Identification of Novel Risk Variants of Non-Syndromic Cleft Palate by Targeted Gene Panel Sequencing
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Population
2.2. The NGS-Based Multi-Gene Panel
2.2.1. Variant Identification and Annotation
2.2.2. Variant Selection and Prioritisation
2.2.3. Variant Validation and Segregation
3. Results
Targeted NGS Sequencing
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
- Mossey, P.A.; Little, J.; Munger, R.G.; Dixon, M.J.; Shaw, W.C. Cleft Lip and Palate. Lancet 2009, 374, 1773–1785. [Google Scholar] [CrossRef]
- Christensen, K.; Juel, K.; Herskind, A.M.; Murray, J.C. Long term follow up study of survival associated with cleft lip and palate at birth. BMJ 2004, 328, 1405. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Wehby, G.; Cassell, C.H. The impact of orofacial clefts on quality of life and healthcare use and costs. Oral Dis. 2010, 16, 3–10. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zhu, J.L.; Basso, O.; Hasle, H.; Winther, J.F.; Olsen, J.H.; Olsen, J. Do parents of children with congenital malformations have a higher cancer risk? A nationwide study in Denmark. Br. J. Cancer 2002, 87, 524–528. [Google Scholar] [CrossRef] [Green Version]
- Mangold, E.; Ludwig, K.U.; Nöthen, M.M. Breakthroughs in the genetics of orofacial clefting. Trends Mol. Med. 2011, 17, 725–733. [Google Scholar] [CrossRef]
- Yu, Y.; Zuo, X.; He, M.; Gao, J.; Fu, Y.; Qin, C.; Meng, L.; Wang, W.; Song, Y.; Cheng, Y.; et al. Genome-wide analyses of non-syndromic cleft lip with palate identify 14 novel loci and genetic heterogeneity. Nat. Commun. 2017, 8, 14364. [Google Scholar] [CrossRef] [Green Version]
- Ferguson, M.W. Palate Development. Development 1988, 103, 41–60. [Google Scholar] [CrossRef] [PubMed]
- Jugessur, A.; Farlie, P.G.; Kilpatrick, N. The genetics of isolated orofacial clefts: From genotypes to subphenotypes. Oral Dis. 2009, 15, 437–453. [Google Scholar] [CrossRef] [PubMed]
- Leslie, E.J.; Marazita, M.L. Genetics of cleft lip and cleft palate. Am. J. Med. Genet. Part C Semin. Med. Genet. 2013, 163, 246–258. [Google Scholar] [CrossRef] [Green Version]
- Watkins, S.E.; Meyer, R.E.; Strauss, R.P.; Aylsworth, A.S. Classification, Epidemiology, and Genetics of Orofacial Clefts. Clin. Plast. Surg. 2014, 41, 149–163. [Google Scholar] [CrossRef]
- Dixon, M.J.; Marazita, M.L.; Beaty, T.H.; Murray, J.C. Cleft lip and palate: Understanding genetic and environmental influences. Nat. Rev. Genet. 2011, 12, 167–178. [Google Scholar] [CrossRef] [Green Version]
- Murray, J. Gene/environment causes of cleft lip and/or palate. Clin. Genet. 2002, 61, 248–256. [Google Scholar] [CrossRef]
- Gowans, L.J.J.; Adeyemo, W.; Eshete, M.; Mossey, P.; Busch, T.; Aregbesola, B.; Donkor, P.; Arthur, F.K.N.; Bello, S.; Martinez, A.; et al. Association Studies and Direct DNA Sequencing Implicate Genetic Susceptibility Loci in the Etiology of Nonsyndromic Orofacial Clefts in Sub-Saharan African Populations. J. Dent. Res. 2016, 95, 1245–1256. [Google Scholar] [CrossRef] [PubMed]
- Ishorst, N.; Francheschelli, P.; Böhmer, A.C.; Khan, M.F.J.; Heilmann-Heimbach, S.; Fricker, N.; Little, J.; Steegers-Theunissen, R.P.M.; Peterlin, B.; Nowak, S.; et al. Nonsyndromic Cleft Palate: An Association Study at GWAS Candidate Loci in a Multiethnic Sample. Birth Defects Res. 2018, 110, 871–882. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Beaty, T.H.; Ruczinski, I.; Murray, J.C.; Marazita, M.L.; Munger, R.G.; Hetmanski, J.B.; Murray, T.; Redett, R.J.; Fallin, M.D.; Liang, K.Y.; et al. Evidence for gene-environment interaction in a genome wide study of nonsyndromic cleft palate. Genet. Epidemiol. 2011, 35, 469–478. [Google Scholar] [CrossRef] [PubMed]
- Leslie, E.J.; Liu, H.; Carlson, J.C.; Shaffer, J.R.; Feingold, E.; Wehby, G.; Laurie, C.A.; Jain, D.; Laurie, C.C.; Doheny, K.F.; et al. A Genome-Wide Association Study of Nonsyndromic Cleft Palate Identifies an Etiologic Missense Variant in GRHL3. Am. J. Hum. Genet. 2016, 98, 744–754. [Google Scholar] [CrossRef] [Green Version]
- Butali, A.; Mossey, P.A.; Adeyemo, W.L.; Eshete, M.A.; Gowans, L.J.J.; Busch, T.D.; Jain, D.; Yu, W.; Huan, L.; Laurie, C.A.; et al. Genomic analyses in African populations identify novel risk loci for cleft palate. Hum. Mol. Genet. 2019, 28, 1038–1051. [Google Scholar] [CrossRef] [Green Version]
- Huang, L.; Jia, Z.; Shi, Y.; Du, Q.; Shi, J.; Wang, Z.; Mou, Y.; Wang, Q.; Zhang, B.; Wang, Q.; et al. Genetic factors define CPO and CLO subtypes of nonsyndromicorofacial cleft. PLoS Genet. 2019, 15, e1008357. [Google Scholar] [CrossRef] [PubMed]
- He, M.; Zuo, X.; Liu, H.; Wang, W.; Zhang, Y.; Fu, Y.; Zhen, Q.; Yu, Y.; Pan, Y.; Qin, C.; et al. Genome-wide Analyses Identify a Novel Risk Locus for Nonsyndromic Cleft Palate. J. Dent. Res. 2020, 99, 1461–1468. [Google Scholar] [CrossRef]
- Mangold, E.; Böhmer, A.C.; Ishorst, N.; Hoebel, A.-K.; Gültepe, P.; Schuenke, H.; Klamt, J.; Hofmann, A.; Gölz, L.; Raff, R.; et al. Sequencing the GRHL3 Coding Region Reveals Rare Truncating Mutations and a Common Susceptibility Variant for Nonsyndromic Cleft Palate. Am. J. Hum. Genet. 2016, 98, 755–762. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Martinelli, M.; Palmieri, A.; Carinci, F.; Scapoli, L. Non-syndromic Cleft Palate: An Overview on Human Genetic and Environmental Risk Factors. Front. Cell Dev. Biol. 2020, 8, 592271. [Google Scholar] [CrossRef] [PubMed]
- Marini, N.J.; Asrani, K.; Yang, W.; Rine, J.; Shaw, G.M. Accumulation of rare coding variants in genes implicated in risk of human cleft lip with or without cleft palate. Am. J. Med. Genet. Part A 2019, 179, 1260–1269. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Leslie, E.J.; Carlson, J.C.; Shaffer, J.R.; Buxó, C.J.; Castilla, E.E.; Christensen, K.; Deleyiannis, F.W.B.; Field, L.L.; Hecht, J.T.; Moreno, L.; et al. Association studies of low-frequency coding variants in nonsyndromic cleft lip with or without cleft palate. Am. J. Med. Genet. Part A 2017, 173, 1531–1538. [Google Scholar] [CrossRef] [PubMed]
- Machado, R.A.; Martelli-Junior, H.; Reis, S.R.D.A.; Küchler, E.C.; Scariot, R.; das Neves, L.T.; Coletta, R.D. Identification of Novel Variants in Cleft Palate-Associated Genes in Brazilian Patients With Non-syndromic Cleft Palate Only. Front. Cell Dev. Biol. 2021, 9, 638522. [Google Scholar] [CrossRef]
- Bureau, A.; Parker, M.; Ruczinski, I.; Taub, M.A.; Marazita, M.L.; Murray, J.C.; Mangold, E.; Noethen, M.M.; Ludwig, K.U.; Hetmanski, J.B.; et al. Whole Exome Sequencing of Distant Relatives in Multiplex Families Implicates Rare Variants in Candidate Genes for Oral Clefts. Genetics 2014, 197, 1039–1044. [Google Scholar] [CrossRef] [Green Version]
- Basha, M.; Demeer, B.; Revencu, N.; Helaers, R.; Theys, S.; Saba, S.B.; Boute, O.; Devauchelle, B.; Francois, G.; Bayet, B.; et al. Whole exome sequencing identifies mutations in 10% of patients with familial non-syndromic cleft lip and/or palate in genes mutated in well-known syndromes. J. Med. Genet. 2018, 55, 449–458. [Google Scholar] [CrossRef] [Green Version]
- Hoebel, A.; Drichel, D.; Van De Vorst, M.; Böhmer, A.; Sivalingam, S.; Ishorst, N.; Klamt, J.; Gölz, L.; Alblas, M.; Maaser-Hecker, A.; et al. Candidate Genes for Nonsyndromic Cleft Palate Detected by Exome Sequencing. J. Dent. Res. 2017, 96, 1314–1321. [Google Scholar] [CrossRef]
- Liu, H.; Busch, T.; Eliason, S.; Anand, D.; Bullard, S.; Gowans, L.J.; Nidey, N.; Petrin, A.; Augustine-Akpan, E.-A.; Saadi, I.; et al. Exome sequencing provides additional evidence for the involvement ofARHGAP29in Mendelian orofacial clefting and extends the phenotypic spectrum to isolated cleft palate. Birth Defects Res. 2017, 109, 27–37. [Google Scholar] [CrossRef] [Green Version]
- Pengelly, R.J.; Arias, L.; Martínez, J.; Upstill-Goddard, R.; Seaby, E.G.; Gibson, J.; Ennis, S.; Collins, A.; Briceño, I. Deleterious coding variants in multi-case families with non-syndromic cleft lip and/or palate phenotypes. Sci. Rep. 2016, 6, 30457. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Sawicka-Gutaj, N.; Gruszczyński, D.; Guzik, P.; Mostowska, A.; Walkowiak, J. Publication Ethics of Human Studies in the Light of the Declaration of Helsinki—A Mini-Review. J. Med. Sci. 2022, 91, e700. [Google Scholar] [CrossRef]
- Dąbrowska, J.; Biedziak, B.; Szponar-Żurowska, A.; Budner, M.; Jagodziński, P.P.; Płoski, R.; Mostowska, A. Identification of Novel Susceptibility Genes for Non-Syndromic Cleft Lip with or without Cleft Palate Using NGS-Based Multigene Panel Testing. Mol. Genet. Genomics 2022, 297, 1315–1327. [Google Scholar] [CrossRef]
- Biedziak, B.; Firlej, E.; Dąbrowska, J.; Bogdanowicz, A.; Zadurska, M.; Mostowska, A. Novel Candidate Genes for Non-Syndromic Tooth Agenesis Identified Using Targeted Next-Generation Sequencing. J. Clin. Med. 2022, 11, 6089. [Google Scholar] [CrossRef] [PubMed]
- Carlson, J.C.; Taub, M.A.; Feingold, E.; Beaty, T.H.; Murray, J.C.; Marazita, M.L.; Leslie, E.J.; Anand, D.; Butali, A.; Buxo, C.J.; et al. Identifying Genetic Sources of Phenotypic Heterogeneity in Orofacial Clefts by Targeted Sequencing. Genet. Epidemiol. 2017, 43, 704–716. [Google Scholar] [CrossRef] [PubMed]
- Carlson, J.C.; Anand, D.; Butali, A.; Buxo, C.J.; Christensen, K.; Deleyiannis, F.; Hecht, J.T.; Moreno, L.M.; Orioli, I.M.; Padilla, C.; et al. A Systematic Genetic Analysis and Visualization of Phenotypic Heterogeneity among Orofacial Cleft GWAS Signals. Genet. Epidemiol. 2019, 43, 704–716. [Google Scholar] [CrossRef]
- Kroeger, J.; Hoppe, E.; Galiger, C.; Has, C.; Franzke, C.W. Amino Acid Substitution in the C-Terminal Domain of Collagen XVII Reduces Laminin-332 Interaction Causing Mild Skin Fragility with Atrophic Scarring. Matrix Biol. 2019, 80, 72–84. [Google Scholar] [CrossRef]
- Funato, N.; Nakamura, M. Identification of shared and unique gene families associated with oral clefts. Int. J. Oral Sci. 2017, 9, 104–109. [Google Scholar] [CrossRef]
- Liu, F.; van der Lijn, F.; Schurmann, C.; Zhu, G.; Chakravarty, M.M.; Hysi, P.G.; Wollstein, A.; Lao, O.; de Bruijne, M.; Ikram, M.A.; et al. A Genome-Wide Association Study Identifies Five Loci Influencing Facial Morphology in Europeans. PLoS Genet. 2012, 8, e1002932. [Google Scholar] [CrossRef] [Green Version]
- Feng, W.; Leach, S.M.; Tipney, H.; Phang, T.; Geraci, M.; Spritz, R.A.; Hunter, L.E.; Williams, T. Spatial and Temporal Analysis of Gene Expression during Growth and Fusion of the Mouse Facial Prominences. PLoS ONE 2009, 4, e8066. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Mangold, E.; Ludwig, K.U.; Birnbaum, S.; Baluardo, C.; Ferrian, M.; Herms, S.; Reutter, H.; de Assis, N.A.; Al Chawa, T.; Mattheisen, M.; et al. Genome-wide association study identifies two susceptibility loci for nonsyndromic cleft lip with or without cleft palate. Nat. Genet. 2010, 42, 24–26. [Google Scholar] [CrossRef] [Green Version]
- Butali, A.; Suzuki, S.; Cooper, M.E.; Mansilla, A.M.; Cuenco, K.; Leslie, E.J.; Suzuki, Y.; Niimi, T.; Yamamoto, M.; Ayanga, G.; et al. Replication of Genome Wide Association Identified Candidate Genes Confirm the Role of Common and Rare Variants in PAX7 and VAX1 in the Etiology of Nonsyndromic CL(P). Am. J. Med. Genet. A 2013, 161, 965–972. [Google Scholar] [CrossRef] [Green Version]
- Mostowska, A.; Gaczkowska, A.; Żukowski, K.; Ludwig, K.U.; Hozyasz, K.K.; Wójcicki, P.; Mangold, E.; Böhmer, A.C.; Heilmann-Heimbach, S.; Knapp, M.; et al. Common Variants in DLG1 Locus Are Associated with Non-Syndromic Cleft Lip with or without Cleft Palate. Clin. Genet. 2018, 93, 784–793. [Google Scholar] [CrossRef]
- Li, Q.; Kim, Y.; Suktitipat, B.; Hetmanski, J.B.; Marazita, M.L.; Duggal, P.; Beaty, T.H.; Bailey-Wilson, J.E. Gene-Gene Interaction Among WNT Genes for Oral Cleft in Trios. Genet. Epidemiol. 2015, 39, 385–394. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Brooks, S.P.; Coccia, M.; Tang, H.R.; Kanuga, N.; Machesky, L.M.; Bailly, M.; Cheetham, M.E.; Hardcastle, A.J. The Nance–Horan syndrome protein encodes a functional WAVE homology domain (WHD) and is important for co-ordinating actin remodelling and maintaining cell morphology. Hum. Mol. Genet. 2010, 19, 2421–2432. [Google Scholar] [CrossRef] [Green Version]
- Burdon, K.P.; McKay, J.D.; Sale, M.M.; Russell-Eggitt, I.M.; Mackey, D.A.; Wirth, M.G.; Elder, J.E.; Nicoll, A.; Clarke, M.; FitzGerald, L.; et al. Mutations in a Novel Gene, NHS, Cause the Pleiotropic Effects of Nance-Horan Syndrome, Including Severe Congenital Cataract, Dental Anomalies, and Mental Retardation. Am. J. Hum. Genet. 2003, 73, 1120–1130. [Google Scholar] [CrossRef] [Green Version]
- Khan, A.O.; Aldahmesh, M.A.; Mohamed, J.Y.; Alkuraya, F.S. Phenotype-genotype Correlation in Potential Female Carriers of X-linked Developmental Cataract (Nance-Horan Syndrome). Ophthalmic Genet. 2012, 33, 89–95. [Google Scholar] [CrossRef] [PubMed]
- Bishop, M.R.; Diaz Perez, K.K.; Sun, M.; Ho, S.; Chopra, P.; Mukhopadhyay, N.; Hetmanski, J.B.; Taub, M.A.; Moreno-Uribe, L.M.; Valencia-Ramirez, L.C.; et al. Genome-Wide Enrichment of De Novo Coding Mutations in Orofacial Cleft Trios. Am. J. Hum. Genet. 2020, 107, 124–136. [Google Scholar] [CrossRef] [PubMed]
- Pakvasa, M.; Haravu, P.; Boachie-Mensah, M.; Jones, A.; Coalson, E.; Liao, J.; Zeng, Z.; Wu, D.; Qin, K.; Wu, X.; et al. Notch signaling: Its essential roles in bone and craniofacial development. Genes Dis. 2021, 8, 8–24. [Google Scholar] [CrossRef] [PubMed]
- Restivo, G.; Nguyen, B.-C.; Dziunycz, P.; Ristorcelli, E.; Ryan, R.J.H.; Özuysal, Ö.Y.; Di Piazza, M.; Radtke, F.; Dixon, M.J.; Hofbauer, G.F.L.; et al. IRF6 is a mediator of Notch pro-differentiation and tumour suppressive function in keratinocytes. EMBO J. 2011, 30, 4571–4585. [Google Scholar] [CrossRef] [PubMed]
- Reynolds, K.; Zhang, S.; Sun, B.; Garland, M.A.; Ji, Y.; Zhou, C.J. Genetics and signaling mechanisms of orofacial clefts. Birth Defects Res. 2020, 112, 1588–1634. [Google Scholar] [CrossRef]
- Li, H.; Jones, K.L.; Hooper, J.E.; Williams, T. The Molecular Anatomy of Mammalian Upper Lip and Primary Palate Fusion at Single Cell Resolution. Development 2019, 146, dev174888. [Google Scholar] [CrossRef] [Green Version]
- Richardson, R.J.; Dixon, J.; Jiang, R.; Dixon, M.J. Integration of IRF6 and Jagged2 signalling is essential for controlling palatal adhesion and fusion competence. Hum. Mol. Genet. 2009, 18, 2632–2642. [Google Scholar] [CrossRef] [Green Version]
- Gilbert, M.A.; Bauer, R.C.; Rajagopalan, R.; Grochowski, C.M.; Chao, G.; McEldrew, D.; Nassur, J.A.; Rand, E.B.; Krock, B.L.; Kamath, B.M.; et al. Alagille syndrome mutation update: Comprehensive overview of JAG1 and NOTCH2 mutation frequencies and insight into missense variant classification. Hum. Mutat. 2019, 40, 2197–2220. [Google Scholar] [CrossRef] [Green Version]
- Kamath, B.M.; Bauer, R.C.; Loomes, K.M.; Chao, G.; Gerfen, J.; Hutchinson, A.; Hardikar, W.; Hirschfield, G.; Jara, P.; Krantz, I.D.; et al. NOTCH2mutations in Alagille syndrome. J. Med. Genet. 2012, 49, 138–144. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Herman, S.B.; Guo, T.; McGinn, D.M.M.; Blonska, A.; Shanske, A.L.; Bassett, A.S.; Chow, E.W.C.; Bowser, M.; Sheridan, M.; Beemer, F.; et al. Overt Cleft Palate Phenotype and TBX1 Genotype Correlations in Velo-Cardio-Facial/DiGeorge/22q11. 2 Deletion Syndrome Patients. Am. J. Med. Genet. A 2012, 158A, 2781–2787. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Vieira, A.R.; Avila, J.R.; Daack-Hirsch, S.; Dragan, E.; Félix, T.M.; Rahimov, F.; Harrington, J.; Schultz, R.R.; Watanabe, Y.; Johnson, M.; et al. Medical Sequencing of Candidate Genes for Nonsyndromic Cleft Lip and Palate. PLoS Genet. 2005, 1, e64. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Mostowska, A.; Hozyasz, K.K.; Wojcicki, P.; Biedziak, B.; Paradowska, P.; Jagodzinski, P.P. Association between genetic variants of reported candidate genes or regions and risk of cleft lip with or without cleft palate in the polish population. Birth Defects Res. Part A Clin. Mol. Teratol. 2010, 88, 538–545. [Google Scholar] [CrossRef] [PubMed]
- Marcano, A.C.B.; Doudney, K.; Braybrook, C.; Squires, R.; Patton, M.A.; Lees, M.M.; Richieri-Costa, A.; Lidral, A.C.; Murray, J.C.; Moore, G.E.; et al. TBX22 mutations are a frequent cause of cleft palate. J. Med. Genet. 2004, 41, 68–74. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Stanier, P.; Moore, G.E. Genetics of Cleft Lip and Palate: Syndromic Genes Contribute to the Incidence of Non-Syndromic Clefts. Hum. Mol. Genet. 2004, 13, 73–81. [Google Scholar] [CrossRef] [PubMed]
- Lansdon, L.A.; Darbro, B.W.; Petrin, A.L.; Hulstrand, A.M.; Standley, J.M.; Brouillette, R.B.; Long, A.; Mansilla, M.A.; Cornell, R.A.; Murray, J.C.; et al. Identification of Isthmin 1 as a Novel Clefting and Craniofacial Patterning Gene in Humans. Genetics 2018, 208, 283–296. [Google Scholar] [CrossRef] [Green Version]
- Kraus, F.; Haenig, B.; Kispert, A. Cloning and expression analysis of the mouse T-box gene Tbx18. Mech. Dev. 2001, 100, 83–86. [Google Scholar] [CrossRef]
- Richardson, B.; Dixon, J.; Malhotra, S.; Hardman, M.; Knowles, L.; Boot-Handford, R.; Shore, P.; Whitmarsh, A.; Dixon, M.J. Irf6 is a key determinant of the keratinocyte proliferation-differentiation switch. Nat. Genet. 2006, 38, 1329–1334. [Google Scholar] [CrossRef]
- Letra, A.; Maili, L.; Mulliken, J.B.; Buchanan, E.; Blanton, S.H.; Hecht, J.T. Further evidence suggesting a role for variation in ARHGAP29 variants in nonsyndromic cleft lip/palate. Birth Defects Res. Part A Clin. Mol. Teratol. 2014, 100, 679–685. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Khandelwal, K.D.; van den Boogaard, M.-J.H.; Mehrem, S.L.; Gebel, J.; Fagerberg, C.; Van Beusekom, E.; Van Binsbergen, E.; Topaloglu, O.; Steehouwer, M.; Gilissen, C.; et al. Deletions and loss-of-function variants in TP63 associated with orofacial clefting. Eur. J. Hum. Genet. 2019, 27, 1101–1112. [Google Scholar] [CrossRef] [PubMed]
- Jugessur, A.; Shi, M.; Gjessing, H.K.; Lie, R.T.; Wilcox, A.J.; Weinberg, C.; Christensen, K.; Boyles, A.L.; Daack-Hirsch, S.; Nguyen, T.T.; et al. Maternal Genes and Facial Clefts in Offspring: A Comprehensive Search for Genetic Associations in Two Population-Based Cleft Studies from Scandinavia. PLoS ONE 2010, 5, e11493. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- He, F.; Chen, Y. Wnt Signaling in Lip and Palate Development. Front. Oral Biol. 2012, 16, 81–90. [Google Scholar] [CrossRef] [PubMed]
- Woods, D.F.; Hough, C.; Peel, D.; Callaini, G.; Bryant, P.J. Dlg Protein Is Required for Junction Structure, Cell Polarity, and Proliferation Control in Drosophila Epithelia. J. Cell Biol. 1996, 134, 1469–1482. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Yamanaka, T.; Ohno, S. Role of Lgl/Dlg/Scribble in the Regulation of Epithelial Junction, Polarity and Growth. Front. Biosci. 2008, 13, 6693–6707. [Google Scholar] [CrossRef] [Green Version]
- Iizuka-Kogo, A.; Senda, T.; Akiyama, T.; Shimomura, A.; Nomura, R.; Hasegawa, Y.; Yamamura, K.-I.; Kogo, H.; Sawai, N.; Matsuzaki, T. Requirement of DLG1 for Cardiovascular Development and Tissue Elongation during Cochlear, Enteric, and Skeletal Development: Possible Role in Convergent Extension. PLoS ONE 2015, 10, e0123965. [Google Scholar] [CrossRef] [Green Version]
- Seelan, R.S.; Mukhopadhyay, P.; Warner, D.R.; Webb, C.L.; Pisano, M.; Greene, R.M.; Hong, C.-S.; Saint-Jeannet, J.-P.; Lefebvre, V.; Bhattaram, P.; et al. Requirement for Dlgh-1 in Planar Cell Polarity and Skeletogenesis during Vertebrate Development. Development 2013, 134, 6693–6707. [Google Scholar]
- Caruana, G.; Bernstein, A. Craniofacial Dysmorphogenesis Including Cleft Palate in Mice with an Insertional Mutation in the discs large Gene. Mol. Cell. Biol. 2001, 21, 1475–1483. [Google Scholar] [CrossRef] [Green Version]
- Iizuka-Kogo, A.; Ishidao, T.; Akiyama, T.; Senda, T. Abnormal development of urogenital organs in Dlgh1-deficient mice. Development 2007, 134, 1799–1807. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Menezes, R.; Letra, A.; Kim, A.H.; Küchler, E.C.; Day, A.; Tannure, P.N.; Gomes da Motta, L.; Paiva, K.B.S.; Granjeiro, J.M.; Vieira, A.R. Studies with Wnt Genes and Nonsyndromic Cleft Lip and Palate. Birth Defects Res. A Clin. Mol. Teratol. 2010, 88, 995–1000. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Chiquet, B.T.; Blanton, S.H.; Burt, A.; Ma, D.; Stal, S.; Mulliken, J.B.; Hecht, J.T. Variation in WNT genes is associated with non-syndromic cleft lip with or without cleft palate. Hum. Mol. Genet. 2008, 17, 2212–2218. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Rochard, L.; Monica, S.D.; Ling, I.T.C.; Kong, Y.; Roberson, S.; Harland, R.; Halpern, M.; Liao, E.C. Roles of Wnt Pathway Genes Wls, Wnt9a, Wnt5b, Frzb and Gpc4 in Regulating Convergent-Extension during Zebrafish Palate Morphogenesis. Development 2016, 143, 2541–2547. [Google Scholar]
- Song, L.; Li, Y.; Wang, K.; Wang, Y.-Z.; Molotkov, A.; Gao, L.; Zhao, T.; Yamagami, T.; Wang, Y.; Gan, Q.; et al. Lrp6-mediated canonical Wnt signaling is required for lip formation and fusion. Development 2009, 136, 3161–3171. [Google Scholar] [CrossRef] [Green Version]
- Lei, Y.; Fathe, K.; McCartney, D.; Zhu, H.; Yang, W.; Ross, M.E.; Shaw, G.M.; Finnell, R.H. Rare LRP6 Variants Identified in Spina Bifida P atients. Hum. Mutat. 2015, 36, 342–349. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Ockeloen, C.W.; Khandelwal, K.D.; Dreesen, K.; Ludwig, K.U.; Sullivan, R.; Van Rooij, I.A.L.M.; Thonissen, M.; Swinnen, S.; Phan, M.; Conte, F.; et al. Novel mutations in LRP6 highlight the role of WNT signaling in tooth agenesis. Genet. Med. 2016, 18, 1158–1162. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Phan, M.; Conte, F.; Khandelwal, K.D.; Ockeloen, C.W.; Bartzela, T.; Kleefstra, T.; van Bokhoven, H.; Rubini, M.; Zhou, H.; Carels, C.E.L. Tooth Agenesis and Orofacial Clefting: Genetic Brothers in Arms? Hum. Genet. 2016, 135, 1299–1327. [Google Scholar] [CrossRef] [Green Version]
- Conte, F.; Oti, M.; Dixon, J.; Carels, C.E.L.; Rubini, M.; Zhou, H. Systematic analysis of copy number variants of a large cohort of orofacial cleft patients identifies candidate genes for orofacial clefts. Hum. Genet. 2016, 135, 41–59. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Shi, M.; Mostowska, A.; Jugessur, A.; Johnson, M.K.; Mansilla, M.A.; Christensen, K.; Lie, R.T.; Wilcox, A.J.; Murray, J.C. Identification of Microdeletions in Candidate Genes for Cleft Lip and/or Palate. Birth Defects Res. A Clin. Mol. Teratol. 2009, 85, 42–51. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Osoegawa, K.; Vessere, G.M.; Utami, K.H.; Mansilla, M.A.; Johnson, M.K.; Riley, B.M.; L’Heureux, J.; Pfundt, R.; Staaf, J.; Van Der Vliet, W.A.; et al. Identification of novel candidate genes associated with cleft lip and palate using array comparative genomic hybridisation. J. Med. Genet. 2008, 45, 81–86. [Google Scholar] [CrossRef] [PubMed] [Green Version]
All Patients (n = 38) | ||
---|---|---|
N | % | |
Gender distribution | ||
Males | 17 | 44.74 |
Females | 21 | 55.26 |
Cleft type | ||
Cleft of the soft palate | 3 | 7.89 |
Cleft of the hard and soft palate | 35 | 92.11 |
Associated anomalies | ||
Dental anomalies 1 | 8 | 21.05 |
Positive family history | ||
Extended family | 4 | 10.53 |
Variant Effect | gnomAD | Genotyping Results c | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Patient | Gender | Type of Cleft | Family History a | Gene | Rs Number | DNA Change | Protein Change | Frequency b | Patient | Father | Mother |
De novo Variants | |||||||||||
CP_1 | M | Cleft of the hard and soft palate | NO | IRF6 | novel | c.224A>G | p.Asp75Gly | not found | HET | wt | wt |
CP_2 | F | Cleft of the hard and soft palate | YES—ex. fam. | NHS | novel | c.568G>C | p.Val190Leu | not found | HET | wt | wt |
Variants Inherited from Unaffected Parent | |||||||||||
CP_3 | F | Cleft of the hard and soft palate | NO | COL17A1 | novel | c.2435-1G>A | not found | HET | wt | HET | |
CP_4 | F | Cleft of the hard and soft palate | YES—ex. fam. | DLG1 | rs139789027 | c.1586G>C | p.Glu562Asp | 2.95 × 10−5 | HET | wt | HET |
CP_5 | F | Cleft of the hard and soft palate | NO | FLNB | novel | c.3605A>G | p.Tyr1202Cys | not found | HET | no DNA | HET |
CP_6 | F | Cleft of the hard and soft palate | NO | LRP6 | rs769446193 | c.481C>A | p.Pro161Thr | not found | HET | no DNA | HET |
CP_7 | F | Cleft of the hard and soft palate | NO | NOTCH2 | novel | c.1997A>G | p.Tyr666Cys | not found | HET | HET | wt |
CP_8 | M | Cleft of the hard and soft palate | NO | TP63 | novel | c.353A>T | p.Asn118Ile | not found | HET | wt | HET |
CP_9 | F | Cleft of the hard and soft palate | NO | VAX1 | novel | c.400G>A | p.Ala134Thr | not found | HET | wt | HET |
CP_10 | M | Cleft of the hard and soft palate | NO | WNT5B | rs529807731 | c.716G>T | p.Arg239Leu | 0.000 | HET | HET | wt |
Variants with Unknown Inheritance | |||||||||||
CP_11 | M | Cleft of the hard and soft palate | NO | ARHGAP29 | rs867470445 | c.1706G>A | p.Arg569Gln | 1.47 × 10−5 | HET | no DNA | wt |
CP_12 | F | Cleft of the soft palate | NO | TBX18 | novel | c.674A>T | p.His225Leu | not found | HET | no DNA | wt |
GENE | VARIANT | IN SILICO PATHOGENICITY PREDICTION c | ADA | CADD | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Name | pLi a | Z score b | Alternation | Type | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | Score d | Score e |
De novo Variants | |||||||||||||||||||||||
IRF6 | 1.000 | 2.774 | c.224A>G; p.Asp75Gly | Missense | Dc | M | D | D | D | D | D | P | P | D | D | D | P | P | D | D | D | 28.5 | |
NHS | 1.000 | 1.822 | c.568G>C; p.Val190Leu | Missense | Dc | N | T | D | D | D | T | T, D | T, D | N | B | B | D | T | T | 24.6 | |||
Variants Inherited from Unaffected Parent | |||||||||||||||||||||||
COL17A1 | 0.000 | −0.748 | c.2435-1G>A | Splicing | D | D | P | P | 0.99 | 33.0 | |||||||||||||
DLG1 | 0.994 | 1.496 | c.1586G>C; p.Glu562Asp | Missense | Dc | M | D | D | N | D | T | B | P | D | D | N | B | B | T | D | D | 23.6 | |
FLNB | 0.000 | 2.141 | c.3605A>G; p.Tyr1202Cys | Missense | Dc | M | T | D | D | D | D | P | P | D | D | D | P | P | D | D | D | 29.2 | |
LRP6 | 0.697 | 2.754 | c.481C>A; p.Pro161Thr | Missense | Dc | H | D | D | D | D | D | P | P | D | D | D | P | P | D | D | D | 26.0 | |
NOTCH2 | 1.000 | 3.502 | c.1997A>G; p.Tyr666Cys | Missense | Dc | H | D | D | D | U | D | P | P | D | D | D | P | P | T | D | D | 26.1 | |
TP63 | 0.997 | 2.208 | c.353A>T; p.Asn118Ile | Missense | Dc | L | T, D | D | D | D | D | P | P | D | D | D | P | P | D | D | D | 27.6 | |
VAX1 | 0.771 | 0.869 | c.400G>A; p.Ala134Thr | Missense | Dc | H | D | D | D | D | D | P | P | D | D | D | P | P | D | D | D | 27.6 | |
WNT5B | 0.589 | 1.788 | c.716G>T; p.Arg239Leu | Missense | Dc | H | T | D | D | D | D | P | P | D | D | D | B | P | D | D | D | 32.0 | |
Variants with Unknown Inheritance | |||||||||||||||||||||||
ARHGAP29 | 1.000 | 1.211 | c.1706G>A; p.Arg569Gln | Missense | Dc | M | T | D | D | N | T | P | P | D | D | D | B | B | D | T | T | 28.4 | |
TBX18 | 0.999 | 0.099 | c.674A>T; p.His225Leu | Missense | Dc | H | D | D | D | D | D | P | P | D | D | D | P | P | D | D | D | 31.0 |
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Dąbrowska, J.; Biedziak, B.; Bogdanowicz, A.; Mostowska, A. Identification of Novel Risk Variants of Non-Syndromic Cleft Palate by Targeted Gene Panel Sequencing. J. Clin. Med. 2023, 12, 2051. https://doi.org/10.3390/jcm12052051
Dąbrowska J, Biedziak B, Bogdanowicz A, Mostowska A. Identification of Novel Risk Variants of Non-Syndromic Cleft Palate by Targeted Gene Panel Sequencing. Journal of Clinical Medicine. 2023; 12(5):2051. https://doi.org/10.3390/jcm12052051
Chicago/Turabian StyleDąbrowska, Justyna, Barbara Biedziak, Agnieszka Bogdanowicz, and Adrianna Mostowska. 2023. "Identification of Novel Risk Variants of Non-Syndromic Cleft Palate by Targeted Gene Panel Sequencing" Journal of Clinical Medicine 12, no. 5: 2051. https://doi.org/10.3390/jcm12052051
APA StyleDąbrowska, J., Biedziak, B., Bogdanowicz, A., & Mostowska, A. (2023). Identification of Novel Risk Variants of Non-Syndromic Cleft Palate by Targeted Gene Panel Sequencing. Journal of Clinical Medicine, 12(5), 2051. https://doi.org/10.3390/jcm12052051