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Diaz Perez KK, Chung S, Head ST, Epstein MP, Hecht JT, Wehby GL, Weinberg SM, Murray JC, Marazita ML, Leslie EJ. Rare variants found in multiplex families with orofacial clefts: Does expanding the phenotype make a difference? Am J Med Genet A 2023; 191:2558-2570. [PMID: 37350193 PMCID: PMC10528230 DOI: 10.1002/ajmg.a.63336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/25/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023]
Abstract
Exome sequencing (ES) is now a relatively straightforward process to identify causal variants in Mendelian disorders. However, the same is not true for ES in families where the inheritance patterns are less clear, and a complex etiology is suspected. Orofacial clefts (OFCs) are highly heritable birth defects with both Mendelian and complex etiologies. The phenotypic spectrum of OFCs may include overt clefts and several subclinical phenotypes, such as discontinuities in the orbicularis oris muscle (OOM) in the upper lip, velopharyngeal insufficiency (VPI), microform clefts or bifid uvulas. We hypothesize that expanding the OFC phenotype to include these phenotypes can clarify inheritance patterns in multiplex families, making them appear more Mendelian. We performed exome sequencing to find rare, likely causal genetic variants in 31 multiplex OFC families, which included families with multiple individuals with OFCs and individuals with subclinical phenotypes. We identified likely causal variants in COL11A2, IRF6, SHROOM3, SMC3, TBX3, and TP63 in six families. Although we did not find clear evidence supporting the subclinical phenotype hypothesis, our findings support a role for rare variants in the etiology of OFCs.
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Affiliation(s)
- Kimberly K Diaz Perez
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Sydney Chung
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - S Taylor Head
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jacqueline T Hecht
- Department of Pediatrics, McGovern Medical, School and School of Dentistry, UT Health at Houston, Houston, Texas, USA
| | - George L Wehby
- Department of Health Management and Policy, University of Iowa, Iowa City, Iowa, USA
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh School of Dental Medicine, Pittsburgh, Pennsylvania, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh School of Dental Medicine, Pittsburgh, Pennsylvania, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
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Diaz Perez KK, Curtis SW, Sanchis-Juan A, Zhao X, Head T, Ho S, Carter B, McHenry T, Bishop MR, Valencia-Ramirez LC, Restrepo C, Hecht JT, Uribe LM, Wehby G, Weinberg SM, Beaty TH, Murray JC, Feingold E, Marazita ML, Cutler DJ, Epstein MP, Brand H, Leslie EJ. Rare variants found in clinical gene panels illuminate the genetic and allelic architecture of orofacial clefting. Genet Med 2023; 25:100918. [PMID: 37330696 PMCID: PMC10592535 DOI: 10.1016/j.gim.2023.100918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 05/12/2023] [Accepted: 06/10/2023] [Indexed: 06/19/2023] Open
Abstract
PURPOSE Orofacial clefts (OFCs) are common birth defects including cleft lip, cleft lip and palate, and cleft palate. OFCs have heterogeneous etiologies, complicating clinical diagnostics because it is not always apparent if the cause is Mendelian, environmental, or multifactorial. Sequencing is not currently performed for isolated or sporadic OFCs; therefore, we estimated the diagnostic yield for 418 genes in 841 cases and 294 controls. METHODS We evaluated 418 genes using genome sequencing and curated variants to assess their pathogenicity using American College of Medical Genetics criteria. RESULTS 9.04% of cases and 1.02% of controls had "likely pathogenic" variants (P < .0001), which was almost exclusively driven by heterozygous variants in autosomal genes. Cleft palate (17.6%) and cleft lip and palate (9.09%) cases had the highest yield, whereas cleft lip cases had a 2.80% yield. Out of 39 genes with likely pathogenic variants, 9 genes, including CTNND1 and IRF6, accounted for more than half of the yield (4.64% of cases). Most variants (61.8%) were "variants of uncertain significance", occurring more frequently in cases (P = .004), but no individual gene showed a significant excess of variants of uncertain significance. CONCLUSION These results underscore the etiological heterogeneity of OFCs and suggest sequencing could reduce the diagnostic gap in OFCs.
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Affiliation(s)
| | - Sarah W Curtis
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA
| | - Alba Sanchis-Juan
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, Department of Neurology and Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Xuefang Zhao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, Department of Neurology and Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Taylor Head
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA
| | - Samantha Ho
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA
| | - Bridget Carter
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA; Agnes Scott College, Decatur, GA
| | - Toby McHenry
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA
| | - Madison R Bishop
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA
| | | | | | - Jacqueline T Hecht
- Department of Pediatrics, McGovern Medical, School and School of Dentistry, UT Health at Houston, Houston, TX
| | - Lina M Uribe
- Department of Orthodontics, University of Iowa, Iowa City, IA
| | - George Wehby
- Department of Health Management and Policy, University of Iowa, Iowa City, IA
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | | | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA; Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA
| | - Michael P Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, Department of Neurology and Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA.
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Perez KKD, Chung S, Head ST, Epstein MP, Hecht JT, Wehby GL, Weinberg SM, Murray JC, Marazita ML, Leslie EJ. Rare variants found in multiplex families with orofacial clefts: Does expanding the phenotype make a difference? medRxiv 2023:2023.02.01.23285340. [PMID: 36798250 PMCID: PMC9934724 DOI: 10.1101/2023.02.01.23285340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Whole-exome sequencing (WES) is now a relatively straightforward process to identify causal variants in Mendelian disorders. However, the same is not true for WES in families where the inheritance patterns are less clear, and a complex etiology is suspected. Orofacial clefts (OFCs) are highly heritable birth defects with both Mendelian and complex etiologies. The phenotypic spectrum of OFCs may include overt clefts and several subclinical phenotypes, such as discontinuities in the orbicularis oris muscle (OOM) in the upper lip, velopharyngeal insufficiency (VPI), microform clefts or bifid uvulas. We hypothesize that expanding the OFC phenotype to include these phenotypes can clarify inheritance patterns in multiplex families, making them appear more Mendelian. We performed whole-exome sequencing to find rare, likely causal genetic variants in 31 multiplex OFC families, which included families with multiple individuals with OFCs and individuals with subclinical phenotypes. We identified likely causal variants in COL11A2, IRF6, KLF4, SHROOM3, SMC3, TP63 , and TBX3 in seven families. Although we did not find clear evidence supporting the subclinical phenotype hypothesis, our findings support a role for rare variants in the etiology of OFCs.
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Affiliation(s)
- Kimberly K Diaz Perez
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Sydney Chung
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - S Taylor Head
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jacqueline T Hecht
- Department of Pediatrics, McGovern Medical, School and School of Dentistry, UT Health at Houston, Houston, TX 77030, USA
| | - George L Wehby
- Department of Health Management and Policy, University of Iowa, Iowa City, IA, 52242, USA
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA, 15213, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA, 15213, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
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Bishop MR, Diaz Perez KK, Sun M, Ho S, Chopra P, Mukhopadhyay N, Hetmanski JB, Taub MA, Moreno-Uribe LM, Valencia-Ramirez LC, Restrepo Muñeton CP, Wehby G, Hecht JT, Deleyiannis F, Weinberg SM, Wu-Chou YH, Chen PK, Brand H, Epstein MP, Ruczinski I, Murray JC, Beaty TH, Feingold E, Lipinski RJ, Cutler DJ, Marazita ML, Leslie EJ. Genome-wide Enrichment of De Novo Coding Mutations in Orofacial Cleft Trios. Am J Hum Genet 2020; 107:124-136. [PMID: 32574564 PMCID: PMC7332647 DOI: 10.1016/j.ajhg.2020.05.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/26/2020] [Indexed: 01/05/2023] Open
Abstract
Although de novo mutations (DNMs) are known to increase an individual's risk of congenital defects, DNMs have not been fully explored regarding orofacial clefts (OFCs), one of the most common human birth defects. Therefore, whole-genome sequencing of 756 child-parent trios of European, Colombian, and Taiwanese ancestry was performed to determine the contributions of coding DNMs to an individual's OFC risk. Overall, we identified a significant excess of loss-of-function DNMs in genes highly expressed in craniofacial tissues, as well as genes associated with known autosomal dominant OFC syndromes. This analysis also revealed roles for zinc-finger homeobox domain and SOX2-interacting genes in OFC etiology.
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Affiliation(s)
- Madison R. Bishop
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kimberly K. Diaz Perez
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Miranda Sun
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Samantha Ho
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nandita Mukhopadhyay
- Department of Oral Biology, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA 15219, USA
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Margaret A. Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Lina M. Moreno-Uribe
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA
| | | | | | - George Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical School and School of Dentistry, UT Health at Houston, Houston, TX 77030, USA
| | | | - Seth M. Weinberg
- Department of Oral Biology, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA 15219, USA,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA
| | - Yah Huei Wu-Chou
- Department of Medical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Philip K. Chen
- Craniofacial Centre, Taipei Medical University Hospital and Taipei Medical University, Taipei, Taiwan
| | - Harrison Brand
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Michael P. Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA
| | - Robert J. Lipinski
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - David J. Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mary L. Marazita
- Department of Oral Biology, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA 15219, USA,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA
| | - Elizabeth J. Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA,Corresponding author
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