypes. This expands our understanding of modifiers for OFC subtypes and further elucidates the genetic mechanisms behind the phenotypic heterogeneity in OFCs.
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Affiliation(s)
- Sarah W. Curtis
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Daniel Chang
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - John R. Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15621, USA
| | - Karlijne Indencleef
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | | | - David J. Cutler
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Peter Claes
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15621, USA
| | - Jenna C. Carlson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261, USA
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24
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Huang Y, Li D, Qiao L, Liu Y, Peng Q, Wu S, Zhang M, Yang Y, Tan J, Xu S, Jin L, Wang S, Tang K, Grünewald S. A genome-wide association study of facial morphology identifies novel genetic loci in Han Chinese. J Genet Genomics 2021; 48:198-207. [PMID: 33593615 DOI: 10.1016/j.jgg.2020.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 10/23/2022]
Abstract
The human face is a heritable surface with many complex sensory organs. In recent years, many genetic loci associated with facial features have been reported in different populations, yet there is a lack of studies on the Han Chinese population. Here, we report a genome-wide association study of 3D normal human faces of 2,659 Han Chinese with autosegment phenotypes of facial morphology. We identify single-nucleotide polymorphisms (SNPs) encompassing four genomic regions showing significant associations with different facial regions, including SNPs in DENND1B associated with the chin, SNPs among PISRT1 associated with eyes, SNPs between DCHS2 and SFRP2 associated with the nose, and SNPs in VPS13B associated with the nose. We replicate 24 SNPs from previously reported genetic loci in different populations, whose candidate genes are DCHS2, SUPT3H, HOXD1, SOX9, PAX3, and EDAR. These results provide a more comprehensive understanding of the genetic basis of variation in human facial morphology.
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Affiliation(s)
- Yin Huang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai 200031, China
| | - Dan Li
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai 200031, China; DeepBlue Technology (Shanghai) Co., Ltd, Shanghai 200336, China
| | - Lu Qiao
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai 200031, China
| | - Yu Liu
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai 200031, China
| | - Qianqian Peng
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai 200031, China
| | - Sijie Wu
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai 200031, China; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Manfei Zhang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai 200031, China; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yajun Yang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; Fudan-Taizhou Institute of Health Sciences, Taizhou 225300, China
| | - Jingze Tan
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; Fudan-Taizhou Institute of Health Sciences, Taizhou 225300, China
| | - Shuhua Xu
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai 200031, China; Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Li Jin
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai 200031, China; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; Fudan-Taizhou Institute of Health Sciences, Taizhou 225300, China; Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China
| | - Sijia Wang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai 200031, China; Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
| | - Kun Tang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai 200031, China; DeepBlue Technology (Shanghai) Co., Ltd, Shanghai 200336, China.
| | - Stefan Grünewald
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai 200031, China.
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25
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Bonfante B, Faux P, Navarro N, Mendoza-Revilla J, Dubied M, Montillot C, Wentworth E, Poloni L, Varón-González C, Jones P, Xiong Z, Fuentes-Guajardo M, Palmal S, Chacón-Duque JC, Hurtado M, Villegas V, Granja V, Jaramillo C, Arias W, Barquera R, Everardo-Martínez P, Sánchez-Quinto M, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Hünemeier T, Ramallo V, Liu F, Weinberg SM, Shaffer JR, Stergiakouli E, Howe LJ, Hysi PG, Spector TD, Gonzalez-José R, Schüler-Faccini L, Bortolini MC, Acuña-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Thauvin-Robinet C, Faivre L, Costedoat C, Balding D, Cox T, Kayser M, Duplomb L, Yalcin B, Cotney J, Adhikari K, Ruiz-Linares A. A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation. SCIENCE ADVANCES 2021; 7:eabc6160. [PMID: 33547071 PMCID: PMC7864580 DOI: 10.1126/sciadv.abc6160] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 12/17/2020] [Indexed: 05/25/2023]
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.
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Affiliation(s)
- Betty Bonfante
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France
| | - Pierre Faux
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France
| | - Nicolas Navarro
- Biogéosciences, UMR 6282 CNRS, EPHE, Université Bourgogne Franche-Comté, Dijon 21078, France
- EPHE, PSL University, Paris 75014, France
| | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
- Unit of Human Evolutionary Genetics, Institut Pasteur, Paris 75015, France
| | - Morgane Dubied
- Biogéosciences, UMR 6282 CNRS, EPHE, Université Bourgogne Franche-Comté, Dijon 21078, France
| | - Charlotte Montillot
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
| | - Emma Wentworth
- Department of Genetics and Genome Sciences, University of Connecticut Health, Farmington, CT 06030, USA
| | - Lauriane Poloni
- Biogéosciences, UMR 6282 CNRS, EPHE, Université Bourgogne Franche-Comté, Dijon 21078, France
- EPHE, PSL University, Paris 75014, France
| | - Ceferino Varón-González
- Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, UA, Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris 75005, France
| | - Philip Jones
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Ziyi Xiong
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3015GD, Netherlands
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica 1000000, Chile
| | - Sagnik Palmal
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France
| | - Juan Camilo Chacón-Duque
- Division of Vertebrates and Anthropology, Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena 07745, Germany
| | - Paola Everardo-Martínez
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
| | - Mirsha Sánchez-Quinto
- Forensic Science, Faculty of Medicine, UNAM (Universidad Nacional Autónoma de México), Mexico City 06320, Mexico
| | - Jorge Gómez-Valdés
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | | | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brasil
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3015GD, Netherlands
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100864, China
- University of Chinese Academy of Sciences, Beijing 100864, China
| | - Seth M Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - John R Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Evie Stergiakouli
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol BS1 2LY, UK
- School of Oral and Dental Sciences, University of Bristol, Bristol BS1 2LY, UK
| | - Laurence J Howe
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol BS1 2LY, UK
| | - Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Lavinia Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brasil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brasil
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Arica 1000000, Chile
| | - Christel Thauvin-Robinet
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
- Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs" de l'Est, Centre de Génétique, FHU TRANSLAD, CHU Dijon, Dijon 21000, France
| | - Laurence Faivre
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
- Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs" de l'Est, Centre de Génétique, FHU TRANSLAD, CHU Dijon, Dijon 21000, France
| | | | - David Balding
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Melbourne Integrative Genomics, Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Timothy Cox
- Department of Oral and Craniofacial Sciences, School of Dentistry and Department of Pediatrics, School of Medicine, University of Missouri, Kansas City, MO 64108, USA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3015GD, Netherlands
| | - Laurence Duplomb
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
| | - Binnaz Yalcin
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
| | - Justin Cotney
- Department of Genetics and Genome Sciences, University of Connecticut Health, Farmington, CT 06030, USA
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK.
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Andrés Ruiz-Linares
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France.
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, China
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26
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Liu D, Alhazmi N, Matthews H, Lee MK, Li J, Hecht JT, Wehby GL, Moreno LM, Heike CL, Roosenboom J, Feingold E, Marazita ML, Claes P, Liao EC, Weinberg SM, Shaffer JR. Impact of low-frequency coding variants on human facial shape. Sci Rep 2021; 11:748. [PMID: 33436952 PMCID: PMC7804299 DOI: 10.1038/s41598-020-80661-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/18/2020] [Indexed: 01/29/2023] Open
Abstract
The contribution of low-frequency variants to the genetic architecture of normal-range facial traits is unknown. We studied the influence of low-frequency coding variants (MAF < 1%) in 8091 genes on multi-dimensional facial shape phenotypes in a European cohort of 2329 healthy individuals. Using three-dimensional images, we partitioned the full face into 31 hierarchically arranged segments to model facial morphology at multiple levels, and generated multi-dimensional phenotypes representing the shape variation within each segment. We used MultiSKAT, a multivariate kernel regression approach to scan the exome for face-associated low-frequency variants in a gene-based manner. After accounting for multiple tests, seven genes (AR, CARS2, FTSJ1, HFE, LTB4R, TELO2, NECTIN1) were significantly associated with shape variation of the cheek, chin, nose and mouth areas. These genes displayed a wide range of phenotypic effects, with some impacting the full face and others affecting localized regions. The missense variant rs142863092 in NECTIN1 had a significant effect on chin morphology and was predicted bioinformatically to have a deleterious effect on protein function. Notably, NECTIN1 is an established craniofacial gene that underlies a human syndrome that includes a mandibular phenotype. We further showed that nectin1a mutations can affect zebrafish craniofacial development, with the size and shape of the mandibular cartilage altered in mutant animals. Findings from this study expanded our understanding of the genetic basis of normal-range facial shape by highlighting the role of low-frequency coding variants in several novel genes.
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Affiliation(s)
- Dongjing Liu
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nora Alhazmi
- Department of Oral Biology, Harvard School of Dental Medicine, Boston, MA, USA
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Harold Matthews
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, UZ Gasthuisberg, Leuven, Belgium
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jiarui Li
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Jacqueline T Hecht
- Department of Pediatrics, University of Texas McGovern Medical Center, Houston, TX, USA
| | - George L Wehby
- Department of Health Management and Policy, University of Iowa, Iowa City, IA, USA
| | - Lina M Moreno
- Department of Orthodontics, University of Iowa, Iowa City, IA, USA
| | - Carrie L Heike
- Department of Pediatrics, Seattle Children's Craniofacial Center, University of Washington, Seattle, WA, USA
| | - Jasmien Roosenboom
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mary L Marazita
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Eric C Liao
- Department of Surgery, Center for Regenerative Medicine, Massachusetts General Hospital, Shriners Hospital, Boston, MA, USA
| | - Seth M Weinberg
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
| | - John R Shaffer
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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27
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White JD, Indencleef K, Naqvi S, Eller RJ, Hoskens H, Roosenboom J, Lee MK, Li J, Mohammed J, Richmond S, Quillen EE, Norton HL, Feingold E, Swigut T, Marazita ML, Peeters H, Hens G, Shaffer JR, Wysocka J, Walsh S, Weinberg SM, Shriver MD, Claes P. Insights into the genetic architecture of the human face. Nat Genet 2021; 53:45-53. [PMID: 33288918 PMCID: PMC7796995 DOI: 10.1038/s41588-020-00741-7] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 10/23/2020] [Indexed: 01/28/2023]
Abstract
The human face is complex and multipartite, and characterization of its genetic architecture remains challenging. Using a multivariate genome-wide association study meta-analysis of 8,246 European individuals, we identified 203 genome-wide-significant signals (120 also study-wide significant) associated with normal-range facial variation. Follow-up analyses indicate that the regions surrounding these signals are enriched for enhancer activity in cranial neural crest cells and craniofacial tissues, several regions harbor multiple signals with associations to different facial phenotypes, and there is evidence for potential coordinated actions of variants. In summary, our analyses provide insights into the understanding of how complex morphological traits are shaped by both individual and coordinated genetic actions.
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Affiliation(s)
- Julie D White
- Department of Anthropology, Pennsylvania State University, State College, PA, USA.
| | - Karlijne Indencleef
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium.
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan J Eller
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
| | - Hanne Hoskens
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Jasmien Roosenboom
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Myoung Keun Lee
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jiarui Li
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
| | - Jaaved Mohammed
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen Richmond
- Applied Clinical Research and Public Health, School of Dentistry, Cardiff University, Cardiff, UK
| | - Ellen E Quillen
- Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Heather L Norton
- Department of Anthropology, University of Cincinnati, Cincinnati, OH, USA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mary L Marazita
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hilde Peeters
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Greet Hens
- Department of Neurosciences, Experimental Oto-Rhino-Laryngology, KU Leuven, Leuven, Belgium
| | - John R Shaffer
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
| | - Seth M Weinberg
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mark D Shriver
- Department of Anthropology, Pennsylvania State University, State College, PA, USA
| | - Peter Claes
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
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28
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Dash S, Trainor PA. The development, patterning and evolution of neural crest cell differentiation into cartilage and bone. Bone 2020; 137:115409. [PMID: 32417535 DOI: 10.1016/j.bone.2020.115409] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 05/04/2020] [Indexed: 12/12/2022]
Abstract
Neural crest cells are a vertebrate-specific migratory, multipotent cell population that give rise to a diverse array of cells and tissues during development. Cranial neural crest cells, in particular, generate cartilage, bone, tendons and connective tissue in the head and face as well as neurons, glia and melanocytes. In this review, we focus on the chondrogenic and osteogenic potential of cranial neural crest cells and discuss the roles of Sox9, Runx2 and Msx1/2 transcription factors and WNT, FGF and TGFβ signaling pathways in regulating neural crest cell differentiation into cartilage and bone. We also describe cranioskeletal defects and disorders arising from gain or loss-of-function of genes that are required for patterning and differentiation of cranial neural crest cells. Finally, we discuss the evolution of skeletogenic potential in neural crest cells and their function as a conduit for intraspecies and interspecies variation, and the evolution of craniofacial novelties.
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Affiliation(s)
- Soma Dash
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA.
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29
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Li J, Wang Z, Feng D, Wang W, Feng W. Evaluation of genetic susceptibility of common variants in SOX9 in patients with congenital talipes equinovarus in the Han Chinese population. J Orthop Surg Res 2020; 15:276. [PMID: 32703248 PMCID: PMC7376870 DOI: 10.1186/s13018-020-01802-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 07/14/2020] [Indexed: 11/16/2022] Open
Abstract
Background Congenital talipes equinovarus (CTEV) is a common birth defect that causes severe deformities of one or both feet. Genetics have been proven to play a key role in the risk of CTEV. Our study aimed to evaluate the genetic susceptibility of common variants in the SOX9 gene to CTEV in a Han Chinese population. Methods In this study, we recruited 2,205 study participants, including 692 CTEV patients and 1513 healthy controls. A total of seven selected single-nucleotide polymorphisms (SNPs) within the SOX9 gene were genotyped, and environmental variables, including maternal smoking and alcoholic drinking habits, were assessed. In addition, bioinformatics analyses were performed to explore the potential biological functions of the associated SNPs. Results The SNP rs73354570 was identified to be significantly associated with the risk of CTEV (OR = 1.53, P = 2.11 × 10−5), and the C allele was associated with an increased risk of CTEV. A dose-dependent pattern could be observed in genotypic analyses. The OR for individuals with AC genotypes was 1.37 (95% CI 1.09–1.71), and the OR for individuals with CC homozygotes was 1.47 (95% CI 1.18–1.82). Further analyses identified that rs73354570 is located within a region of multiple binding proteins, including CEBPB and POLR2A, which suggested that this SNP was also part of genetic motifs that are found within several cell types. Conclusion Our results provide evidence supporting the important role of the SOX9 gene in the contribution to the risk of CTEV.
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Affiliation(s)
- Jian Li
- Department of Sports Medicine, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Zhi Wang
- Department of Neonatology, Xi'an Children Hospital, Xi'an, Shaanxi, China
| | - Dongxu Feng
- Department of Orthopaedic Trauma, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Wei Wang
- Department of Sports Medicine, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Weilou Feng
- Department of Orthopaedic Trauma, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
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30
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Nakatomi M, Ludwig KU, Knapp M, Kist R, Lisgo S, Ohshima H, Mangold E, Peters H. Msx1 deficiency interacts with hypoxia and induces a morphogenetic regulation during mouse lip development. Development 2020; 147:dev189175. [PMID: 32467233 DOI: 10.1242/dev.189175] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/16/2020] [Indexed: 12/19/2022]
Abstract
Nonsyndromic clefts of the lip and palate are common birth defects resulting from gene-gene and gene-environment interactions. Mutations in human MSX1 have been linked to orofacial clefting and we show here that Msx1 deficiency causes a growth defect of the medial nasal process (Mnp) in mouse embryos. Although this defect alone does not disrupt lip formation, Msx1-deficient embryos develop a cleft lip when the mother is transiently exposed to reduced oxygen levels or to phenytoin, a drug known to cause embryonic hypoxia. In the absence of interacting environmental factors, the Mnp growth defect caused by Msx1 deficiency is modified by a Pax9-dependent 'morphogenetic regulation', which modulates Mnp shape, rescues lip formation and involves a localized abrogation of Bmp4-mediated repression of Pax9 Analyses of GWAS data revealed a genome-wide significant association of a Gene Ontology morphogenesis term (including assigned roles for MSX1, MSX2, PAX9, BMP4 and GREM1) specifically for nonsyndromic cleft lip with cleft palate. Our data indicate that MSX1 mutations could increase the risk for cleft lip formation by interacting with an impaired morphogenetic regulation that adjusts Mnp shape, or through interactions that inhibit Mnp growth.
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Affiliation(s)
- Mitsushiro Nakatomi
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne NE1 3BZ, UK
- Division of Anatomy, Department of Health Promotion, Kyushu Dental University, Kitakyushu 803-8580, Japan
| | - Kerstin U Ludwig
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, 53127 Bonn, Germany
| | - Ralf Kist
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne NE1 3BZ, UK
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4BW, UK
| | - Steven Lisgo
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne NE1 3BZ, UK
| | - Hayato Ohshima
- Division of Anatomy and Cell Biology of the Hard Tissue, Department of Tissue Regeneration and Reconstruction, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8514, Japan
| | - Elisabeth Mangold
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
| | - Heiko Peters
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne NE1 3BZ, UK
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31
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Katz DC, Aponte JD, Liu W, Green RM, Mayeux JM, Pollard KM, Pomp D, Munger SC, Murray SA, Roseman CC, Percival CJ, Cheverud J, Marcucio RS, Hallgrímsson B. Facial shape and allometry quantitative trait locus intervals in the Diversity Outbred mouse are enriched for known skeletal and facial development genes. PLoS One 2020; 15:e0233377. [PMID: 32502155 PMCID: PMC7274373 DOI: 10.1371/journal.pone.0233377] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 05/04/2020] [Indexed: 02/06/2023] Open
Abstract
The biology of how faces are built and come to differ from one another is complex. Discovering normal variants that contribute to differences in facial morphology is one key to untangling this complexity, with important implications for medicine and evolutionary biology. This study maps quantitative trait loci (QTL) for skeletal facial shape using Diversity Outbred (DO) mice. The DO is a randomly outcrossed population with high heterozygosity that captures the allelic diversity of eight inbred mouse lines from three subspecies. The study uses a sample of 1147 DO animals (the largest sample yet employed for a shape QTL study in mouse), each characterized by 22 three-dimensional landmarks, 56,885 autosomal and X-chromosome markers, and sex and age classifiers. We identified 37 facial shape QTL across 20 shape principal components (PCs) using a mixed effects regression that accounts for kinship among observations. The QTL include some previously identified intervals as well as new regions that expand the list of potential targets for future experimental study. Three QTL characterized shape associations with size (allometry). Median support interval size was 3.5 Mb. Narrowing additional analysis to QTL for the five largest magnitude shape PCs, we found significant overrepresentation of genes with known roles in growth, skeletal and facial development, and sensory organ development. For most intervals, one or more of these genes lies within 0.25 Mb of the QTL's peak. QTL effect sizes were small, with none explaining more than 0.5% of facial shape variation. Thus, our results are consistent with a model of facial diversity that is influenced by key genes in skeletal and facial development and, simultaneously, is highly polygenic.
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Affiliation(s)
- David C. Katz
- Department of Cell Biology & Anatomy, Alberta Children’s Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, AB, Canada
| | - J. David Aponte
- Department of Cell Biology & Anatomy, Alberta Children’s Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, AB, Canada
| | - Wei Liu
- Department of Cell Biology & Anatomy, Alberta Children’s Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, AB, Canada
| | - Rebecca M. Green
- Department of Cell Biology & Anatomy, Alberta Children’s Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, AB, Canada
| | - Jessica M. Mayeux
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
| | - K. Michael Pollard
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Daniel Pomp
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC, United States of America
| | - Steven C. Munger
- The Jackson Laboratory, Bar Harbor, ME, United States of America
| | | | - Charles C. Roseman
- Department of Evolution, Ecology, and Behavior, University of Illinois Urbana Champaign, Urbana, IL, United States of America
| | - Christopher J. Percival
- Department of Anthropology, Stony Brook University, Stony Brook, NY, United States of America
| | - James Cheverud
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - Ralph S. Marcucio
- Department of Orthopaedic Surgery, School of Medicine, University of California San Francisco, San Francisco, CA, United States of America
| | - Benedikt Hallgrímsson
- Department of Cell Biology & Anatomy, Alberta Children’s Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, AB, Canada
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32
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Salek Ardestani S, Aminafshar M, Zandi Baghche Maryam MB, Banabazi MH, Sargolzaei M, Miar Y. Signatures of selection analysis using whole-genome sequence data reveals novel candidate genes for pony and light horse types. Genome 2020; 63:387-396. [PMID: 32407640 DOI: 10.1139/gen-2020-0001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Natural selection and domestication have shaped modern horse populations, resulting in a vast range of phenotypically diverse breeds. Horse breeds are classified into three types (pony, light, and draft) generally based on their body type. Understanding the genetic basis of horse type variation and selective pressures related to the evolutionary trend can be particularly important for current selection strategies. Whole-genome sequences were generated for 14 pony and 32 light horses to investigate the genetic signatures of selection of the horse type in pony and light horses. In the overlapping extremes of the fixation index and nucleotide diversity results, we found novel genomic signatures of selective sweeps near key genes previously implicated in body measurements including C4ORF33, CRB1, CPN1, FAM13A, and FGF12 that may influence variation in pony and light horse types. This study contributes to a better understanding of the genetic background of differences between pony and light horse types.
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Affiliation(s)
- Siavash Salek Ardestani
- Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran
| | - Mehdi Aminafshar
- Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran
| | | | - Mohammad Hossein Banabazi
- Department of Biotechnology, Animal Science Research Institute of Iran, Agricultural Research, Education & Extension Organization, Karaj 3146618361, Iran
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON NIG 2W1, Canada.,Select Sires Inc., Plain City, OH 43064, USA
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada
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33
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Gupta P, Tripathi T, Singh N, Bhutiani N, Rai P, Gopal R. A review of genetics of nasal development and morphological variation. J Family Med Prim Care 2020; 9:1825-1833. [PMID: 32670926 PMCID: PMC7346930 DOI: 10.4103/jfmpc.jfmpc_1265_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/06/2020] [Accepted: 03/26/2020] [Indexed: 11/04/2022] Open
Abstract
The nose is central in the determination of facial esthetics. The variations in its structural characteristics greatly influence the ultimate dentoskeletal positioning at the end of an orthodontic therapy. A careful insight into its developmental etiology will greatly aid the health care professional in identifying patient's real concern about the facial appearance. This in turn will aid in the fabrication of a better treatment plan regarding the end placement goals for the teeth and jaws in all the three dimensions of space. However, this important structure is often missed as a part of the diagnostic and treatment planning regime owing to the lack of meticulous understanding of its developmental etiology by the orthodontists. The development of the nose in the embryo occurs in pre skeletal and skeletal phases by a well-coordinated and regulated interaction of multiple signaling cascades with the crucial importance of each factor in the entire mechanism. The five key factors, which control frontonasal development are sonic hedgehog (SHH), fibroblast growth factors (FGF), transforming growth factor β (TGFβ), wingless (WNT) proteins, and bone morphogenetic protein (BMP). The recent evidence suggests the association of various nasal dimensions and their related syndromes with multiple genes. The revelation of nasal genetic makeup in totality will aid in ascertaining the direction of growth, which will govern our orthodontic treatment results and will also act as a harbinger for potential genetic editing and tissue engineering. This article describes at length the morphological and genetic aspect of nasal growth and development in light of the gender and racial variability along with the emphasis on the importance of knowing these nasal features with regard to diagnosis and treatment planning in orthodontics.
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Affiliation(s)
- Prateek Gupta
- Department of Orthodontics and Dentofacial Orthopaedics, Maulana Azad Institute of Dental Sciences, Bahadur Shah ZafarMarg, New Delhi, India
| | - Tulika Tripathi
- Department of Orthodontics and Dentofacial Orthopaedics, Maulana Azad Institute of Dental Sciences, Bahadur Shah ZafarMarg, New Delhi, India
| | - Navneet Singh
- Department of Orthodontics and Dentofacial Orthopaedics, Maulana Azad Institute of Dental Sciences, Bahadur Shah ZafarMarg, New Delhi, India
| | - Neha Bhutiani
- Department of Orthodontics and Dentofacial Orthopaedics, Maulana Azad Institute of Dental Sciences, Bahadur Shah ZafarMarg, New Delhi, India
| | - Priyank Rai
- Department of Orthodontics and Dentofacial Orthopaedics, Maulana Azad Institute of Dental Sciences, Bahadur Shah ZafarMarg, New Delhi, India
| | - Ram Gopal
- Department of Orthodontics and Dentofacial Orthopaedics, Maulana Azad Institute of Dental Sciences, Bahadur Shah ZafarMarg, New Delhi, India
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34
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Xiong Z, Dankova G, Howe LJ, Lee MK, Hysi PG, de Jong MA, Zhu G, Adhikari K, Li D, Li Y, Pan B, Feingold E, Marazita ML, Shaffer JR, McAloney K, Xu SH, Jin L, Wang S, de Vrij FMS, Lendemeijer B, Richmond S, Zhurov A, Lewis S, Sharp GC, Paternoster L, Thompson H, Gonzalez-Jose R, Bortolini MC, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Uitterlinden AG, Ikram MA, Wolvius E, Kushner SA, Nijsten TEC, Palstra RJTS, Boehringer S, Medland SE, Tang K, Ruiz-Linares A, Martin NG, Spector TD, Stergiakouli E, Weinberg SM, Liu F, Kayser M. Novel genetic loci affecting facial shape variation in humans. eLife 2019; 8:e49898. [PMID: 31763980 PMCID: PMC6905649 DOI: 10.7554/elife.49898] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/22/2019] [Indexed: 12/14/2022] Open
Abstract
The human face represents a combined set of highly heritable phenotypes, but knowledge on its genetic architecture remains limited, despite the relevance for various fields. A series of genome-wide association studies on 78 facial shape phenotypes quantified from 3-dimensional facial images of 10,115 Europeans identified 24 genetic loci reaching study-wide suggestive association (p < 5 × 10-8), among which 17 were previously unreported. A follow-up multi-ethnic study in additional 7917 individuals confirmed 10 loci including six unreported ones (padjusted < 2.1 × 10-3). A global map of derived polygenic face scores assembled facial features in major continental groups consistent with anthropological knowledge. Analyses of epigenomic datasets from cranial neural crest cells revealed abundant cis-regulatory activities at the face-associated genetic loci. Luciferase reporter assays in neural crest progenitor cells highlighted enhancer activities of several face-associated DNA variants. These results substantially advance our understanding of the genetic basis underlying human facial variation and provide candidates for future in-vivo functional studies.
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Affiliation(s)
- Ziyi Xiong
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Gabriela Dankova
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Laurence J Howe
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
| | - Pirro G Hysi
- Department of Twin Research and Genetic EpidemiologyKing’s College LondonLondonUnited Kingdom
| | - Markus A de Jong
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Oral & Maxillofacial Surgery, Special Dental Care, and OrthodonticsErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenNetherlands
| | - Gu Zhu
- QIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Kaustubh Adhikari
- Department of Genetics, Evolution, and EnvironmentUniversity College LondonLondonUnited Kingdom
| | - Dan Li
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
| | - Yi Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Bo Pan
- Department of Auricular ReconstructionPlastic Surgery HospitalBeijingChina
| | - Eleanor Feingold
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
| | - John R Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
| | | | - Shu-Hua Xu
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | - Li Jin
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life SciencesFudan UniversityShanghaiChina
| | - Sijia Wang
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | - Femke MS de Vrij
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Bas Lendemeijer
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Stephen Richmond
- Applied Clinical Research and Public Health, University Dental SchoolCardiff UniversityCardiffUnited Kingdom
| | - Alexei Zhurov
- Applied Clinical Research and Public Health, University Dental SchoolCardiff UniversityCardiffUnited Kingdom
| | - Sarah Lewis
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Gemma C Sharp
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
- School of Oral and Dental SciencesUniversity of BristolBristolUnited Kingdom
| | - Lavinia Paternoster
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Holly Thompson
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Rolando Gonzalez-Jose
- Instituto Patagonico de Ciencias Sociales y Humanas, CENPAT-CONICETPuerto MadrynArgentina
| | | | - Samuel Canizales-Quinteros
- UNAM-Instituto Nacional de Medicina Genomica, Facultad de QuımicaUnidad de Genomica de Poblaciones Aplicada a la SaludMexico CityMexico
| | - Carla Gallo
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y FilosofıaUniversidad Peruana Cayetano HerediaLimaPeru
| | - Giovanni Poletti
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y FilosofıaUniversidad Peruana Cayetano HerediaLimaPeru
| | - Gabriel Bedoya
- GENMOL (Genetica Molecular)Universidad de AntioquiaMedellınColombia
| | | | - André G Uitterlinden
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Internal MedicineErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - M Arfan Ikram
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Eppo Wolvius
- Department of Oral & Maxillofacial Surgery, Special Dental Care, and OrthodonticsErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Steven A Kushner
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Tamar EC Nijsten
- Department of DermatologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Robert-Jan TS Palstra
- Department of BiochemistryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Stefan Boehringer
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenNetherlands
| | | | - Kun Tang
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
| | - Andres Ruiz-Linares
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life SciencesFudan UniversityShanghaiChina
- Aix-Marseille Université, CNRS, EFS, ADESMarseilleFrance
| | | | - Timothy D Spector
- Department of Twin Research and Genetic EpidemiologyKing’s College LondonLondonUnited Kingdom
| | - Evie Stergiakouli
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
- School of Oral and Dental SciencesUniversity of BristolBristolUnited Kingdom
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
- Department of AnthropologyUniversity of PittsburghPittsburghUnited States
| | - Fan Liu
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Manfred Kayser
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
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35
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Weinberg SM, Roosenboom J, Shaffer JR, Shriver MD, Wysocka J, Claes P. Hunting for genes that shape human faces: Initial successes and challenges for the future. Orthod Craniofac Res 2019; 22 Suppl 1:207-212. [PMID: 31074157 DOI: 10.1111/ocr.12268] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 12/08/2018] [Indexed: 12/19/2022]
Abstract
There is ample evidence from heritability studies, genetic syndromes and experimental animal models that facial morphology is strongly influenced by genes. In this brief review, we present an up-to-date overview of the efforts to identify genes associated with the size and shape of human facial features. We discuss recent methodological advances that have led to breakthroughs, but also the multitude of challenges facing the field. We offer perspective on possible applications of this line of research, particularly in the context of the precision genomics movement.
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Affiliation(s)
- Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Anthropology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jasmien Roosenboom
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - John R Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mark D Shriver
- Department of Anthropology, Pennsylvania State University, State College, Pennsylvania
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California
| | - Peter Claes
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.,Medical Imaging Research Center, MIRC, UZ Leuven, Leuven, Belgium.,Murdoch Childrens Research Institute, Melbourne, Vic., Australia
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36
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Lee HY, Cha S, Ban HJ, Kim IY, Park BR, Kim IJ, Hong KW. The age distribution of facial metrics in two large Korean populations. Sci Rep 2019; 9:14564. [PMID: 31601901 PMCID: PMC6786987 DOI: 10.1038/s41598-019-51121-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 09/25/2019] [Indexed: 11/19/2022] Open
Abstract
Growth and alterations in craniofacial morphology have attracted interest in many fields of science, especially physical anthropology, genetics and forensic sciences. We performed an analysis of craniofacial morphology alterations by gender and ageing stage in Korean populations. We studied 15 facial metrics using two large Korean populations (1,926 samples from the Korea Medicine Data Center cohort and 5,643 samples from the Ansan-Ansung cohort). Among the 15 metrics, 12 showed gender differences and tended to change with age. In both of the independent populations, brow ridge height, upper lip height, nasal tip height, and profile nasal length tended to increase with age, whereas outer canthal width, right palpebral fissure height, left palpebral fissure height, right upper lip thickness, left upper lip thickness, nasal tip protrusion, facial base width, and lower facial width tended to decrease. In conclusion, our findings suggest that ageing (past 40 years of age) might affect eye size, nose length, upper lip thickness, and facial width, possibly due to loss of elasticity in the face. Therefore, these facial metric changes could be applied to individual age prediction and aesthetic facial care.
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Affiliation(s)
- Hae-Young Lee
- Theragenetex Bioinstitute Co. Ltd, Suwon, 16229, Republic of Korea
| | - Seongwon Cha
- Future Medicine Division, Korea Institute of Oriental Medicine, Daejeon, 34054, Republic of Korea
| | - Hyo-Jeong Ban
- Future Medicine Division, Korea Institute of Oriental Medicine, Daejeon, 34054, Republic of Korea
| | - In-Young Kim
- Theragenetex Bioinstitute Co. Ltd, Suwon, 16229, Republic of Korea
| | - Bo-Reum Park
- Theragenetex Bioinstitute Co. Ltd, Suwon, 16229, Republic of Korea
| | - Ig-Jae Kim
- Center for Imaging Media Research, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Kyung-Won Hong
- Theragenetex Bioinstitute Co. Ltd, Suwon, 16229, Republic of Korea.
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37
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Lee HY, Cha S, Ban HJ, Kim IY, Park BR, Kim IJ, Hong KW. The age distribution of facial metrics in two large Korean populations. Sci Rep 2019. [PMID: 31601901 DOI: 10.1038/s41598-019-51121-z.pmid:31601901;pmcid:pmc6786987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Growth and alterations in craniofacial morphology have attracted interest in many fields of science, especially physical anthropology, genetics and forensic sciences. We performed an analysis of craniofacial morphology alterations by gender and ageing stage in Korean populations. We studied 15 facial metrics using two large Korean populations (1,926 samples from the Korea Medicine Data Center cohort and 5,643 samples from the Ansan-Ansung cohort). Among the 15 metrics, 12 showed gender differences and tended to change with age. In both of the independent populations, brow ridge height, upper lip height, nasal tip height, and profile nasal length tended to increase with age, whereas outer canthal width, right palpebral fissure height, left palpebral fissure height, right upper lip thickness, left upper lip thickness, nasal tip protrusion, facial base width, and lower facial width tended to decrease. In conclusion, our findings suggest that ageing (past 40 years of age) might affect eye size, nose length, upper lip thickness, and facial width, possibly due to loss of elasticity in the face. Therefore, these facial metric changes could be applied to individual age prediction and aesthetic facial care.
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Affiliation(s)
- Hae-Young Lee
- Theragenetex Bioinstitute Co. Ltd, Suwon, 16229, Republic of Korea
| | - Seongwon Cha
- Future Medicine Division, Korea Institute of Oriental Medicine, Daejeon, 34054, Republic of Korea
| | - Hyo-Jeong Ban
- Future Medicine Division, Korea Institute of Oriental Medicine, Daejeon, 34054, Republic of Korea
| | - In-Young Kim
- Theragenetex Bioinstitute Co. Ltd, Suwon, 16229, Republic of Korea
| | - Bo-Reum Park
- Theragenetex Bioinstitute Co. Ltd, Suwon, 16229, Republic of Korea
| | - Ig-Jae Kim
- Center for Imaging Media Research, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Kyung-Won Hong
- Theragenetex Bioinstitute Co. Ltd, Suwon, 16229, Republic of Korea.
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38
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Han X, Qassim A, An J, Marshall H, Zhou T, Ong JS, Hassall MM, Hysi PG, Foster PJ, Khaw PT, Mackey DA, Gharahkhani P, Khawaja AP, Hewitt AW, Craig JE, MacGregor S. Genome-wide association analysis of 95 549 individuals identifies novel loci and genes influencing optic disc morphology. Hum Mol Genet 2019; 28:3680-3690. [DOI: 10.1093/hmg/ddz193] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/30/2019] [Accepted: 08/04/2019] [Indexed: 12/13/2022] Open
Abstract
Abstract
Optic nerve head morphology is affected by several retinal diseases. We measured the vertical optic disc diameter (DD) of the UK Biobank (UKBB) cohort (N = 67 040) and performed the largest genome-wide association study (GWAS) of DD to date. We identified 81 loci (66 novel) for vertical DD. We then replicated the novel loci in International Glaucoma Genetic Consortium (IGGC, N = 22 504) and European Prospective Investigation into Cancer–Norfolk (N = 6005); in general the concordance in effect sizes was very high (correlation in effect size estimates 0.90): 44 of the 66 novel loci were significant at P < 0.05, with 19 remaining significant after Bonferroni correction. We identified another 26 novel loci in the meta-analysis of UKBB and IGGC data. Gene-based analyses identified an additional 57 genes. Human ocular tissue gene expression analysis showed that most of the identified genes are enriched in optic nerve head tissue. Some of the identified loci exhibited pleiotropic effects with vertical cup-to-disc ratio, intraocular pressure, glaucoma and myopia. These results can enhance our understanding of the genetics of optic disc morphology and shed light on the genetic findings for other ophthalmic disorders such as glaucoma and other optic nerve diseases.
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Affiliation(s)
- Xikun Han
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Medicine, University of Queensland, St Lucia, Brisbane, Australia
| | - Ayub Qassim
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
| | - Jiyuan An
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Henry Marshall
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
| | - Tiger Zhou
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
| | - Jue-Sheng Ong
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Mark M Hassall
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
| | - Pirro G Hysi
- Department of Ophthalmology, King’s College London, St. Thomas’ Hospital, London, UK
| | - Paul J Foster
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Peng T Khaw
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - David A Mackey
- Menzies Institute for Medical Research, University of Tasmania, Australia
- Lions Eye Institute, Centre for Ophthalmology and Visual Science, University of Western Australia, Perth, Australia
| | - Puya Gharahkhani
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Anthony P Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Australia
- Centre for Eye Research Australia, University of Melbourne, Melbourne, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
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39
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SOX9 in cartilage development and disease. Curr Opin Cell Biol 2019; 61:39-47. [PMID: 31382142 DOI: 10.1016/j.ceb.2019.07.008] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 07/06/2019] [Indexed: 12/18/2022]
Abstract
SOX9 is a pivotal transcription factor in chondrocytes, a lineage essential in skeletogenesis. Its mandatory role in transactivating many cartilage-specific genes is well established, whereas its pioneer role in lineage specification, which along with transactivation defines master transcription factors, remains to be better defined. Abundant, but yet incomplete evidence exists that intricate molecular networks control SOX9 activity during the multi-step chondrogenesis pathway. They include a highly modular genetic regulation, post-transcriptional and post-translational modifications, and varying sets of functional partners. Fully uncovering SOX9 actions and regulation is fundamental to explain mechanisms underlying many diseases that directly or indirectly affect SOX9 activities and to design effective disease treatments. We here review current knowledge, highlight recent discoveries, and propose new research directions to answer remaining questions.
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40
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Li Y, Zhao W, Li D, Tao X, Xiong Z, Liu J, Zhang W, Ji A, Tang K, Liu F, Li C. EDAR, LYPLAL1, PRDM16, PAX3, DKK1, TNFSF12, CACNA2D3, and SUPT3H gene variants influence facial morphology in a Eurasian population. Hum Genet 2019; 138:681-689. [PMID: 31025105 DOI: 10.1007/s00439-019-02023-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/20/2019] [Indexed: 12/19/2022]
Abstract
In human society, the facial surface is visible and recognizable based on the facial shape variation which represents a set of highly polygenic and correlated complex traits. Understanding the genetic basis underlying facial shape traits has important implications in population genetics, developmental biology, and forensic science. A number of single nucleotide polymorphisms (SNPs) are associated with human facial shape variation, mostly in European populations. To bridge the gap between European and Asian populations in term of the genetic basis of facial shape variation, we examined the effect of these SNPs in a European-Asian admixed Eurasian population which included a total of 612 individuals. The coordinates of 17 facial landmarks were derived from high resolution 3dMD facial images, and 136 Euclidean distances between all pairs of landmarks were quantitatively derived. DNA samples were genotyped using the Illumina Infinium Global Screening Array and imputed using the 1000 Genomes reference panel. Genetic association between 125 previously reported facial shape-associated SNPs and 136 facial shape phenotypes was tested using linear regression. As a result, a total of eight SNPs from different loci demonstrated significant association with one or more facial shape traits after adjusting for multiple testing (significance threshold p < 1.28 × 10-3), together explaining up to 6.47% of sex-, age-, and BMI-adjusted facial phenotype variance. These included EDAR rs3827760, LYPLAL1 rs5781117, PRDM16 rs4648379, PAX3 rs7559271, DKK1 rs1194708, TNFSF12 rs80067372, CACNA2D3 rs56063440, and SUPT3H rs227833. Notably, the EDAR rs3827760 and LYPLAL1 rs5781117 SNPs displayed significant association with eight and seven facial phenotypes, respectively (2.39 × 10-5 < p < 1.28 × 10-3). The majority of these SNPs showed a distinct allele frequency between European and East Asian reference panels from the 1000 Genomes Project. These results showed the details of above eight genes influence facial shape variation in a Eurasian population.
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Affiliation(s)
- Yi Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Wenting Zhao
- Key Laboratory of Forensic Genetics, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, China
| | - Dan Li
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xianming Tao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ziyi Xiong
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jing Liu
- Key Laboratory of Forensic Genetics, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, China
| | - Wei Zhang
- Key Laboratory of Forensic Genetics, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, China
| | - Anquan Ji
- Key Laboratory of Forensic Genetics, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, China
| | - Kun Tang
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Caixia Li
- Key Laboratory of Forensic Genetics, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, China.
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41
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Wu W, Zhai G, Xu Z, Hou B, Liu D, Liu T, Liu W, Ren F. Whole-exome sequencing identified four loci influencing craniofacial morphology in northern Han Chinese. Hum Genet 2019; 138:601-611. [PMID: 30968251 PMCID: PMC6554238 DOI: 10.1007/s00439-019-02008-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/02/2019] [Indexed: 11/30/2022]
Abstract
Facial shape differences are one of the most significant phenotypes in humans. It is affected largely by skull shape. However, research into the genetic basis of the craniofacial morphology has rarely been reported. The present study aimed to identify genetic variants influencing craniofacial morphology in northern Han Chinese through whole-exome sequencing (WES). Phenotypic data of the volunteers’ faces and skulls were obtained through three-dimensional CT scan of the skull. A total of 48 phenotypes (35 facial and 13 cranial phenotypes) were used for the bioinformatics analysis. Four genetic loci were identified affecting the craniofacial shapes. The four candidate genes are RGPD3, IGSF3, SLC28A3, and USP40. Four single-nucleotide polymorphism (SNP) site mutations in RGPD3, IGSF3, and USP40 were significantly associated with the skull shape (p < 1×10−6), and three SNP site mutations in RGPD3, IGSF3, and SLC28A3 were significantly associated with the facial shape (p < 1×10−6). The rs62152530 site mutation in the RGPD3 gene may be closely associated with the nasal length, ear length, and alar width. The rs647711 site mutation in the IGSF3 gene may be closely associated with the nasal length, mandibular width, and width between the mental foramina. The rs10868138 site mutation in the SLC28A3 gene may be associated with the nasal length, alar width, width between tragus, and width between the mental foramina. The rs1048603 and rs838543 site mutations in the USP40 gene may be closely associated with the pyriform aperture width. Our findings provide useful genetic information for the determination of face morphology.
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Affiliation(s)
- Wei Wu
- School of Humanities and Management, Jinzhou Medical University, Jinzhou, 121001, Liaoning, People's Republic of China.,Biological Anthropology Institute, Jinzhou Medical University, No. 40, Section 3, Songpo Road, Linghe District, Jinzhou, 121001, Liaoning, People's Republic of China.,Liaoning Province Key Laboratory of Chinese Physical Characteristics Research (LPKL-CPCR), Jinzhou, 121001, Liaoning, People's Republic of China
| | - Guiying Zhai
- Biological Anthropology Institute, Jinzhou Medical University, No. 40, Section 3, Songpo Road, Linghe District, Jinzhou, 121001, Liaoning, People's Republic of China.,Liaoning Province Key Laboratory of Chinese Physical Characteristics Research (LPKL-CPCR), Jinzhou, 121001, Liaoning, People's Republic of China
| | - Zejun Xu
- Biological Anthropology Institute, Jinzhou Medical University, No. 40, Section 3, Songpo Road, Linghe District, Jinzhou, 121001, Liaoning, People's Republic of China.,Liaoning Province Key Laboratory of Chinese Physical Characteristics Research (LPKL-CPCR), Jinzhou, 121001, Liaoning, People's Republic of China
| | - Bo Hou
- Biological Anthropology Institute, Jinzhou Medical University, No. 40, Section 3, Songpo Road, Linghe District, Jinzhou, 121001, Liaoning, People's Republic of China.,Liaoning Province Key Laboratory of Chinese Physical Characteristics Research (LPKL-CPCR), Jinzhou, 121001, Liaoning, People's Republic of China
| | - Dahua Liu
- Biological Anthropology Institute, Jinzhou Medical University, No. 40, Section 3, Songpo Road, Linghe District, Jinzhou, 121001, Liaoning, People's Republic of China.,Liaoning Province Key Laboratory of Chinese Physical Characteristics Research (LPKL-CPCR), Jinzhou, 121001, Liaoning, People's Republic of China
| | - Tianyi Liu
- Department of Plastic and Maxillofacial Surgery, Uppsala University, Uppsala, Sweden
| | - Wei Liu
- Biological Anthropology Institute, Jinzhou Medical University, No. 40, Section 3, Songpo Road, Linghe District, Jinzhou, 121001, Liaoning, People's Republic of China.,Liaoning Province Key Laboratory of Chinese Physical Characteristics Research (LPKL-CPCR), Jinzhou, 121001, Liaoning, People's Republic of China
| | - Fu Ren
- Biological Anthropology Institute, Jinzhou Medical University, No. 40, Section 3, Songpo Road, Linghe District, Jinzhou, 121001, Liaoning, People's Republic of China. .,Liaoning Province Key Laboratory of Chinese Physical Characteristics Research (LPKL-CPCR), Jinzhou, 121001, Liaoning, People's Republic of China.
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42
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Yang C, Ren J, Li B, Jin C, Ma C, Cheng C, Sun Y, Shi X. Identification of gene biomarkers in patients with postmenopausal osteoporosis. Mol Med Rep 2018; 19:1065-1073. [PMID: 30569177 PMCID: PMC6323213 DOI: 10.3892/mmr.2018.9752] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 09/18/2018] [Indexed: 12/17/2022] Open
Abstract
Postmenopausal osteoporosis (PMOP) is a major public health concern worldwide. The present study aimed to provide evidence to assist in the development of specific novel biomarkers for PMOP. Differentially expressed genes (DEGs) were identified between PMOP and normal controls by integrated microarray analyses of the Gene Expression Omnibus (GEO) database, and the optimal diagnostic gene biomarkers for PMOP were identified with LASSO and Boruta algorithms. Classification models, including support vector machine (SVM), decision tree and random forests models, were established to test the diagnostic value of identified gene biomarkers for PMOP. Functional annotations and protein‑protein interaction (PPI) network constructions were also conducted. Integrated microarray analyses (GSE56815, GSE13850 and GSE7429) of the GEO database were employed, and 1,320 DEGs were identified between PMOP and normal controls. An 11‑gene combination was also identified as an optimal biomarker for PMOP by feature selection and classification methods using SVM, decision tree and random forest models. This combination was comprised of the following genes: Dehydrogenase E1 and transketolase domain containing 1 (DHTKD1), osteoclast stimulating factor 1 (OSTF1), G protein‑coupled receptor 116 (GPR116), BCL2 interacting killer, adrenoceptor β1 (ADRB1), neogenin 1 (NEO1), RB binding protein 4 (RBBP4), GPR87, cylicin 2, EF‑hand calcium binding domain 1 and DEAH‑box helicase 35. RBBP4 (degree=12) was revealed to be the hub gene of this PMOP‑specific PPI network. Among these 11 genes, three genes (OSTF1, ADRB1 and NEO1) were speculated to serve roles in PMOP by regulating the balance between bone formation and bone resorption, while two genes (GPR87 and GPR116) may be involved in PMOP by regulating the nuclear factor‑κB signaling pathway. Furthermore, DHTKD1 and RBBP4 may be involved in PMOP by regulating mitochondrial dysfunction and interacting with ESR1, respectively. In conclusion, the findings of the current study provided an insight for exploring the mechanism and developing novel biomarkers for PMOP. Further studies are required to test the diagnostic value for PMOP prior to use in a clinical setting.
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Affiliation(s)
- Chenggang Yang
- Department of Research and Development, Gu'an Bojian Bio‑Technology Co., Ltd., Langfang, Hebei 065000, P.R. China
| | - Jing Ren
- Department of Big Data, Beijing Medintell Bioinformatic Technology Co., Ltd., Beijing 100081, P.R. China
| | - Bangling Li
- Department of Big Data, Beijing Medintell Bioinformatic Technology Co., Ltd., Beijing 100081, P.R. China
| | - Chuandi Jin
- Department of Big Data, Beijing Medintell Bioinformatic Technology Co., Ltd., Beijing 100081, P.R. China
| | - Cui Ma
- Department of Research and Development, Gu'an Bojian Bio‑Technology Co., Ltd., Langfang, Hebei 065000, P.R. China
| | - Cheng Cheng
- Department of Big Data, Beijing Medintell Bioinformatic Technology Co., Ltd., Beijing 100081, P.R. China
| | - Yaolan Sun
- Department of Big Data, Beijing Medintell Bioinformatic Technology Co., Ltd., Beijing 100081, P.R. China
| | - Xiaofeng Shi
- Department of Research and Development, Gu'an Bojian Bio‑Technology Co., Ltd., Langfang, Hebei 065000, P.R. China
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43
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Richmond S, Howe LJ, Lewis S, Stergiakouli E, Zhurov A. Facial Genetics: A Brief Overview. Front Genet 2018; 9:462. [PMID: 30386375 PMCID: PMC6198798 DOI: 10.3389/fgene.2018.00462] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/20/2018] [Indexed: 12/20/2022] Open
Abstract
Historically, craniofacial genetic research has understandably focused on identifying the causes of craniofacial anomalies and it has only been within the last 10 years, that there has been a drive to detail the biological basis of normal-range facial variation. This initiative has been facilitated by the availability of low-cost hi-resolution three-dimensional systems which have the ability to capture the facial details of thousands of individuals quickly and accurately. Simultaneous advances in genotyping technology have enabled the exploration of genetic influences on facial phenotypes, both in the present day and across human history. There are several important reasons for exploring the genetics of normal-range variation in facial morphology. - Disentangling the environmental factors and relative parental biological contributions to heritable traits can help to answer the age-old question "why we look the way that we do?" - Understanding the etiology of craniofacial anomalies; e.g., unaffected family members of individuals with non-syndromic cleft lip/palate (nsCL/P) have been shown to differ in terms of normal-range facial variation to the general population suggesting an etiological link between facial morphology and nsCL/P. - Many factors such as ancestry, sex, eye/hair color as well as distinctive facial features (such as, shape of the chin, cheeks, eyes, forehead, lips, and nose) can be identified or estimated using an individual's genetic data, with potential applications in healthcare and forensics. - Improved understanding of historical selection and adaptation relating to facial phenotypes, for example, skin pigmentation and geographical latitude. - Highlighting what is known about shared facial traits, medical conditions and genes.
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Affiliation(s)
- Stephen Richmond
- Applied Clinical Research and Public Health, School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff, United Kingdom
| | - Laurence J. Howe
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
- Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Sarah Lewis
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
- School of Oral and Dental Sciences, University of Bristol, Bristol, United Kingdom
| | - Evie Stergiakouli
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
- School of Oral and Dental Sciences, University of Bristol, Bristol, United Kingdom
| | - Alexei Zhurov
- Applied Clinical Research and Public Health, School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff, United Kingdom
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