1
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Vanneste M, Hoskens H, Goovaerts S, Matthews H, Aponte JD, Cole J, Shriver M, Marazita ML, Weinberg SM, Walsh S, Richmond S, Klein OD, Spritz RA, Peeters H, Hallgrímsson B, Claes P. Syndrome-informed phenotyping identifies a polygenic background for achondroplasia-like facial variation in the general population. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570544. [PMID: 38106188 PMCID: PMC10723447 DOI: 10.1101/2023.12.07.570544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Human craniofacial shape is highly variable yet highly heritable with genetic variants interacting through multiple layers of development. Here, we hypothesize that Mendelian phenotypes represent the extremes of a phenotypic spectrum and, using achondroplasia as an example, we introduce a syndrome-informed phenotyping approach to identify genomic loci associated with achondroplasia-like facial variation in the normal population. We compared three-dimensional facial scans from 43 individuals with achondroplasia and 8246 controls to calculate achondroplasia-like facial scores. Multivariate GWAS of the control scores revealed a polygenic basis for normal facial variation along an achondroplasia-specific shape axis, identifying genes primarily involved in skeletal development. Jointly modeling these genes in two independent control samples showed craniofacial effects approximating the characteristic achondroplasia phenotype. These findings suggest that both complex and Mendelian genetic variation act on the same developmentally determined axes of facial variation, providing new insights into the genetic intersection of complex traits and Mendelian disorders.
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Affiliation(s)
| | - Hanne Hoskens
- Department of Cell Biology & Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Seppe Goovaerts
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Harold Matthews
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Jose D Aponte
- Department of Cell Biology & Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Joanne Cole
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Mark Shriver
- Department of Anthropology, Pennsylvania State University, State College, PA, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
| | - Stephen Richmond
- Applied Clinical Research and Public Health, School of Dentistry, Cardiff University, Cardiff, UK
| | - Ophir D Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, CA, 94143, USA
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Richard A Spritz
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Hilde Peeters
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Benedikt Hallgrímsson
- Department of Cell Biology & Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
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2
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Goovaerts S, Hoskens H, Eller RJ, Herrick N, Musolf AM, Justice CM, Yuan M, Naqvi S, Lee MK, Vandermeulen D, Szabo-Rogers HL, Romitti PA, Boyadjiev SA, Marazita ML, Shaffer JR, Shriver MD, Wysocka J, Walsh S, Weinberg SM, Claes P. Joint multi-ancestry and admixed GWAS reveals the complex genetics behind human cranial vault shape. Nat Commun 2023; 14:7436. [PMID: 37973980 PMCID: PMC10654897 DOI: 10.1038/s41467-023-43237-8] [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: 12/07/2022] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
The cranial vault in humans is highly variable, clinically relevant, and heritable, yet its genetic architecture remains poorly understood. Here, we conduct a joint multi-ancestry and admixed multivariate genome-wide association study on 3D cranial vault shape extracted from magnetic resonance images of 6772 children from the ABCD study cohort yielding 30 genome-wide significant loci. Follow-up analyses indicate that these loci overlap with genomic risk loci for sagittal craniosynostosis, show elevated activity cranial neural crest cells, are enriched for processes related to skeletal development, and are shared with the face and brain. We present supporting evidence of regional localization for several of the identified genes based on expression patterns in the cranial vault bones of E15.5 mice. Overall, our study provides a comprehensive overview of the genetics underlying normal-range cranial vault shape and its relevance for understanding modern human craniofacial diversity and the etiology of congenital malformations.
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Affiliation(s)
- Seppe Goovaerts
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium.
| | - Hanne Hoskens
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Ryan J Eller
- Department of Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Noah Herrick
- Department of Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Anthony M Musolf
- Statistical Genetics Section, Computational and Statistical Genomics Branch, NHGRI, NIH, MD, Baltimore, USA
| | - Cristina M Justice
- Genometrics Section, Computational and Statistical Genomics Branch, Division of Intramural Research, NHGRI, NIH, Baltimore, MD, USA
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Meng Yuan
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Genetics and Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Myoung Keun Lee
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dirk Vandermeulen
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Heather L Szabo-Rogers
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatchewan, Canada
| | - Paul A Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, IA, USA
| | - Simeon A Boyadjiev
- Department of Pediatrics, University of California Davis, Sacramento, CA, USA
| | - Mary L Marazita
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - John R Shaffer
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mark D Shriver
- Department of Anthropology, Pennsylvania State University, State College, 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 Indianapolis, Indianapolis, IN, USA
| | - Seth M Weinberg
- Department of Oral and Craniofacial Sciences, 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.
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium.
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.
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3
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Cho HW, Ban HJ, Jin HS, Cha S, Eom YB. A genome-wide association scan reveals novel loci for facial traits of Koreans. Genomics 2023; 115:110710. [PMID: 37734486 DOI: 10.1016/j.ygeno.2023.110710] [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: 07/05/2023] [Revised: 09/07/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023]
Abstract
DNA-based prediction of externally visible characteristics (EVC) with SNPs is one of the research areas of interest in the forensic field. Based on a previous study performing GWAS on facial traits in a Korean population, herein, we present results stemming from GWA analysis with KoreanChip and novel genetic loci satisfying genome-wide significant level. We discovered a total of 20 signals and 12 loci were found to have novel associations with facial traits, including six loci located in intergenic regions and six loci located at UBE2O, HECTD2, CCDC108, TPK1, FCN2, and FRMPD1. Additionally, we performed a polygenic score analysis for 33 distance-related traits in facial phenotyping and determined genetic relationships between facial traits and SNPs using the GCTA program. The results of the current study offer an understanding of how facial morphology is influenced by complex genetic structures and provide insights into forensic investigation and population genetics.
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Affiliation(s)
- Hye-Won Cho
- Department of Medical Sciences, Graduate School, Soonchunhyang University, Asan, Chungnam 31538, Republic of Korea
| | - Hyo-Jeong Ban
- Korea Medicine (KM) Data Division, Korea Institute of Oriental Medicine, Daejeon 34054, Republic of Korea
| | - Hyun-Seok Jin
- Department of Biomedical Laboratory Science, College of Life and Health Sciences, Hoseo University, Asan, Chungnam 31499, Republic of Korea
| | - Seongwon Cha
- Korea Medicine (KM) Data Division, Korea Institute of Oriental Medicine, Daejeon 34054, Republic of Korea.
| | - Yong-Bin Eom
- Department of Medical Sciences, Graduate School, Soonchunhyang University, Asan, Chungnam 31538, Republic of Korea; Department of Biomedical Laboratory Science, College of Medical Sciences, Soonchunhyang University, Asan, Chungnam 31538, Republic of Korea.
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4
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Kaucka M. Cis-regulatory landscapes in the evolution and development of the mammalian skull. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220079. [PMID: 37183897 PMCID: PMC10184250 DOI: 10.1098/rstb.2022.0079] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Extensive morphological variation found in mammals reflects the wide spectrum of their ecological adaptations. The highest morphological diversity is present in the craniofacial region, where geometry is mainly dictated by the bony skull. Mammalian craniofacial development represents complex multistep processes governed by numerous conserved genes that require precise spatio-temporal control. A central question in contemporary evolutionary biology is how a defined set of conserved genes can orchestrate formation of fundamentally different structures, and therefore how morphological variability arises. In principle, differential gene expression patterns during development are the source of morphological variation. With the emergence of multicellular organisms, precise regulation of gene expression in time and space is attributed to cis-regulatory elements. These elements contribute to higher-order chromatin structure and together with trans-acting factors control transcriptional landscapes that underlie intricate morphogenetic processes. Consequently, divergence in cis-regulation is believed to rewire existing gene regulatory networks and form the core of morphological evolution. This review outlines the fundamental principles of the genetic code and genomic regulation interplay during development. Recent work that deepened our comprehension of cis-regulatory element origin, divergence and function is presented here to illustrate the state-of-the-art research that uncovered the principles of morphological novelty. This article is part of the theme issue 'The mammalian skull: development, structure and function'.
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Affiliation(s)
- Marketa Kaucka
- Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
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5
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Kienkas K, Jakobsone G, Salms G. The Facial Characteristics of Individuals with Posterior Crossbite: A Cross-Sectional Study. Healthcare (Basel) 2023; 11:1881. [PMID: 37444714 DOI: 10.3390/healthcare11131881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/21/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Facial morphology is known to be influenced by genetic and environmental factors. Scientific evidence regarding facial parameters in patients with posterior crossbite is lacking. This study aimed to investigate the association between posterior crossbite and facial parameters. This cross-sectional study included 34 adolescents with and 34 adolescents without posterior crossbite in the age range from 13 to 15 years. Facial surface scans were acquired with a 3dMD imaging system, and landmark-based analysis was performed. Data were analyzed using the Mann-Whitney U test and Spearman's correlations. Individuals in the control group had lower face heights (females: p = 0.003, r = 0.45; males: p = 0.005, r = 0.57). The control group females presented with smaller intercanthal width (p = 0.04; r = 0.31) and anatomical nose width (p = 0.004; r = 0.43) compared with the crossbite group females. The males in the control group had wider nostrils. In the control group, significant correlations among different facial parameters were more common, including the correlations between eye width and other transversal face measurements. On the contrary, the facial width was correlated with nasal protrusion (r = 0.657; p < 0.01) and the morphological width of the nose (r = 0.505; p < 0.05) in the crossbite group alone. In both groups, the philtrum width was linked with the anatomical and morphological widths of the nose. Conclusions: Patients with posterior crossbites have increased face height and different patterns of facial proportions compared with individuals without crossbites.
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Affiliation(s)
- Karlina Kienkas
- Department of Orthodontics, Institute of Stomatology, Riga Stradins University, LV-1007 Riga, Latvia
| | - Gundega Jakobsone
- Department of Orthodontics, Institute of Stomatology, Riga Stradins University, LV-1007 Riga, Latvia
| | - Girts Salms
- Department of Oral and Maxillofacial Surgery, Institute of Stomatology, Riga Stradins University, LV-1007 Riga, Latvia
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6
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Ma L, Xiao D, Kim D, Lian C, Kuang T, Liu Q, Deng H, Yang E, Liebschner MAK, Gateno J, Xia JJ, Yap PT. Simulation of Postoperative Facial Appearances via Geometric Deep Learning for Efficient Orthognathic Surgical Planning. IEEE TRANSACTIONS ON MEDICAL IMAGING 2023; 42:336-345. [PMID: 35657829 PMCID: PMC10037541 DOI: 10.1109/tmi.2022.3180078] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Orthognathic surgery corrects jaw deformities to improve aesthetics and functions. Due to the complexity of the craniomaxillofacial (CMF) anatomy, orthognathic surgery requires precise surgical planning, which involves predicting postoperative changes in facial appearance. To this end, most conventional methods involve simulation with biomechanical modeling methods, which are labor intensive and computationally expensive. Here we introduce a learning-based framework to speed up the simulation of postoperative facial appearances. Specifically, we introduce a facial shape change prediction network (FSC-Net) to learn the nonlinear mapping from bony shape changes to facial shape changes. FSC-Net is a point transform network weakly-supervised by paired preoperative and postoperative data without point-wise correspondence. In FSC-Net, a distance-guided shape loss places more emphasis on the jaw region. A local point constraint loss restricts point displacements to preserve the topology and smoothness of the surface mesh after point transformation. Evaluation results indicate that FSC-Net achieves 15× speedup with accuracy comparable to a state-of-the-art (SOTA) finite-element modeling (FEM) method.
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7
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Head Shape Heritability in the Hungarian Meadow Viper Vipera ursinii rakosiensis. Animals (Basel) 2023; 13:ani13020322. [PMID: 36670862 PMCID: PMC9854840 DOI: 10.3390/ani13020322] [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: 12/07/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
Understanding heritability patterns in functionally relevant traits is a cornerstone for evaluating their evolutionary potential and their role in local adaptation. In this study, we investigated patterns of heritability in the head shape of the Hungarian meadow viper (Vipera ursinii rakosiensis). To this end, we used geometric morphometric data from 12 families composed of 8 mothers, 6 fathers and 221 offspring, bred in captivity at the Hungarian Meadow Viper Conservation Centre (Hungary). We separately evaluated maternal and paternal contributions to the offspring phenotype, in addition to additive genetic effects, all determined using a mixed animal model. Our results indicate a strong genetic and maternal contribution to head shape variations. In contrast, the paternal effects-which are rarely evaluated in wild-ranging species-as well as residual environmental variance, were minimal. Overall, our results indicate a high evolutionary potential for head shape in the Hungarian meadow viper, which suggests a strong contribution of this ecologically important trait in shaping the ability of this endangered species to adapt to changing conditions and/or habitats. Furthermore, our results suggest that maternal phenotypes should be carefully considered when designing captive breeding parental pairs for reinforcing the adaptive capacity of threatened populations, whereas the paternal phenotypes seem less relevant.
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8
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Ogbunugafor CB, Edge MD. Gattaca as a lens on contemporary genetics: marking 25 years into the film's "not-too-distant" future. Genetics 2022; 222:iyac142. [PMID: 36218390 PMCID: PMC9713434 DOI: 10.1093/genetics/iyac142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
The 1997 film Gattaca has emerged as a canonical pop culture reference used to discuss modern controversies in genetics and bioethics. It appeared in theaters a few years prior to the announcement of the "completion" of the human genome (2000), as the science of human genetics was developing a renewed sense of its social implications. The story is set in a near-future world in which parents can, with technological assistance, influence the genetic composition of their offspring on the basis of predicted life outcomes. The current moment-25 years after the film's release-offers an opportunity to reflect on where society currently stands with respect to the ideas explored in Gattaca. Here, we review and discuss several active areas of genetic research-genetic prediction, embryo selection, forensic genetics, and others-that interface directly with scenes and concepts in the film. On its silver anniversary, we argue that Gattaca remains an important reflection of society's expectations and fears with respect to the ways that genetic science has manifested in the real world. In accompanying supplemental material, we offer some thought questions to guide group discussions inside and outside of the classroom.
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Affiliation(s)
- C Brandon Ogbunugafor
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
- Vermont Complex Systems Center, Burlington, VT 05401, USA
| | - Michael D Edge
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
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Hardin AM, Knigge RP, Duren DL, Williams-Blangero S, Subedi J, Mahaney MC, Sherwood RJ. Genetic influences on dentognathic morphology in the Jirel population of Nepal. Anat Rec (Hoboken) 2022; 305:2137-2157. [PMID: 34981668 PMCID: PMC9250551 DOI: 10.1002/ar.24857] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022]
Abstract
Patterns of genetic variation and covariation impact the evolution of the craniofacial complex and contribute to clinically significant malocclusions in modern human populations. Previous quantitative genetic studies have estimated the heritabilities and genetic correlations of skeletal and dental traits in humans and nonhuman primates, but none have estimated these quantitative genetic parameters across the dentognathic complex. A large and powerful pedigree from the Jirel population of Nepal was leveraged to estimate heritabilities and genetic correlations in 62 maxillary and mandibular arch dimensions, incisor and canine lengths, and post-canine tooth crown areas (N ≥ 739). Quantitative genetic parameter estimation was performed using maximum likelihood-based variance decomposition. Residual heritability estimates were significant for all traits, ranging from 0.269 to 0.898. Genetic correlations were positive for all trait pairs. Principal components analyses of the phenotypic and genetic correlation matrices indicate an overall size effect across all measurements on the first principal component. Additional principal components demonstrate positive relationships between post-canine tooth crown areas and arch lengths and negative relationships between post-canine tooth crown areas and arch widths, and between arch lengths and arch widths. Based on these findings, morphological variation in the human dentognathic complex may be constrained by genetic relationships between dental dimensions and arch lengths, with weaker genetic correlations between these traits and arch widths allowing for variation in arch shape. The patterns identified are expected to have impacted the evolution of the dentognathic complex and its genetic architecture as well as the prevalence of dental crowding in modern human populations.
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Affiliation(s)
- Anna M. Hardin
- Biology Department, Western Oregon University
- Craniofacial Research Center, Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine
- Department of Orthopaedic Surgery, University of Missouri School of Medicine
| | - Ryan P. Knigge
- Craniofacial Research Center, Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine
- Department of Orthopaedic Surgery, University of Missouri School of Medicine
- Department of Integrative Biology and Physiology, University of Minnesota Medical School
| | - Dana L. Duren
- Craniofacial Research Center, Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine
- Department of Orthopaedic Surgery, University of Missouri School of Medicine
| | - Sarah Williams-Blangero
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley
| | | | - Michael C. Mahaney
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley
| | - Richard J. Sherwood
- Craniofacial Research Center, Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine
- Department of Orthopaedic Surgery, University of Missouri School of Medicine
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10
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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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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: Challenges and Progress 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] [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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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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13
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Null M, Yilmaz F, Astling D, Yu HC, Cole JB, Hallgrímsson B, Santorico SA, Spritz RA, Shaikh TH, Hendricks AE. Genome-wide analysis of copy number variants and normal facial variation in a large cohort of Bantu Africans. HGG ADVANCES 2022; 3:100082. [PMID: 35047866 PMCID: PMC8756499 DOI: 10.1016/j.xhgg.2021.100082] [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: 07/15/2021] [Accepted: 12/21/2021] [Indexed: 11/28/2022] Open
Abstract
Similarity in facial characteristics between relatives suggests a strong genetic component underlies facial variation. While there have been numerous studies of the genetics of facial abnormalities and, more recently, single nucleotide polymorphism (SNP) genome-wide association studies (GWASs) of normal facial variation, little is known about the role of genetic structural variation in determining facial shape. In a sample of Bantu African children, we found that only 9% of common copy number variants (CNVs) and 10-kb CNV analysis windows are well tagged by SNPs (r2 ≥ 0.8), indicating that associations with our internally called CNVs were not captured by previous SNP-based GWASs. Here, we present a GWAS and gene set analysis of the relationship between normal facial variation and CNVs in a sample of Bantu African children. We report the top five regions, which had p values ≤ 9.35 × 10−6 and find nominal evidence of independent CNV association (p < 0.05) in three regions previously identified in SNP-based GWASs. The CNV region with strongest association (p = 1.16 × 10−6, 55 losses and seven gains) contains NFATC1, which has been linked to facial morphogenesis and Cherubism, a syndrome involving abnormal lower facial development. Genomic loss in the region is associated with smaller average lower facial depth. Importantly, new loci identified here were not identified in a SNP-based GWAS, suggesting that CNVs are likely involved in determining facial shape variation. Given the plethora of SNP-based GWASs, calling CNVs from existing data may be a relatively inexpensive way to aid in the study of complex traits.
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Affiliation(s)
- Megan Null
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO, USA.,Department of Mathematics and Physical Sciences, The College of Idaho, Caldwell, ID 83605, USA
| | - Feyza Yilmaz
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.,Department of Integrative Biology, University of Colorado Denver, Denver, CO 80204, USA
| | - David Astling
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Hung-Chun Yu
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joanne B Cole
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.,Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Benedikt Hallgrímsson
- Department of Cell Biology & Anatomy, Alberta Children Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Stephanie A Santorico
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO, USA.,Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.,Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA
| | - Richard A Spritz
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.,Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Tamim H Shaikh
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.,Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Audrey E Hendricks
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO, USA.,Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.,Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA
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14
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Aponte JD, Katz DC, Roth DM, Vidal-García M, Liu W, Andrade F, Roseman CC, Murray SA, Cheverud J, Graf D, Marcucio RS, Hallgrímsson B. Relating multivariate shapes to genescapes using phenotype-biological process associations for craniofacial shape. eLife 2021; 10:68623. [PMID: 34779766 PMCID: PMC8631940 DOI: 10.7554/elife.68623] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 11/12/2021] [Indexed: 12/20/2022] Open
Abstract
Realistic mappings of genes to morphology are inherently multivariate on both sides of the equation. The importance of coordinated gene effects on morphological phenotypes is clear from the intertwining of gene actions in signaling pathways, gene regulatory networks, and developmental processes underlying the development of shape and size. Yet, current approaches tend to focus on identifying and localizing the effects of individual genes and rarely leverage the information content of high-dimensional phenotypes. Here, we explicitly model the joint effects of biologically coherent collections of genes on a multivariate trait – craniofacial shape – in a sample of n = 1145 mice from the Diversity Outbred (DO) experimental line. We use biological process Gene Ontology (GO) annotations to select skeletal and facial development gene sets and solve for the axis of shape variation that maximally covaries with gene set marker variation. We use our process-centered, multivariate genotype-phenotype (process MGP) approach to determine the overall contributions to craniofacial variation of genes involved in relevant processes and how variation in different processes corresponds to multivariate axes of shape variation. Further, we compare the directions of effect in phenotype space of mutations to the primary axis of shape variation associated with broader pathways within which they are thought to function. Finally, we leverage the relationship between mutational and pathway-level effects to predict phenotypic effects beyond craniofacial shape in specific mutants. We also introduce an online application that provides users the means to customize their own process-centered craniofacial shape analyses in the DO. The process-centered approach is generally applicable to any continuously varying phenotype and thus has wide-reaching implications for complex trait genetics.
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Affiliation(s)
- Jose D 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, Calgary, Canada
| | - 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, Calgary, Canada
| | - Daniela M Roth
- School of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Marta Vidal-García
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, 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, Calgary, Canada
| | - Fernando Andrade
- Department of Biology, Loyola University Chicago, Chicago, United States
| | - Charles C Roseman
- Department of Biology, Loyola University Chicago, Chicago, United States
| | | | - James Cheverud
- Department of Biology, Loyola University Chicago, Chicago, United States
| | - Daniel Graf
- School of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada.,Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Ralph S Marcucio
- Department of Orthopaedic Surgery, School of Medicine, University of California, San Francisco, San Francisco, United States
| | - 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, Calgary, Canada.,Department of Animal Biology, University of Illinois Urbana Champaign, Urbana, United States
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15
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Katsanis SH, Claes P, Doerr M, Cook-Deegan R, Tenenbaum JD, Evans BJ, Lee MK, Anderton J, Weinberg SM, Wagner JK. A survey of U.S. public perspectives on facial recognition technology and facial imaging data practices in health and research contexts. PLoS One 2021; 16:e0257923. [PMID: 34648520 PMCID: PMC8516205 DOI: 10.1371/journal.pone.0257923] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/13/2021] [Indexed: 12/01/2022] Open
Abstract
Facial imaging and facial recognition technologies, now common in our daily lives, also are increasingly incorporated into health care processes, enabling touch-free appointment check-in, matching patients accurately, and assisting with the diagnosis of certain medical conditions. The use, sharing, and storage of facial data is expected to expand in coming years, yet little is documented about the perspectives of patients and participants regarding these uses. We developed a pair of surveys to gather public perspectives on uses of facial images and facial recognition technologies in healthcare and in health-related research in the United States. We used Qualtrics Panels to collect responses from general public respondents using two complementary and overlapping survey instruments; one focused on six types of biometrics (including facial images and DNA) and their uses in a wide range of societal contexts (including healthcare and research) and the other focused on facial imaging, facial recognition technology, and related data practices in health and research contexts specifically. We collected responses from a diverse group of 4,048 adults in the United States (2,038 and 2,010, from each survey respectively). A majority of respondents (55.5%) indicated they were equally worried about the privacy of medical records, DNA, and facial images collected for precision health research. A vignette was used to gauge willingness to participate in a hypothetical precision health study, with respondents split as willing to (39.6%), unwilling to (30.1%), and unsure about (30.3%) participating. Nearly one-quarter of respondents (24.8%) reported they would prefer to opt out of the DNA component of a study, and 22.0% reported they would prefer to opt out of both the DNA and facial imaging component of the study. Few indicated willingness to pay a fee to opt-out of the collection of their research data. Finally, respondents were offered options for ideal governance design of their data, as "open science"; "gated science"; and "closed science." No option elicited a majority response. Our findings indicate that while a majority of research participants might be comfortable with facial images and facial recognition technologies in healthcare and health-related research, a significant fraction expressed concern for the privacy of their own face-based data, similar to the privacy concerns of DNA data and medical records. A nuanced approach to uses of face-based data in healthcare and health-related research is needed, taking into consideration storage protection plans and the contexts of use.
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Affiliation(s)
- Sara H. Katsanis
- Mary Ann & J. Milburn Smith Child Health Outcomes, Research and Evaluation Center, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, United States of America
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Peter Claes
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, MIRC, KU Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Megan Doerr
- Sage Bionetworks, Seattle, Washington, United States of America
| | - Robert Cook-Deegan
- School for the Future of Innovation in Society, Arizona State University, Washington, District of Columbia, United States of America
| | - Jessica D. Tenenbaum
- Department of Biostatistics & Bioinformatics, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Barbara J. Evans
- Levin College of Law, University of Florida, Gainesville, Florida, United States of America
- Wertheim College of Engineering, University of Florida, Gainesville, Florida, United States of America
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Joel Anderton
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jennifer K. Wagner
- School of Engineering Design, Technology, and Professional Programs, Pennsylvania State University, University Park, Pennsylvania, United States of America
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16
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Samra R, Alsulaiman AA, Motro M, Will LA. Heritability of nasal characteristics assessed using lateral cephalograms. Am J Orthod Dentofacial Orthop 2021; 161:263-271. [PMID: 34629235 DOI: 10.1016/j.ajodo.2020.08.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 08/01/2020] [Accepted: 08/01/2020] [Indexed: 11/25/2022]
Abstract
INTRODUCTION The midface and nasal bones have a significant influence on facial esthetics. Being able to predict the ultimate size of a growing patient's nose may influence the orthodontic treatment plan. Our study aimed to determine whether significant heritability exists between parents and children using multiple soft and hard tissue measurements of nasal dimensions. METHODS This cross-sectional study comprised 47 Western European families from the Forsyth Moorrees Twin Study. The lateral cephalograms of each parent and postpubertal child were evaluated using 14 cephalometric variables. The resemblance and heritability patterns were estimated from the Pearson correlation coefficient and Falconer's heritability test (ie, h2 = 2 × β estimate). RESULTS We found significant heritability between 1 or both parents to sons, daughters, or both children for 11 measurements. Daughters were more strongly influenced by their mothers than fathers, and sons showed relatively few features strongly heritable from either parent. The nasal bone length and ANB were strongly heritable with the mother, and the nose length alone was strongly heritable with the father. In addition, 4 of the 6 measurements that were significantly heritable for daughters were horizontal measurements. CONCLUSIONS Many nasal dimensions are significantly heritable. However, fathers more strongly influenced their daughters than sons, but mothers and daughters shared stronger and more numerous traits than fathers and daughters. Finally, horizontal traits were significantly more heritable between parents and daughters than sons.
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Affiliation(s)
| | - Ahmed A Alsulaiman
- Department of Preventive Dental Sciences, Imam Abdulrahman Bin Faisal University, College of Dentistry, Dammam, Saudi Arabia
| | - Melih Motro
- Department of Orthodontics and Dentofacial Orthopedics, Henry M. Goldman School of Dental Medicine, Boston University, Boston, Mass
| | - Leslie A Will
- Department of Orthodontics and Dentofacial Orthopedics, Henry M. Goldman School of Dental Medicine, Boston University, Boston, Mass.
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17
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Tan DW, Gilani SZ, Boutrus M, Alvares GA, Whitehouse AJO, Mian A, Suter D, Maybery MT. Facial asymmetry in parents of children on the autism spectrum. Autism Res 2021; 14:2260-2269. [PMID: 34529361 DOI: 10.1002/aur.2612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 07/05/2021] [Accepted: 08/25/2021] [Indexed: 11/08/2022]
Abstract
Greater facial asymmetry has been consistently found in children with autism spectrum disorder (ASD) relative to children without ASD. There is substantial evidence that both facial structure and the recurrence of ASD diagnosis are highly heritable within a nuclear family. Furthermore, sub-clinical levels of autistic-like behavioural characteristics have also been reported in first-degree relatives of individuals with ASD, commonly known as the 'broad autism phenotype'. Therefore, the aim of the current study was to examine whether a broad autism phenotype expresses as facial asymmetry among 192 biological parents of autistic individuals (134 mothers) compared to those of 163 age-matched adults without a family history of ASD (113 females). Using dense surface-modelling techniques on three dimensional facial images, we found evidence for greater facial asymmetry in parents of autistic individuals compared to age-matched adults in the comparison group (p = 0.046, d = 0.21 [0.002, 0.42]). Considering previous findings and the current results, we conclude that facial asymmetry expressed in the facial morphology of autistic children may be related to heritability factors. LAY ABSTRACT: In a previous study, we showed that autistic children presented with greater facial asymmetry than non-autistic children. In the current study, we examined the amount of facial asymmetry shown on three-dimensional facial images of 192 parents of autistic children compared to a control group consisting of 163 similarly aged adults with no known history of autism. Although parents did show greater levels of facial asymmetry than those in the control group, this effect is statistically small. We concluded that the facial asymmetry previously found in autistic children may be related to genetic factors.
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Affiliation(s)
- Diana Weiting Tan
- School of Psychological Science, The University of Western Australia, Perth, Western Australia, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Syed Zulqarnain Gilani
- School of Sciences, Edith Cowan University, Perth, Western Australia, Australia.,School of Computer Science and Software Engineering, The University of Western Australia, Perth, Western Australia, Australia
| | - Maryam Boutrus
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Gail A Alvares
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Andrew J O Whitehouse
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Ajmal Mian
- School of Computer Science and Software Engineering, The University of Western Australia, Perth, Western Australia, Australia
| | - David Suter
- School of Sciences, Edith Cowan University, Perth, Western Australia, Australia
| | - Murray T Maybery
- School of Psychological Science, The University of Western Australia, Perth, Western Australia, Australia
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18
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Maciejewska-Turek A, Bilińska M, Wellens HLL, Fudalej PS. Craniofacial shape from pre- to post-adolescence. Eur J Orthod 2021; 44:332-339. [PMID: 34458910 DOI: 10.1093/ejo/cjab061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AIM Craniofacial growth demonstrates significant variation and is difficult to predict. The aim of the present investigation was twofold: (1) to assess the association (covariation) between craniofacial shape at pre- and post-adolescence and (2) to evaluate if pre-adolescent craniofacial shape is related (covaries) with growth magnitude and direction. SUBJECTS AND METHODS One hundred fifty subjects (86 males and 64 females) untreated orthodontically were selected from AAOF Craniofacial Growth Legacy Collection. Each subject had cephalograms taken before 9 (pre-adolescent stage) and after 15 years of age (post-adolescent). Fourteen curves comprising 123 points (10 fixed and 113 sliding semilandmarks) comprehensively covering the craniofacial skeleton were digitally traced on each cephalogram. Procrustes alignment, principal component analysis, 2-block partial least squares (2B-PLS) analysis, and regression analysis were done after sliding the semilandmarks to minimize bending energy. RESULTS The first 16 principal components (PCs) were non-trivial and explained 85.2% of total shape variability in the sample. PC1 depicted mainly variability in the vertical direction, PC2 represented mostly variability in the saddle angle and in the antero-posterior position of the mandible, and PC3 depicted primarily variability of the mandibular shape (steep versus flat mandibular plane). The covariation between pre- and post-adolescent facial shape was statistically significant, both in the pooled sample (RV coefficient = 0.604) and in boys (RV = 0.639) and girls (RV = 0.629). The pre-adolescent shape was weakly associated with the magnitude of facial change-2-block PLS analysis demonstrated that blocks 1 and 2 were independent (P = 0.118, RV = 0.035). CONCLUSIONS The pre-adolescent shape of the craniofacial complex explained approximately 60% of the post-adolescent shape of the craniofacial complex; however, the relationship between pre-adolescent shape of the craniofacial complex and magnitude of its change was weak.
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Affiliation(s)
| | - Małgorzata Bilińska
- Section of Orthodontics, Department of Dentistry and Oral Health, Aarhus University, Aarhus C, Denmark
| | | | - Piotr S Fudalej
- Department of Orthodontics, Jagiellonian University in Krakow, Krakow, Poland.,Department of Orthodontics, Institute of Dentistry and Oral Sciences, Palacky University Olomouc, Olomouc, Czech Republic.,Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
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19
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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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20
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Ghosh S, Kasher M, Malkina I, Livshits G. Is craniofacial morphology and body composition related by common genes: Comparative analysis of two ethnically diverse populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 176:249-261. [PMID: 34297355 DOI: 10.1002/ajpa.24373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 01/18/2023]
Abstract
OBJECTIVES The overarching hypothesis of the present paper is that ethnically and/or genetically diverse human populations may exhibit similarity in correlations between various aspects of human phenotypes due to the morphological integration process during the ontogenetic stages. To test this we investigated whether an association between craniofacial (CF) features and body composition (BC) variations is present in humans and the extent to which such possible associations are comparable in different populations. Furthermore, the paper examines the contribution of common genetic (additive) and shared familial environmental factors in assessing the correlation between CF and BC characteristics in humans. MATERIALS AND METHODS Two pedigree-based samples were collected from two distinct populations, including India (Santhal) and Europe (Chuvash). Canonical correlation analysis was used to compare the association between CF and BC characteristics in the two studied samples. The contribution of genetic and familial environmental factors on the correlation between CF and BC features was analyzed through variance decomposition analysis by implementing the Mendelian Analysis package (MAN). RESULTS Our study suggests that CF morphology is significantly (p < 0.001) associated with BC variation in both samples. CF characteristics and BC phenotypes revealed a consistent trend in both samples where condensed and broad CF morphology was significantly associated with increased fat accumulation, with slight variations between the Santhal and Chuvash samples. Despite the variations observed between the samples, the heritability estimates were impressively equivalent for traits like total facial height (55.6%Santhal vs.56.1%Chuvash ) and nasal index (42.8%Santhal vs. 43.3%Chuvash ). DISCUSSION The genetic contribution of CF morphology appeared to be extensive and the contribution of common genetic and shared family environmental correlations between CF and BC measures were suggestively substantial. Accordingly, these correlations were consistently observed across ethnically diverse populations, despite drastic morphological differences between the samples under comparison.
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Affiliation(s)
- Sudipta Ghosh
- Department of Anthropology, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Melody Kasher
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Ida Malkina
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Gregory Livshits
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel.,Adelson School of Medicine, Ariel University, Ariel, Israel
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21
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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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22
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Marchini M, Hu D, Lo Vercio L, Young NM, Forkert ND, Hallgrímsson B, Marcucio R. Wnt Signaling Drives Correlated Changes in Facial Morphology and Brain Shape. Front Cell Dev Biol 2021; 9:644099. [PMID: 33855022 PMCID: PMC8039397 DOI: 10.3389/fcell.2021.644099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/08/2021] [Indexed: 11/20/2022] Open
Abstract
Canonical Wnt signaling plays multiple roles critical to normal craniofacial development while its dysregulation is known to be involved in structural birth defects of the face. However, when and how Wnt signaling influences phenotypic variation, including those associated with disease, remains unclear. One potential mechanism is via Wnt signaling’s role in the patterning of an early facial signaling center, the frontonasal ectodermal zone (FEZ), and its subsequent regulation of early facial morphogenesis. For example, Wnt signaling may directly alter the shape and/or magnitude of expression of the sonic hedgehog (SHH) domain in the FEZ. To test this idea, we used a replication-competent avian sarcoma retrovirus (RCAS) encoding Wnt3a to modulate its expression in the facial mesenchyme. We then quantified and compared ontogenetic changes in treated to untreated embryos in the three-dimensional (3D) shape of both the SHH expression domain of the FEZ, and the morphology of the facial primordia and brain using iodine-contrast microcomputed tomography imaging and 3D geometric morphometrics (3DGM). We found that increased Wnt3a expression in early stages of head development produces correlated variation in shape between both structural and signaling levels of analysis. In addition, altered Wnt3a activation disrupted the integration between the forebrain and other neural tube derivatives. These results show that activation of Wnt signaling influences facial shape through its impact on the forebrain and SHH expression in the FEZ, and highlights the close relationship between morphogenesis of the forebrain and midface.
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Affiliation(s)
- Marta Marchini
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada.,McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Diane Hu
- Department of Orthopaedic Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Lucas Lo Vercio
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada.,McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Nathan M Young
- Department of Orthopaedic Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Nils D Forkert
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.,Department of Radiology, University of Calgary, Calgary, AB, Canada
| | - Benedikt Hallgrímsson
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada.,McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Ralph Marcucio
- Department of Orthopaedic Surgery, University of California, San Francisco, San Francisco, CA, United States
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23
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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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24
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Abstract
Our ability to unravel the mysteries of human health and disease have changed dramatically over the past 2 decades. Decoding health and disease has been facilitated by the recent availability of high-throughput genomics and multi-omics analyses and the companion tools of advanced informatics and computational science. Understanding of the human genome and its influence on phenotype continues to advance through genotyping large populations and using “light phenotyping” approaches in combination with smaller subsets of the population being evaluated using “deep phenotyping” approaches. Using our capability to integrate and jointly analyze genomic data with other multi-omic data, the knowledge of genotype-phenotype relationships and associated genetic pathways and functions is being advanced. Understanding genotype-phenotype relationships that discriminate human health from disease is speculated to facilitate predictive, precision health care and change modes of health care delivery. The American Association for Dental Research Fall Focused Symposium assembled experts to discuss how studies of genotype-phenotype relationships are illuminating the pathophysiology of craniofacial diseases and developmental biology. Although the breadth of the topic did not allow all areas of dental, oral, and craniofacial research to be addressed (e.g., cancer), the importance and power of integrating genomic, phenomic, and other -omic data are illustrated using a variety of examples. The 8 Fall Focused talks presented different methodological approaches for ascertaining study populations and evaluating population variance and phenotyping approaches. These advances are reviewed in this summary.
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Affiliation(s)
- J T Wright
- Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M C Herzberg
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA
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25
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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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26
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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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27
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Charpentier MJE, Harté M, Poirotte C, de Bellefon JM, Laubi B, Kappeler PM, Renoult JP. Same father, same face: Deep learning reveals selection for signaling kinship in a wild primate. SCIENCE ADVANCES 2020; 6:eaba3274. [PMID: 32537486 PMCID: PMC7253159 DOI: 10.1126/sciadv.aba3274] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
Many animals rely on facial traits to recognize their kin; however, whether these traits have been selected specifically for this function remains unknown. Using deep learning for face recognition, we present the first evidence that interindividual facial resemblance has been selected to signal paternal kinship. Mandrills (Mandrillus sphinx) live in matrilineal societies, in which females spend their entire lives not only with maternal half-sisters (MHS) but also with paternal half-sisters (PHS). We show that PHS have more differentiated social relationships compared to nonkin, suggesting the existence of kin recognition mechanisms. We further demonstrate that facial resemblance increases with genetic relatedness. However, PHS resemble each other visually more than MHS do, despite both kin categories sharing similar degrees of genetic relatedness. This paternally derived facial resemblance among PHS indicates selection to facilitate kin recognition. This study also highlights the potential of artificial intelligence to study phenotypic evolution.
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Affiliation(s)
- M. J. E. Charpentier
- ISEM, UMR5554, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon (cc065), 34095 Montpellier cedex 05, France
| | - M. Harté
- ISEM, UMR5554, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon (cc065), 34095 Montpellier cedex 05, France
| | - C. Poirotte
- Behavioral Ecology and Sociobiology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | | | - B. Laubi
- Projet Mandrillus, SODEPAL, BP 52, Bakoumba, Gabon
| | - P. M. Kappeler
- Behavioral Ecology and Sociobiology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - J. P. Renoult
- CEFE, UMR5175, CNRS, University of Montpellier, University Paul Valery Montpellier, EPHE, 1919 route de Mende, 34293 Montpellier, France
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28
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Vilas R, Ceballos FC, Al-Soufi L, González-García R, Moreno C, Moreno M, Villanueva L, Ruiz L, Mateos J, González D, Ruiz J, Cinza A, Monje F, Álvarez G. Is the "Habsburg jaw" related to inbreeding? Ann Hum Biol 2019; 46:553-561. [PMID: 31786955 DOI: 10.1080/03014460.2019.1687752] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Background: The "Habsburg jaw" has long been associated with inbreeding due to the high prevalence of consanguineous marriages in the Habsburg dynasty. However, it is thought that mandibular prognathism (MP) is under the influence of a dominant major gene.Aim: To investigate the relationship between the "Habsburg jaw" and the pedigree-based inbreeding coefficient (F) as a relative measure of genome homozygosity.Subjects and methods: The degree of MP and maxillary deficiency (MD) of 15 members of the Habsburg dynasty was quantified through the clinical analysis of 18 dysmorphic features diagnosed from 66 portraits.Results: A statistically significant correlation (r = 0.711, p = 0.003) between MP and MD was observed among individuals. Only MP showed a statistically significant positive regression on F as evidenced from univariate analysis (b = 6.36 ± 3.34, p = 0.040) and multivariate analysis (PCA) performed from single dysmorphic features (b = 14.10 ± 6.62, p = 0.027, for the first PC).Conclusion: Both MP and MD are generally involved in the "Habsburg jaw." The results showed a greater sensitivity to inbreeding for the lower third of the face and suggest a positive association between the "Habsburg jaw" and homozygosity and therefore a basically recessive inheritance pattern.
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Affiliation(s)
- Román Vilas
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Francisco C Ceballos
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Laila Al-Soufi
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Raúl González-García
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - Carlos Moreno
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - Manuel Moreno
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - Laura Villanueva
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - Luis Ruiz
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - Jesús Mateos
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - David González
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - Jennifer Ruiz
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - Aitor Cinza
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - Florencio Monje
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - Gonzalo Álvarez
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, Santiago de Compostela, Spain
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29
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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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30
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Hallgrímsson B, Katz DC, Aponte JD, Larson JR, Devine J, Gonzalez PN, Young NM, Roseman CC, Marcucio RS. Integration and the Developmental Genetics of Allometry. Integr Comp Biol 2019; 59:1369-1381. [PMID: 31199435 PMCID: PMC6934422 DOI: 10.1093/icb/icz105] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Allometry refers to the ways in which organismal shape is associated with size. It is a special case of integration, or the tendency for traits to covary, in that variation in size is ubiquitous and evolutionarily important. Allometric variation is so commonly observed that it is routinely removed from morphometric analyses or invoked as an explanation for evolutionary change. In this case, familiarity is mistaken for understanding because rarely do we know the mechanisms by which shape correlates with size or understand their significance. As with other forms of integration, allometric variation is generated by variation in developmental processes that affect multiple traits, resulting in patterns of covariation. Given this perspective, we can dissect the genetic and developmental determinants of allometric variation. Our work on the developmental and genetic basis for allometric variation in craniofacial shape in mice and humans has revealed that allometric variation is highly polygenic. Different measures of size are associated with distinct but overlapping patterns of allometric variation. These patterns converge in part on a common genetic basis. Finally, environmental modulation of size often generates variation along allometric trajectories, but the timing of genetic and environmental perturbations can produce deviations from allometric patterns when traits are differentially sensitive over developmental time. These results question the validity of viewing allometry as a singular phenomenon distinct from morphological integration more generally.
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Affiliation(s)
- Benedikt Hallgrímsson
- Department of Cell Biology & Anatomy, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - David C Katz
- Department of Cell Biology & Anatomy, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jose D Aponte
- Department of Cell Biology & Anatomy, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jacinda R Larson
- Department of Cell Biology & Anatomy, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jay Devine
- Department of Cell Biology & Anatomy, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Paula N Gonzalez
- Unidad Ejecutora de Estudios en Neurociencias y Sistemas Complejos (CONICET-HEC-UNAJ), Buenos Aires, Argentina
| | - Nathan M Young
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, USA
| | - Charles C Roseman
- Department of Animal Biology, University of Illinois Urbana Champaign, Urbana, IL 61801, USA
| | - Ralph S Marcucio
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, USA
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31
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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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32
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Coombs MC, She X, Brown TR, Slate EH, Lee JS, Yao H. Temporomandibular Joint Condyle-Disc Morphometric Sexual Dimorphisms Independent of Skull Scaling. J Oral Maxillofac Surg 2019; 77:2245-2257. [PMID: 31125537 DOI: 10.1016/j.joms.2019.04.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 04/18/2019] [Accepted: 04/18/2019] [Indexed: 10/27/2022]
Abstract
PURPOSE Approximately 2 to 4% of the US population have been estimated to seek treatment for temporomandibular symptoms, predominately women. The study purpose was to determine whether sex-specific differences in temporomandibular morphometry result from scaling with sex differences in skull size and shape or intrinsic sex-specific differences. MATERIALS AND METHODS A total of 22 (11 male [aged 74.5 ± 9.1 years]; 11 female [aged 73.6 ± 12.8 years]) human cadaveric heads with no history of temporomandibular disc derangement underwent cone beam computed tomography and high-resolution magnetic resonance imaging scanning to determine 3-dimensional cephalometric parameters and temporomandibular morphometric outcomes. Regression models between morphometric outcomes and cephalometric parameters were developed, and intrinsic sex-specific differences in temporomandibular morphometry normalized by cephalometric parameters were determined. Subject-specific finite element (FE) models of the extreme male and extreme female conditions were developed to predict variations in articular disc stress-strain under the same joint loading. RESULTS In some cases, sex differences in temporomandibular morphometric parameters could be explained by linear scaling with skull size and shape; however, scaling alone could not fully account for some differences between sexes, indicating intrinsic sex-specific differences. The intrinsic sex-specific differences in temporomandibular morphometry included an increased condylar medial length and mediolateral disc lengths in men and a longer anteroposterior disc length in women. Considering the extreme male and female temporomandibular morphometry observed in the present study, subject-specific FE models resulted in sex differences, with the extreme male joint having a broadly distributed stress field and peak stress of 5.28 MPa. The extreme female joint had a concentrated stress field and peak stress of 7.37 MPa. CONCLUSIONS Intrinsic sex-specific differences independent of scaling with donor skull size were identified in temporomandibular morphometry. Understanding intrinsic sex-specific morphometric differences is critical to determining the temporomandibular biomechanics given the effect of anatomy on joint contact mechanics and stress-strain distributions and requires further study as one potential factor for the increased predisposition of women to temporomandibular disc derangement.
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Affiliation(s)
- Matthew C Coombs
- Postdoctoral Fellow, Department of Bioengineering, Clemson University, Clemson, SC; and Department of Oral Health Sciences, Medical University of South Carolina, Charleston, SC
| | - Xin She
- Graduate Assistant, Department of Bioengineering, Clemson University, Clemson, SC
| | - Truman R Brown
- Professor, Center for Biomedical Imaging, Medical University of South Carolina, Charleston, SC
| | - Elizabeth H Slate
- Professor, Department of Statistics, Florida State University, Tallahassee, FL
| | - Janice S Lee
- Clinical Director, National Institutes of Health National Institute of Dental and Craniofacial Research, Bethesda, MD
| | - Hai Yao
- Professor, Department of Bioengineering, Clemson University, Clemson, SC; and Department of Oral Health Sciences, Medical University of South Carolina, Charleston, SC.
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33
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He L, Liu W, Temple DH, Wang M, Zhang Q, Cramon‐Taubadel N. Diachronic changes in craniofacial morphology among the middle–late Holocene populations from Hehuang region, Northwest China. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 169:55-65. [DOI: 10.1002/ajpa.23807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/11/2019] [Accepted: 02/13/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Letian He
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of Sciences Beijing, 100044 China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences Beijing, 100044 China
- School of Earth Sciences, University of Chinese Academy of Sciences Beijing, 100049 China
- Department of Sociology and AnthropologyGeorge Mason University Virginia, 22030‐4444
| | - Wu Liu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of Sciences Beijing, 100044 China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences Beijing, 100044 China
| | - Daniel H. Temple
- Department of Sociology and AnthropologyGeorge Mason University Virginia, 22030‐4444
| | - Minghui Wang
- Institute of ArchaeologyChinese Academy of Social Sciences Beijing, 100710 China
| | - Quanchao Zhang
- School of Archaeology, Jilin University Changchun, 130012 China
| | - Noreen Cramon‐Taubadel
- Buffalo Human Evolutionary Morphology Lab, Department of AnthropologyUniversity at Buffalo Buffalo, 14261 New York
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34
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Jacobs LF. The navigational nose: a new hypothesis for the function of the human external pyramid. ACTA ACUST UNITED AC 2019; 222:222/Suppl_1/jeb186924. [PMID: 30728230 DOI: 10.1242/jeb.186924] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
One of the outstanding questions in evolution is why Homo erectus became the first primate species to evolve the external pyramid, i.e. an external nose. The accepted hypothesis for this trait has been its role in respiration, to warm and humidify air as it is inspired. However, new studies testing the key assumptions of the conditioning hypothesis, such as the importance of turbulence to enhance heat and moisture exchange, have called this hypothesis into question. The human nose has two functions, however, respiration and olfaction. It is thus also possible that the external nose evolved in response to selection for olfaction. The genus Homo had many adaptations for long-distance locomotion, which allowed Homo erectus to greatly expand its species range, from Africa to Asia. Long-distance navigation in birds and other species is often accomplished by orientation to environmental odors. Such olfactory navigation, in turn, is enhanced by stereo olfaction, made possible by the separation of the olfactory sensors. By these principles, the human external nose could have evolved to separate olfactory inputs to enhance stereo olfaction. This could also explain why nose shape later became so variable: as humans became more sedentary in the Neolithic, a decreasing need for long-distance movements could have been replaced by selection for other olfactory functions, such as detecting disease, that would have been critical to survival in newly dense human settlements.
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Affiliation(s)
- Lucia F Jacobs
- Department of Psychology and Helen Wills Neuroscience Institute, University of California, 2121 Berkeley Way, Berkeley, CA 94720-1650, USA
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35
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Atukorala ADS, Bhatia V, Ratnayake R. Craniofacial skeleton of MEXICAN tetra (Astyanax mexicanus): As a bone disease model. Dev Dyn 2018; 248:153-161. [PMID: 30450697 DOI: 10.1002/dvdy.4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/12/2018] [Accepted: 11/12/2018] [Indexed: 12/16/2022] Open
Abstract
A small fresh water fish, the Mexican tetra (Astyanax mexicanus) is a novel animal model in evolutionary developmental biology. The existence of morphologically distinct surface and cave morphs of this species allows simultaneous comparative analysis of phenotypic changes at different life stages. The cavefish harbors many favorable constructive traits (i.e., large jaws with an increased number of teeth, neuromast cells, enlarged olfactory pits and excess storage of adipose tissues) and regressive traits (i.e., reduced eye structures and pigmentation) which are essential for cave adaptation. A wide spectrum of natural craniofacial morphologies can be observed among the different cave populations. Recently, the Mexican tetra has been identified as a human disease model. The fully sequenced genome along with modern genome editing tools has allowed researchers to generate transgenic and targeted gene knockouts with phenotypes that resemble human pathological conditions. This review will discuss the anatomy of the craniofacial skeleton of A. mexicanus with a focus on morphologically variable facial bones, jaws that house continuously replacing teeth and pharyngeal skeleton. Furthermore, the possible applications of this model animal in identifying human congenital and metabolic skeletal disorders is addressed. Developmental Dynamics 248:153-161, 2019. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Atukorallaya Devi Sewvandini Atukorala
- Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Vikram Bhatia
- Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ravindra Ratnayake
- Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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36
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Hoskens H, Li J, Indencleef K, Gors D, Larmuseau MHD, Richmond S, Zhurov AI, Hens G, Peeters H, Claes P. Spatially Dense 3D Facial Heritability and Modules of Co-heritability in a Father-Offspring Design. Front Genet 2018; 9:554. [PMID: 30510565 PMCID: PMC6252335 DOI: 10.3389/fgene.2018.00554] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/29/2018] [Indexed: 12/04/2022] Open
Abstract
Introduction: The human face is a complex trait displaying a strong genetic component as illustrated by various studies on facial heritability. Most of these start from sparse descriptions of facial shape using a limited set of landmarks. Subsequently, facial features are preselected as univariate measurements or principal components and the heritability is estimated for each of these features separately. However, none of these studies investigated multivariate facial features, nor the co-heritability between different facial features. Here we report a spatially dense multivariate analysis of facial heritability and co-heritability starting from data from fathers and their children available within ALSPAC. Additionally, we provide an elaborate overview of related craniofacial heritability studies. Methods: In total, 3D facial images of 762 father-offspring pairs were retained after quality control. An anthropometric mask was applied to these images to establish spatially dense quasi-landmark configurations. Partial least squares regression was performed and the (co-)heritability for all quasi-landmarks (∼7160) was computed as twice the regression coefficient. Subsequently, these were used as input to a hierarchical facial segmentation, resulting in the definition of facial modules that are internally integrated through the biological mechanisms of inheritance. Finally, multivariate heritability estimates were obtained for each of the resulting modules. Results: Nearly all modular estimates reached statistical significance under 1,000,000 permutations and after multiple testing correction (p ≤ 1.3889 × 10-3), displaying low to high heritability scores. Particular facial areas showing the greatest heritability were similar for both sons and daughters. However, higher estimates were obtained in the former. These areas included the global face, upper facial part (encompassing the nasion, zygomas and forehead) and nose, with values reaching 82% in boys and 72% in girls. The lower parts of the face only showed low to moderate levels of heritability. Conclusion: In this work, we refrain from reducing facial variation to a series of individual measurements and analyze the heritability and co-heritability from spatially dense landmark configurations at multiple levels of organization. Finally, a multivariate estimation of heritability for global-to-local facial segments is reported. Knowledge of the genetic determination of facial shape is useful in the identification of genetic variants that underlie normal-range facial variation.
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Affiliation(s)
- Hanne Hoskens
- Department of Human Genetics, KU Leuven, Leuven, Belgium.,Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Jiarui Li
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium.,Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Karlijne Indencleef
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium.,Research Group Experimental Otorhinolaryngology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Dorothy Gors
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium.,Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Maarten H D Larmuseau
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Stephen Richmond
- Applied Clinical Research and Public Health, School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff, United Kingdom
| | - Alexei I Zhurov
- Applied Clinical Research and Public Health, School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff, United Kingdom
| | - Greet Hens
- Research Group Experimental Otorhinolaryngology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Hilde Peeters
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Peter Claes
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium.,Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.,Murdoch Childrens Research Institute, Melbourne, VIC, Australia
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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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Motofei IG. Biology of Cancer; From Cellular Cancerogenesis to Supracellular Evolution of Malignant Phenotype. Cancer Invest 2018; 36:309-317. [DOI: 10.1080/07357907.2018.1477955] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ion G. Motofei
- Department of Surgery/Oncology, Carol Davila University, St. Pantelimon Hospital, Bucharest, Romania
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Cole JB, Manyama MF, Nikitovic D, Gonzalez PN, Liberton DK, Wilson WM, Rolian C, Larson JR, Kimwaga E, Mathayo J, Roseman CC, Santorico SA, Lukowiak K, Spritz RA, Hallgrimsson B. Facial shape manifestations of growth faltering in Tanzanian children. J Anat 2017; 232:250-262. [PMID: 29193055 DOI: 10.1111/joa.12748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2017] [Indexed: 12/18/2022] Open
Abstract
Variation in the shape of the human face and in stature is determined by complex interactions between genetic and environmental influences. One such environmental influence is malnourishment, which can result in growth faltering, usually diagnosed by means of comparing an individual's stature with a set of age-appropriate standards. These standards for stature, however, are typically ascertained in groups where people are at low risk for growth faltering. Moreover, genetic differences among populations with respect to stature are well established, further complicating the generalizability of stature-based diagnostic tools. In a large sample of children aged 5-19 years, we obtained high-resolution genomic data, anthropometric measures and 3D facial images from individuals within and around the city of Mwanza, Tanzania. With genome-wide complex trait analysis, we partitioned genetic and environmental variance for growth outcomes and facial shape. We found that children with growth faltering have faces that look like those of older and taller children, in a direction opposite to the expected allometric trajectory, and in ways predicted by the environmental portion of covariance at the community and individual levels. The environmental variance for facial shape varied subtly but significantly among communities, whereas genetic differences were minimal. These results reveal that facial shape preserves information about exposure to undernourishment, with important implications for refining assessments of nutritional status in children and the developmental-genetics of craniofacial variation alike.
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Affiliation(s)
- Joanne B Cole
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - Mange F Manyama
- Weill-Cornell Medicine-Qatar, Doha, Qatar.,Department of Anatomy, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Dejana Nikitovic
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada
| | - Paula N Gonzalez
- ENyS. Estudios en Neurociencias y Sistemas Complejos, CONICET-HEC-UNAJ., Av. Calchaquí 5401. CP1882, Buenos Aires, Argentina
| | - Denise K Liberton
- National Institute for Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Warren M Wilson
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada
| | - Campbell Rolian
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Jacinda R Larson
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Emmanuel Kimwaga
- Department of Anatomy, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Joshua Mathayo
- Department of Anatomy, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Charles C Roseman
- Department of Animal Biology, School of Integrative Biology, University of Illinois, Urbana, IL, USA
| | - Stephanie A Santorico
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, CO, USA.,Mathematical and Statistical Sciences, University of Colorado, Denver, CO, USA
| | - Ken Lukowiak
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - Benedikt Hallgrimsson
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.,Department of Anatomy and Cell Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
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40
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Larson JR, Manyama MF, Cole JB, Gonzalez PN, Percival CJ, Liberton DK, Ferrara TM, Riccardi SL, Kimwaga EA, Mathayo J, Spitzmacher JA, Rolian C, Jamniczky HA, Weinberg SM, Roseman CC, Klein O, Lukowiak K, Spritz RA, Hallgrimsson B. Body size and allometric variation in facial shape in children. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 165:327-342. [PMID: 29178597 DOI: 10.1002/ajpa.23356] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 10/22/2017] [Accepted: 10/24/2017] [Indexed: 11/06/2022]
Abstract
OBJECTIVES Morphological integration, or the tendency for covariation, is commonly seen in complex traits such as the human face. The effects of growth on shape, or allometry, represent a ubiquitous but poorly understood axis of integration. We address the question of to what extent age and measures of size converge on a single pattern of allometry for human facial shape. METHODS Our study is based on two large cross-sectional cohorts of children, one from Tanzania and the other from the United States (N = 7,173). We employ 3D facial imaging and geometric morphometrics to relate facial shape to age and anthropometric measures. RESULTS The two populations differ significantly in facial shape, but the magnitude of this difference is small relative to the variation within each group. Allometric variation for facial shape is similar in both populations, representing a small but significant proportion of total variation in facial shape. Different measures of size are associated with overlapping but statistically distinct aspects of shape variation. Only half of the size-related variation in facial shape can be explained by the first principal component of four size measures and age while the remainder associates distinctly with individual measures. CONCLUSIONS Allometric variation in the human face is complex and should not be regarded as a singular effect. This finding has important implications for how size is treated in studies of human facial shape and for the developmental basis for allometric variation more generally.
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Affiliation(s)
- Jacinda R Larson
- Department of Cell Biology & Anatomy, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Mange F Manyama
- Division of Medical Education, Weill Cornell Medicine - Qatar, Doha, Qatar.,Department of Anatomy, Catholic University of Health and Allied Science, Mwanza, Tanzania
| | - Joanne B Cole
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Human Medical Genetics and Genomics Program and Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado
| | - Paula N Gonzalez
- Department of Anthropology, University of La Plata, La Plata, Argentina
| | | | - Denise K Liberton
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland
| | - Tracey M Ferrara
- Human Medical Genetics and Genomics Program and Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado
| | - Sheri L Riccardi
- Human Medical Genetics and Genomics Program and Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado
| | - Emmanuel A Kimwaga
- Department of Anatomy, Catholic University of Health and Allied Science, Mwanza, Tanzania
| | - Joshua Mathayo
- Department of Anatomy, Catholic University of Health and Allied Science, Mwanza, Tanzania
| | | | - Campbell Rolian
- Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.,McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Canada
| | - Heather A Jamniczky
- Department of Cell Biology & Anatomy, Cumming School of Medicine, University of Calgary, Calgary, Canada.,McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Canada
| | - Seth M Weinberg
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Charles C Roseman
- Department of Animal Biology, College of Liberal Arts and Science, University of Illinois, Urbana-Champaign, Urbana, Illinois
| | - Ophir Klein
- Departments of Orofacial Sciences and Pediatrics, and Program in Craniofacial Biology, University of California San Francisco, San Francisco, California
| | - Ken Lukowiak
- Department of Physiology & Pharmacology and the Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program and Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado
| | - Benedikt Hallgrimsson
- Department of Cell Biology & Anatomy, Cumming School of Medicine, University of Calgary, Calgary, Canada.,McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
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41
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Li M, Cole JB, Manyama M, Larson JR, Liberton DK, Riccardi SL, Ferrara TM, Santorico SA, Bannister JJ, Forkert ND, Spritz RA, Mio W, Hallgrimsson B. Rapid automated landmarking for morphometric analysis of three-dimensional facial scans. J Anat 2017; 230:607-618. [PMID: 28078731 DOI: 10.1111/joa.12576] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2016] [Indexed: 12/01/2022] Open
Abstract
Automated phenotyping is essential for the creation of large, highly standardized datasets from anatomical imaging data. Such datasets can support large-scale studies of complex traits or clinical studies related to precision medicine or clinical trials. We have developed a method that generates three-dimensional landmark data that meet the requirements of standard geometric morphometric analyses. The method is robust and can be implemented without high-performance computing resources. We validated the method using both direct comparison to manual landmarking on the same individuals and also analyses of the variation patterns and outlier patterns in a large dataset of automated and manual landmark data. Direct comparison of manual and automated landmarks reveals that automated landmark data are less variable, but more highly integrated and reproducible. Automated data produce covariation structure that closely resembles that of manual landmarks. We further find that while our method does produce some landmarking errors, they tend to be readily detectable and can be fixed by adjusting parameters used in the registration and control-point steps. Data generated using the method described here have been successfully used to study the genomic architecture of facial shape in two different genome-wide association studies of facial shape.
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Affiliation(s)
- Mao Li
- Department of Mathematics, Florida State University, Tallahassee, FL, USA
| | - Joanne B Cole
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - Mange Manyama
- Department of Anatomy, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Jacinda R Larson
- Department of Anatomy and Cell Biology, McCaig Institute for Bone and Joint Health, and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | | | - Sheri L Riccardi
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - Tracey M Ferrara
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - Stephanie A Santorico
- Department of Mathematical and Statistical Science, University of Colorado Denver, Denver, CO, USA
| | - Jordan J Bannister
- Department of Radiology and Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Nils D Forkert
- Department of Radiology and Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, CO, USA.,Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Washington Mio
- Department of Mathematics, Florida State University, Tallahassee, FL, USA
| | - Benedikt Hallgrimsson
- Department of Anatomy and Cell Biology, McCaig Institute for Bone and Joint Health, and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
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