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Hallgrímsson B, Aponte JD, Katz DC, Bannister JJ, Riccardi SL, Mahasuwan N, McInnes BL, Ferrara TM, Lipman DM, Neves AB, Spitzmacher JAJ, Larson JR, Bellus GA, Pham AM, Aboujaoude E, Benke TA, Chatfield KC, Davis SM, Elias ER, Enzenauer RW, French BM, Pickler LL, Shieh JTC, Slavotinek A, Harrop AR, Innes AM, McCandless SE, McCourt EA, Meeks NJL, Tartaglia NR, Tsai ACH, Wyse JPH, Bernstein JA, Sanchez-Lara PA, Forkert ND, Bernier FP, Spritz RA, Klein OD. Automated syndrome diagnosis by three-dimensional facial imaging. Genet Med 2020; 22:1682-1693. [PMID: 32475986 PMCID: PMC7521994 DOI: 10.1038/s41436-020-0845-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 12/27/2022] Open
Abstract
Purpose Deep phenotyping is an emerging trend in precision medicine for genetic disease. The shape of the face is affected in 30–40% of known genetic syndromes. Here, we determine whether syndromes can be diagnosed from 3D images of human faces. Methods We analyzed variation in three-dimensional (3D) facial images of 7057 subjects: 3327 with 396 different syndromes, 727 of their relatives, and 3003 unrelated, unaffected subjects. We developed and tested machine learning and parametric approaches to automated syndrome diagnosis using 3D facial images. Results Unrelated, unaffected subjects were correctly classified with 96% accuracy. Considering both syndromic and unrelated, unaffected subjects together, balanced accuracy was 73% and mean sensitivity 49%. Excluding unrelated, unaffected subjects substantially improved both balanced accuracy (78.1%) and sensitivity (56.9%) of syndrome diagnosis. The best predictors of classification accuracy were phenotypic severity and facial distinctiveness of syndromes. Surprisingly, unaffected relatives of syndromic subjects were frequently classified as syndromic, often to the syndrome of their affected relative. Conclusion Deep phenotyping by quantitative 3D facial imaging has considerable potential to facilitate syndrome diagnosis. Furthermore, 3D facial imaging of “unaffected” relatives may identify unrecognized cases or may reveal novel examples of semidominant inheritance.
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Affiliation(s)
- 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, 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, Calgary, AB, 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, AB, Canada
| | - Jordan J Bannister
- Biomedical Engineering Graduate Program, University of Calgary, Calgary, AB, Canada
| | - Sheri L Riccardi
- Human Medical Genetics and Genomics Program and Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Nick Mahasuwan
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, CA, USA
| | - Brenda L McInnes
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Tracey M Ferrara
- Human Medical Genetics and Genomics Program and Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Danika M Lipman
- 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, AB, Canada
| | - Amanda B Neves
- 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, AB, Canada
| | - Jared A J Spitzmacher
- 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, AB, Canada
| | - Jacinda R Larson
- 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, AB, Canada
| | - Gary A Bellus
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA.,Department of Pediatrics, Geisinger Medical Center, Danville, PA, USA
| | - Anh M Pham
- Department of Pediatrics, Cedars Sinai Medical Center & David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Elias Aboujaoude
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Timothy A Benke
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Kathryn C Chatfield
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Shanlee M Davis
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ellen R Elias
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Robert W Enzenauer
- Department of Pediatric Ophthalmology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Brooke M French
- Department of Surgery, Division of Plastic and Reconstructive Surgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Laura L Pickler
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Joseph T C Shieh
- Department of Pediatrics and Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Anne Slavotinek
- Department of Pediatrics and Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - A Robertson Harrop
- Department of Surgery, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - A Micheil Innes
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Shawn E McCandless
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Emily A McCourt
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Naomi J L Meeks
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Nicole R Tartaglia
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Anne C-H Tsai
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - J Patrick H Wyse
- Division of Ophthalmology, Department of Surgery & Department of Medical Genetics, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Pedro A Sanchez-Lara
- Department of Pediatrics, Cedars Sinai Medical Center & David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Nils D Forkert
- Department of Radiology, Alberta Children's Hospital Research Institute, and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Francois P Bernier
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program and Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA.
| | - Ophir D Klein
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, CA, USA. .,Department of Pediatrics and Institute for Human Genetics, University of California, San Francisco, CA, USA.
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