1
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Robinson K, Curtis SW, Leslie EJ. The heterogeneous genetic architectures of orofacial clefts. Trends Genet 2024; 40:410-421. [PMID: 38480105 DOI: 10.1016/j.tig.2024.02.004] [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: 11/20/2023] [Revised: 02/13/2024] [Accepted: 02/13/2024] [Indexed: 05/09/2024]
Abstract
Orofacial clefts (OFCs) are common, affecting 1:1000 live births. OFCs occur across a phenotypic spectrum - including cleft lip (CL), cleft lip and palate (CLP), or cleft palate (CP) - and can be further subdivided based on laterality, severity, or specific structures affected. Herein we review what is known about the genetic architecture underlying each of these subtypes, considering both shared and subtype-specific risks. While there are more known genetic similarities between CL and CLP than CP, recent research supports both shared and subtype-specific genetic risk factors within and between phenotypic classifications of OFCs. Larger sample sizes and deeper phenotyping data will be of increasing importance for the discovery of novel genetic risk factors for OFCs and various subtypes going forward.
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Affiliation(s)
- Kelsey Robinson
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sarah W Curtis
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
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2
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Sun B, Reynolds K, Saha SK, Zhang S, McMahon M, Zhou CJ. Ezh2-dependent methylation in oral epithelia promotes secondary palatogenesis. Birth Defects Res 2023; 115:1851-1865. [PMID: 37435868 PMCID: PMC10784412 DOI: 10.1002/bdr2.2216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/30/2023] [Accepted: 06/12/2023] [Indexed: 07/13/2023]
Abstract
BACKGROUND In addition to genomic risk variants and environmental influences, increasing evidence suggests epigenetic modifications are important for orofacial development and their alterations can contribute to orofacial clefts. Ezh2 encodes a core catalytic component of the Polycomb repressive complex responsible for addition of methyl marks to Histone H3 as a mechanism of repressing target genes. The role of Ezh2 in orofacial clefts remains unknown. AIMS To investigate the epithelial role of Ezh2-dependent methylation in secondary palatogenesis. METHODS We used conditional gene-targeting methods to ablate Ezh2 in the surface ectoderm-derived oral epithelium of mouse embryos. We then performed single-cell RNA sequencing combined with immunofluorescence and RT-qPCR to investigate gene expression in conditional mutant palate. We also employed double knockout analyses of Ezh1 and Ezh2 to address if they have synergistic roles in palatogenesis. RESULTS We found that conditional inactivation of Ezh2 in oral epithelia results in partially penetrant cleft palate. Double knockout analyses revealed that another family member Ezh1 is dispensable in orofacial development, and it does not have synergistic roles with Ezh2 in palatogenesis. Histochemistry and single-cell RNA-seq analyses revealed dysregulation of cell cycle regulators in the palatal epithelia of Ezh2 mutant mouse embryos disrupts palatogenesis. CONCLUSION Ezh2-dependent histone H3K27 methylation represses expression of cell cycle regulator Cdkn1a and promotes proliferation in the epithelium of the developing palatal shelves. Loss of this regulation may perturb movement of the palatal shelves, causing a delay in palate elevation which may result in failure of the secondary palate to close altogether.
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Affiliation(s)
| | | | - Subbroto Kuma Saha
- Institute for Pediatric Regenerative Medicine of Shriners Hospital for Children – Northern California & Department of Biochemistry and Molecular Medicine, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
| | - Shuwen Zhang
- Institute for Pediatric Regenerative Medicine of Shriners Hospital for Children – Northern California & Department of Biochemistry and Molecular Medicine, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
| | - Moira McMahon
- Institute for Pediatric Regenerative Medicine of Shriners Hospital for Children – Northern California & Department of Biochemistry and Molecular Medicine, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
| | - Chengji J Zhou
- Institute for Pediatric Regenerative Medicine of Shriners Hospital for Children – Northern California & Department of Biochemistry and Molecular Medicine, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
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3
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Pham LNG, Niimi T, Suzuki S, Nguyen MD, Nguyen LCH, Nguyen TD, Hoang KA, Nguyen DM, Sakuma C, Hayakawa T, Hiyori M, Natsume N, Furukawa H, Imura H, Akashi J, Ohta T, Natsume N. Association between IRF6, TP63, GREM1 Gene Polymorphisms and Non-Syndromic Orofacial Cleft Phenotypes in Vietnamese Population: A Case-Control and Family-Based Study. Genes (Basel) 2023; 14:1995. [PMID: 38002937 PMCID: PMC10671090 DOI: 10.3390/genes14111995] [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: 10/03/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
This study aims to identify potential variants in the TP63-IRF6 pathway and GREM1 for the etiology of non-syndromic orofacial cleft (NSOFC) among the Vietnamese population. By collecting 527 case-parent trios and 527 control samples, we conducted a stratified analysis based on different NSOFC phenotypes, using allelic, dominant, recessive and over-dominant models for case-control analyses, and family-based association tests for case-parent trios. Haplotype and linkage disequilibrium analyses were also conducted. IRF6 rs2235375 showed a significant association with an increased risk for non-syndromic cleft lip and palate (NSCLP) and cleft lip with or without cleft palate (NSCL/P) in the G allele, with pallele values of 0.0018 and 0.0003, respectively. Due to the recessive model (p = 0.0011) for the NSCL/P group, the reduced frequency of the GG genotype of rs2235375 was associated with a protective effect against NSCL/P. Additionally, offspring who inherited the G allele at rs2235375 had a 1.34-fold increased risk of NSCL/P compared to the C allele holders. IRF6 rs846810 and a G-G haplotype at rs2235375-rs846810 of IRF6 impacted NSCL/P, with p-values of 0.0015 and 0.0003, respectively. In conclusion, our study provided additional evidence for the association of IRF6 rs2235375 with NSCLP and NSCL/P. We also identified IRF6 rs846810 as a novel marker associated with NSCL/P, and haplotypes G-G and C-A at rs2235375-rs846810 of IRF6 associated with NSOFC.
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Affiliation(s)
- Loc Nguyen Gia Pham
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University, 2–11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (L.N.G.P.); (T.N.); (S.S.); (D.M.N.); (C.S.); (N.N.); (H.I.)
- Odonto-Maxillo Facial Hospital of Ho Chi Minh City, 263-265 Tran Hung Dao Street, District 1, Ho Chi Minh City 71000, Vietnam; (M.D.N.); (L.C.H.N.); (T.D.N.); (K.A.H.)
| | - Teruyuki Niimi
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University, 2–11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (L.N.G.P.); (T.N.); (S.S.); (D.M.N.); (C.S.); (N.N.); (H.I.)
- Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan;
- Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (T.H.); (M.H.)
| | - Satoshi Suzuki
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University, 2–11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (L.N.G.P.); (T.N.); (S.S.); (D.M.N.); (C.S.); (N.N.); (H.I.)
| | - Minh Duc Nguyen
- Odonto-Maxillo Facial Hospital of Ho Chi Minh City, 263-265 Tran Hung Dao Street, District 1, Ho Chi Minh City 71000, Vietnam; (M.D.N.); (L.C.H.N.); (T.D.N.); (K.A.H.)
| | - Linh Cao Hoai Nguyen
- Odonto-Maxillo Facial Hospital of Ho Chi Minh City, 263-265 Tran Hung Dao Street, District 1, Ho Chi Minh City 71000, Vietnam; (M.D.N.); (L.C.H.N.); (T.D.N.); (K.A.H.)
| | - Tuan Duc Nguyen
- Odonto-Maxillo Facial Hospital of Ho Chi Minh City, 263-265 Tran Hung Dao Street, District 1, Ho Chi Minh City 71000, Vietnam; (M.D.N.); (L.C.H.N.); (T.D.N.); (K.A.H.)
| | - Kien Ai Hoang
- Odonto-Maxillo Facial Hospital of Ho Chi Minh City, 263-265 Tran Hung Dao Street, District 1, Ho Chi Minh City 71000, Vietnam; (M.D.N.); (L.C.H.N.); (T.D.N.); (K.A.H.)
| | - Duc Minh Nguyen
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University, 2–11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (L.N.G.P.); (T.N.); (S.S.); (D.M.N.); (C.S.); (N.N.); (H.I.)
- School of Odonto-Stomatology, Hanoi Medical University, Hanoi 10000, Vietnam
| | - Chisato Sakuma
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University, 2–11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (L.N.G.P.); (T.N.); (S.S.); (D.M.N.); (C.S.); (N.N.); (H.I.)
- Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan;
- Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (T.H.); (M.H.)
| | - Toko Hayakawa
- Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (T.H.); (M.H.)
| | - Makino Hiyori
- Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (T.H.); (M.H.)
| | - Nagana Natsume
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University, 2–11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (L.N.G.P.); (T.N.); (S.S.); (D.M.N.); (C.S.); (N.N.); (H.I.)
- Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan;
- Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (T.H.); (M.H.)
| | - Hiroo Furukawa
- Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan;
- Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (T.H.); (M.H.)
| | - Hideto Imura
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University, 2–11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (L.N.G.P.); (T.N.); (S.S.); (D.M.N.); (C.S.); (N.N.); (H.I.)
- Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan;
- Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (T.H.); (M.H.)
| | - Junko Akashi
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University, 2–11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (L.N.G.P.); (T.N.); (S.S.); (D.M.N.); (C.S.); (N.N.); (H.I.)
| | - Tohru Ohta
- Advanced Research Promotion Center, Health Sciences University of Hokkaido, Ishikari-Tobetsu 061-0293, Japan;
| | - Nagato Natsume
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University, 2–11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (L.N.G.P.); (T.N.); (S.S.); (D.M.N.); (C.S.); (N.N.); (H.I.)
- Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan;
- Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (T.H.); (M.H.)
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Yu Y, Zhen Q, Chen W, Yu Y, Li Z, Wang Y, Fan W, Luo S, Wang D, Bai Y, Bian Z, He M, Sun L. Genome-wide meta-analyses identify five new risk loci for nonsyndromic orofacial clefts in the Chinese Han population. Mol Genet Genomic Med 2023; 11:e2226. [PMID: 37326468 PMCID: PMC10568389 DOI: 10.1002/mgg3.2226] [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: 11/23/2022] [Revised: 05/12/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Nonsyndromic orofacial clefts (NSOFCs) are the most common craniofacial birth malformations in humans and are generally classified as nonsyndromic cleft lip with or without cleft palate (NSCL/P) and nonsyndromic cleft palate only (NSCPO). Genome-wide association studies (GWASs) of NSOFCs have demonstrated multiple risk loci and candidate genes; however, published risk factors are able to explain only a small fraction of the observed NSOFCs heritability. METHODS Here, we performed GWASs of 1615 NSCPO cases and 2340 controls, and then conducted genome-wide meta-analyses of NSOFCs, totaling 6812 NSCL/P cases, 2614 NSCPO cases, and 19,165 controls from the Chinese Han population. RESULTS We identify 47 risk loci with genome-wide pmeta -value <5.0 × 10-8 , 5 risk loci (1p32.1, 3p14.1, 3p14.3, 3p21.31, and 13q22.1) of which are new. All of the 47 susceptibility loci conjointly account for 44.12% of the NSOFCs' heritability in the Chinese Han population. CONCLUSION Our results improve the comprehending of genetic susceptibility to NSOFCs and provide new views into the genetic etiology of craniofacial anomalies.
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Affiliation(s)
- Yafen Yu
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
| | - Qi Zhen
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
| | - Weiwei Chen
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
| | - Yanqin Yu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of StomatologyWuhan UniversityWuhanChina
| | - Zhuo Li
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
| | - Yirui Wang
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
| | - Wencheng Fan
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
| | - Sihan Luo
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
| | - Daiyue Wang
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
| | - Yuanming Bai
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
| | - Zhuan Bian
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of StomatologyWuhan UniversityWuhanChina
| | - Miao He
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of StomatologyWuhan UniversityWuhanChina
| | - Liangdan Sun
- Department of Dermatologythe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
- Institute of DermatologyAnhui Medical UniversityHefeiChina
- Key Laboratory of Dermatology, Ministry of EducationAnhui Medical UniversityHefeiChina
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceHefeiChina
- Anhui Provincial Institute of Translational MedicineHefeiChina
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Curtis SW, Carlson JC, Beaty TH, Murray JC, Weinberg SM, Marazita ML, Cotney JL, Cutler DJ, Epstein MP, Leslie EJ. Rare variant modifier analysis identifies variants in SEC24D associated with orofacial cleft subtypes. Hum Genet 2023; 142:1531-1541. [PMID: 37676273 DOI: 10.1007/s00439-023-02596-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/18/2023] [Indexed: 09/08/2023]
Abstract
As one of the most common structural birth defects, orofacial clefts (OFCs) have been studied for decades, and recent studies have demonstrated that there are genetic differences between the different phenotypic presentations of OFCs. However, the contribution of rare genetic variation genome-wide to different subtypes of OFCs has been understudied, with most studies focusing on common genetic variation or rare variation within targeted regions of the genome. Therefore, we used whole-genome sequencing data from the Gabriella Miller Kids First Pediatric Research Program to conduct a gene-based burden analysis to test for genetic modifiers of cleft lip (CL) vs cleft lip and palate (CLP). We found that there was a significantly increased burden of rare variants in SEC24D in CL cases compared to CLP cases (p = 6.86 [Formula: see text] 10-7). Of the 15 variants within SEC24D, 53.3% were synonymous, but overlapped a known craniofacial enhancer. We then tested whether these variants could alter predicted transcription factor binding sites (TFBS), and found that the rare alleles destroyed binding sites for 9 transcription factors (TFs), including Pax1 (p = 0.0009), and created binding sites for 23 TFs, including Pax6 (p = 6.12 [Formula: see text] 10-5) and Pax9 (p = 0.0001), which are known to be involved in normal craniofacial development, suggesting a potential mechanism by which these synonymous variants could have a functional impact. Overall, this study indicates that rare genetic variation may contribute to the phenotypic heterogeneity of OFCs and suggests that regulatory variation may also contribute and warrant further investigation in future studies of genetic variants controlling risk to OFC.
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Affiliation(s)
- Sarah W Curtis
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Jenna C Carlson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Seth M Weinberg
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mary L Marazita
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Justin L Cotney
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, 06030, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA.
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6
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Mason W, Levin AM, Buhl K, Ouchi T, Parker B, Tan J, Ashammakhi N, Jones LR. Translational Research Techniques for the Facial Plastic Surgeon: An Overview. Facial Plast Surg 2023; 39:466-473. [PMID: 37339663 DOI: 10.1055/a-2113-5023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023] Open
Abstract
The field of facial plastic and reconstructive surgery (FPRS) is an incredibly diverse, multispecialty field that seeks innovative and novel solutions for the management of physical defects on the head and neck. To aid in the advancement of medical and surgical treatments for these defects, there has been a recent emphasis on the importance of translational research. With recent technological advancements, there are now a myriad of research techniques that are widely accessible for physician and scientist use in translational research. Such techniques include integrated multiomics, advanced cell culture and microfluidic tissue models, established animal models, and emerging computer models generated using bioinformatics. This study discusses these various research techniques and how they have and can be used for research in the context of various important diseases within the field of FPRS.
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Affiliation(s)
- William Mason
- Department of Otolaryngology, Henry Ford Hospital, Detroit, Michigan
| | - Albert M Levin
- Department of Public Health Science, Henry Ford Health, Detroit, Michigan
- Center for Bioinformatics, Henry Ford Health, Detroit, Michigan
| | - Katherine Buhl
- Department of Otolaryngology, Henry Ford Hospital, Detroit, Michigan
| | - Takahiro Ouchi
- Department of Otolaryngology, Henry Ford Hospital, Detroit, Michigan
| | - Bianca Parker
- Department of Otolaryngology, Henry Ford Hospital, Detroit, Michigan
| | - Jessica Tan
- Department of Otolaryngology, Henry Ford Hospital, Detroit, Michigan
| | - Nureddin Ashammakhi
- Institute for Quantitative Health Science and Engineering, Michigan State University, Michigan
- Department of Biomedical Engineering, College of Engineering, Michigan State University, Michigan
- College of Human Medicine, Michigan State University, Michigan
| | - Lamont R Jones
- Department of Otolaryngology, Henry Ford Hospital, Detroit, Michigan
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7
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Curtis SW, Carlson JC, Beaty TH, Murray JC, Weinberg SM, Marazita ML, Cotney JL, Cutler DJ, Epstein MP, Leslie EJ. Rare genetic variants in SEC24D modify orofacial cleft phenotypes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.24.23287714. [PMID: 37034635 PMCID: PMC10081436 DOI: 10.1101/2023.03.24.23287714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
As one of the most common structural birth defects, orofacial clefts (OFCs) have been studied for decades, and recent studies have demonstrated that there are genetic differences between the different phenotypic presentations of OFCs. However, the contribution of rare genetic variation genome-wide to different subtypes of OFCs has been understudied, with most studies focusing on common genetic variation or rare variation within targeted regions of the genome. Therefore, we used whole-genome sequencing data from the Gabriella Miller Kids First Pediatric Research Program to conduct a gene-based burden analysis to test for genetic modifiers of cleft lip (CL) vs cleft lip and palate (CLP). We found that there was a significantly increased burden of rare variants in SEC24D in CL cases compared to CLP cases (p=6.86×10-7). Of the 15 variants within SEC24D, 53.3% were synonymous, but overlapped a known craniofacial enhancer. We then tested whether these variants could alter predicted transcription factor binding sites (TFBS), and found that the rare alleles destroyed binding sites for 9 transcription factors (TFs), including Pax1 (p=0.0009), and created binding sites for 23 TFs, including Pax6 (p=6.12×10-5) and Pax9 (p= 0.0001), which are known to be involved in normal craniofacial development, suggesting a potential mechanism by which these synonymous variants could have a functional impact. Overall, this study demonstrates that rare genetic variation contributes to the phenotypic heterogeneity of OFCs and suggests that regulatory variation may also contribute and warrant further investigation in future studies of genetic variants controlling risk to OFC.
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Affiliation(s)
- Sarah W Curtis
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Jenna C Carlson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205,USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Seth M Weinberg
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mary L Marazita
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Justin L Cotney
- Department of Genetics and Genome Sciences, University of Connecticut, CT, 06030, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
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8
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Genome Analysis Using Whole-Exome Sequencing of Non-Syndromic Cleft Lip and/or Palate from Malagasy Trios Identifies Variants Associated with Cilium-Related Pathways and Asian Genetic Ancestry. Genes (Basel) 2023; 14:genes14030665. [PMID: 36980938 PMCID: PMC10048728 DOI: 10.3390/genes14030665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/01/2023] [Accepted: 03/05/2023] [Indexed: 03/10/2023] Open
Abstract
Background: Orofacial clefts (OFCs) are common congenital disabilities that can occur as isolated non-syndromic events or as part of Mendelian syndromes. OFC risk factors vary due to differences in regional environmental exposures, genetic variants, and ethnicities. In recent years, significant progress has been made in understanding OFCs, due to advances in sequencing and genotyping technologies. Despite these advances, very little is known about the genetic interplay in the Malagasy population. Methods: Here, we performed high-resolution whole-exome sequencing (WES) on non-syndromic cleft lip with or without palate (nCL/P) trios in the Malagasy population (78 individuals from 26 families (trios)). To integrate the impact of genetic ancestry admixture, we computed both global and local ancestries. Results: Participants demonstrated a high percentage of both African and Asian admixture. We identified damaging variants in primary cilium-mediated pathway genes WNT5B (one family), GPC4 (one family), co-occurrence in MSX1 (five families), WDR11 (one family), and tubulin stabilizer SEPTIN9 (one family). Furthermore, we identified an autosomal homozygous damaging variant in PHGDH (one family) gene that may impact metabiotic activity. Lastly, all variants were predicted to reside on local Asian genetic ancestry admixed alleles. Conclusion: Our results from examining the Malagasy genome provide limited support for the hypothesis that germline variants in primary cilia may be risk factors for nCL/P, and outline the importance of integrating local ancestry components better to understand the multi-ethnic impact on nCL/P.
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9
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Zieger HK, Weinhold L, Schmidt A, Holtgrewe M, Juranek SA, Siewert A, Scheer AB, Thieme F, Mangold E, Ishorst N, Brand FU, Welzenbach J, Beule D, Paeschke K, Krawitz PM, Ludwig KU. Prioritization of non-coding elements involved in non-syndromic cleft lip with/without cleft palate through genome-wide analysis of de novo mutations. HGG ADVANCES 2022; 4:100166. [PMID: 36589413 PMCID: PMC9795529 DOI: 10.1016/j.xhgg.2022.100166] [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: 06/01/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Non-syndromic cleft lip with/without cleft palate (nsCL/P) is a highly heritable facial disorder. To date, systematic investigations of the contribution of rare variants in non-coding regions to nsCL/P etiology are sparse. Here, we re-analyzed available whole-genome sequence (WGS) data from 211 European case-parent trios with nsCL/P and identified 13,522 de novo mutations (DNMs) in nsCL/P cases, 13,055 of which mapped to non-coding regions. We integrated these data with DNMs from a reference cohort, with results of previous genome-wide association studies (GWASs), and functional and epigenetic datasets of relevance to embryonic facial development. A significant enrichment of nsCL/P DNMs was observed at two GWAS risk loci (4q28.1 (p = 8 × 10-4) and 2p21 (p = 0.02)), suggesting a convergence of both common and rare variants at these loci. We also mapped the DNMs to 810 position weight matrices indicative of transcription factor (TF) binding, and quantified the effect of the allelic changes in silico. This revealed a nominally significant overrepresentation of DNMs (p = 0.037), and a stronger effect on binding strength, for DNMs located in the sequence of the core binding region of the TF Musculin (MSC). Notably, MSC is involved in facial muscle development, together with a set of nsCL/P genes located at GWAS loci. Supported by additional results from single-cell transcriptomic data and molecular binding assays, this suggests that variation in MSC binding sites contributes to nsCL/P etiology. Our study describes a set of approaches that can be applied to increase the added value of WGS data.
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Affiliation(s)
- Hanna K. Zieger
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Leonie Weinhold
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn 53127, Germany
| | - Axel Schmidt
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany
| | - Stefan A. Juranek
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn 53127, Germany
| | - Anna Siewert
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Annika B. Scheer
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Frederic Thieme
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Nina Ishorst
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Fabian U. Brand
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn 53127, Germany
| | - Julia Welzenbach
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany,Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn 53127, Germany
| | - Peter M. Krawitz
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn 53127, Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany,Corresponding author
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10
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Abstract
This chapter reviews the evidence of gene×environment interactions (G×E) in the etiology of orofacial cleft birth defects (OFCs), specifically cleft lip (CL), cleft palate (CP), and cleft lip with or without cleft palate (CL/P). We summarize the current state of our understanding of the genetic architecture of nonsyndromic OFCs and the evidence that maternal exposures during pregnancy influence risk of OFCs. Further, we present possible candidate gene pathways for these exposures including metabolism of folates, metabolism of retinoids, retinoic acid receptor signaling, aryl hydrocarbon receptor signaling, glucocorticoid receptor signaling, and biotransformation and transport. We review genes in these pathways with prior evidence of association with OFCs, genes with evidence from prior candidate gene G×E studies, and genes identified from genome-wide searches specifically for identifying G×E. Finally, we suggest future directions for G×E research in OFCs.
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Affiliation(s)
- Mary L Marazita
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, United States; Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States; Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States; Clinical and Translational Science Institute, Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.
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11
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Yu Y, Alvarado R, Petty LE, Bohlender RJ, Shaw DM, Below JE, Bejar N, Ruiz OE, Tandon B, Eisenhoffer GT, Kiss DL, Huff CD, Letra A, Hecht JT. Polygenic risk impacts PDGFRA mutation penetrance in non-syndromic cleft lip and palate. Hum Mol Genet 2022; 31:2348-2357. [PMID: 35147171 PMCID: PMC9307317 DOI: 10.1093/hmg/ddac037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 11/12/2022] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common, severe craniofacial malformation that imposes significant medical, psychosocial and financial burdens. NSCL/P is a multifactorial disorder with genetic and environmental factors playing etiologic roles. Currently, only 25% of the genetic variation underlying NSCL/P has been identified by linkage, candidate gene and genome-wide association studies. In this study, whole-genome sequencing and genome-wide genotyping followed by polygenic risk score (PRS) and linkage analyses were used to identify the genetic etiology of NSCL/P in a large three-generation family. We identified a rare missense variant in PDGFRA (c.C2740T; p.R914W) as potentially etiologic in a gene-based association test using pVAAST (P = 1.78 × 10-4) and showed decreased penetrance. PRS analysis suggested that variant penetrance was likely modified by common NSCL/P risk variants, with lower scores found among unaffected carriers. Linkage analysis provided additional support for PRS-modified penetrance, with a 7.4-fold increase in likelihood after conditioning on PRS. Functional characterization experiments showed that the putatively causal variant was null for signaling activity in vitro; further, perturbation of pdgfra in zebrafish embryos resulted in unilateral orofacial clefting. Our findings show that a rare PDGFRA variant, modified by additional common NSCL/P risk variants, have a profound effect on NSCL/P risk. These data provide compelling evidence for multifactorial inheritance long postulated to underlie NSCL/P and may explain some unusual familial patterns.
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Affiliation(s)
- Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rolando Alvarado
- Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Lauren E Petty
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ryan J Bohlender
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Douglas M Shaw
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nada Bejar
- Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Oscar E Ruiz
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bhavna Tandon
- Department of Pediatrics and Pediatric Research Center, UTHealth McGovern Medical School, Houston, TX 77030, USA
| | - George T Eisenhoffer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Daniel L Kiss
- Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ariadne Letra
- Department of Diagnostic and Biomedical Sciences, UTHealth School of Dentistry at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, UTHealth School of Dentistry at Houston, Houston 77054, TX, USA
| | - Jacqueline T Hecht
- Department of Pediatrics and Pediatric Research Center, UTHealth McGovern Medical School, Houston, TX 77030, USA
- Center for Craniofacial Research, UTHealth School of Dentistry at Houston, Houston 77054, TX, USA
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12
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Dąbrowska J, Biedziak B, Szponar-Żurowska A, Budner M, Jagodziński PP, 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. [PMID: 35778651 DOI: 10.1007/s00438-022-01919-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/12/2022] [Indexed: 01/02/2023]
Abstract
For non-syndromic cleft lip with or without cleft palate (ns-CL/P), the proportion of heritability explained by the known risk loci is estimated to be about 30% and is captured mainly by common variants identified in genome-wide association studies. To contribute to the explanation of the "missing heritability" problem for orofacial clefts, a candidate gene approach was taken to investigate the potential role of rare and private variants in the ns-CL/P risk. Using the next-generation sequencing technology, the coding sequence of a set of 423 candidate genes was analysed in 135 patients from the Polish population. After stringent multistage filtering, 37 rare coding and splicing variants of 28 genes were identified. 35% of these genetic alternations that may play a role of genetic modifiers influencing an individual's risk were detected in genes not previously associated with the ns-CL/P susceptibility, including COL11A1, COL17A1, DLX1, EFTUD2, FGF4, FGF8, FLNB, JAG1, NOTCH2, SHH, WNT5A and WNT9A. Significant enrichment of rare alleles in ns-CL/P patients compared with controls was also demonstrated for ARHGAP29, CHD7, COL17A1, FGF12, GAD1 and SATB2. In addition, analysis of panoramic radiographs of patients with identified predisposing variants may support the hypothesis of a common genetic link between orofacial clefts and dental abnormalities. In conclusion, our study has confirmed that rare coding variants might contribute to the genetic architecture of ns-CL/P. Since only single predisposing variants were identified in novel cleft susceptibility genes, future research will be required to confirm and fully understand their role in the aetiology of ns-CL/P.
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Affiliation(s)
- Justyna Dąbrowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781, Poznan, Poland
| | - Barbara Biedziak
- Department of Orthodontics and Craniofacial Anomalies, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Szponar-Żurowska
- Department of Orthodontics and Craniofacial Anomalies, Poznan University of Medical Sciences, Poznan, Poland
| | - Margareta Budner
- Eastern Poland Burn Treatment and Reconstructive Center, Leczna, Poland
| | - Paweł P Jagodziński
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781, Poznan, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781, Poznan, Poland.
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13
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Yang M, Wang Y, Yin B, Zheng Q, Shi B, Jia Z. Association of soluble epoxide hydrolase 2 gene with the risk of non-syndromic cleft lip with or without cleft palate in western Han Chinese population. HUA XI KOU QIANG YI XUE ZA ZHI = HUAXI KOUQIANG YIXUE ZAZHI = WEST CHINA JOURNAL OF STOMATOLOGY 2022; 40:279-284. [PMID: 38597007 PMCID: PMC9207791 DOI: 10.7518/hxkq.2022.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/20/2022] [Indexed: 04/11/2024]
Abstract
OBJECTIVES This study aimed to explore the associations between soluble epoxide hydrolase 2 gene (EPHX2) variants and non-syndromic cleft lip with or without cleft palate (NSCL/P) in Chinese Han population. METHODS We recruited 159 NSCL/P cases from Chinese Han population and carried out targeted resequencing using the whole genome sequencing data of 542 healthy Chinese individuals from Novegene internal database as controls. We classified EPHX2 variants as common or rare according to their minor allele frequency and performed an association analysis for common variations and a burden analysis for rare variations. RESULTS The lowest P-value in NSCL/P was observed at rs57699806 (P=0.000 13, OR=2.849 and 95% CI: 1.691-4.800), followed by rs4732723 (P=0.006 50, OR=0.662 and 95%CI: 0.491-0.892), rs7829267 (P=0.009 20, OR=1.496 and 95%CI: 1.117-2.005), rs721619 (P=0.011 00, OR=1.474 and 95%CI: 1.098-1.980), and rs7816586 (P=0.040 00, OR=1.310 and 95%CI: 1.015-1.691). The odds ratios suggested the C allele at rs4732723 as a protective factor for NSCL/P and the reference alleles at other single nucleotide polymorphisms (SNPs) as the risk factors for NSCL/P. Burden analysis showed no statistical significance (P>0.05). CONCLUSIONS Through targeted resequencing, this study identified five SNPs named rs57699806, rs4732723, rs7829267, rs721619, and rs7816586 around the region of EPHX2 gene associated with NSCL/P in Chinese Han population. Four SNPs of rs57699806, rs4732723, rs7829267, and rs7816586 were first identified.
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Affiliation(s)
- Mengxi Yang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yiru Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Bin Yin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Qian Zheng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Zhonglin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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14
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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: 16] [Impact Index Per Article: 8.0] [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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15
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Li B, Yong L, Yu Y, Yu Y, Zhen Q, Ge H, Mao Y, Chen W, Yu Y, Wang Y, Li Z, Fan W, Zhang C, Hu X, Zhang R, Cao L, Liu H, Bian Z, He M, Sun L. Genome-wide analyses of nonsyndromic cleft lip with or without palate identify 20 new risk loci in the Chinese Han population. J Genet Genomics 2022; 49:903-905. [PMID: 35217232 DOI: 10.1016/j.jgg.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/16/2022] [Accepted: 02/13/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Bao Li
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China; Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Liang Yong
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China; Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Yafen Yu
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China; Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Yanqin Yu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Qi Zhen
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China; Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Huiyao Ge
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China; Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Yiwen Mao
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China; Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Weiwei Chen
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China; Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Yanxia Yu
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China; Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Yirui Wang
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China; Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Zhuo Li
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China; Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Wencheng Fan
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China; Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Chang Zhang
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China; Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Xia Hu
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China; Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Ruixue Zhang
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China; Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Lu Cao
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China; Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Hao Liu
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China; Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Zhuan Bian
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Miao He
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China.
| | - Liangdan Sun
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China; Anhui Provincial Institute of Translational Medicine, Hefei, China.
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16
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Ruff KLM, Hollstein R, Fazaal J, Thieme F, Gehlen J, Mangold E, Knapp M, Welzenbach J, Ludwig KU. Allele-specific transcription factor binding in a cellular model of orofacial clefting. Sci Rep 2022; 12:1807. [PMID: 35110662 PMCID: PMC8810875 DOI: 10.1038/s41598-022-05876-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/17/2022] [Indexed: 11/09/2022] Open
Abstract
Non-syndromic cleft lip with/without cleft palate (nsCL/P) is a frequent congenital malformation with multifactorial etiology. While recent genome-wide association studies (GWAS) have identified several nsCL/P risk loci, the functional effects of the associated non-coding variants are largely unknown. Furthermore, additional risk loci remain undetected due to lack of power. As genetic variants might alter binding of transcription factors (TF), we here hypothesized that the integration of data from TF binding sites, expression analyses and nsCL/P GWAS might help to (i) identify functionally relevant variants at GWAS loci, and (ii) highlight novel risk variants that have been previously undetected. Analysing the craniofacial TF TFAP2A in human embryonic palatal mesenchyme (HEPM) cells, we identified 2845 TFAP2A ChIP-seq peaks, several of which were located near nsCL/P candidate genes (e.g. MSX1 and SPRY2). Comparison with independent data suggest that 802 of them might be specific to craniofacial development, and genes near these peaks are enriched in processes relevant to nsCL/P. Integration with nsCL/P GWAS data, however, did not show robust evidence for co-localization of common nsCL/P risk variants with TFAP2A ChIP-seq peaks. This data set represents a new resource for the analyses of craniofacial processes, and similar approaches with additional cell lines and TFs could be applied to generate further insights into nsCL/P etiology.
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Affiliation(s)
- Katharina L M Ruff
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Ronja Hollstein
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Julia Fazaal
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Frederic Thieme
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Jan Gehlen
- Centre for Human Genetics, University of Marburg, Marburg, Germany
| | - Elisabeth Mangold
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Michael Knapp
- Institute for Medical Biometry, Informatics and Epidemiology IMBIE, University of Bonn, Bonn, Germany
| | - Julia Welzenbach
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Kerstin U Ludwig
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany.
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17
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Wang X, Guo S, Zhou X, Wang Y, Zhang T, Chen R. Exploring the Molecular Mechanism of lncRNA-miRNA-mRNA Networks in Non-Syndromic Cleft Lip with or without Cleft Palate. Int J Gen Med 2021; 14:9931-9943. [PMID: 34938111 PMCID: PMC8687630 DOI: 10.2147/ijgm.s339504] [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: 09/15/2021] [Accepted: 11/01/2021] [Indexed: 11/23/2022] Open
Abstract
Background Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common craniofacial birth defect. Growing evidence has demonstrated the competing endogenous RNA (ceRNA) hypothesis has played a role in the pathogenesis of NSCL/P. Here, we identified the important lncRNAs in NSCL/P and constructed a ceRNA regulatory network to predict their underlying functional mechanism. Methods Total RNA isolated from the peripheral blood samples were analyzed by the Human Clariom D Affymetrix platform and differentially expressed genes (DEGs) were identified. Using the limma package in R software, DEGs in the expression profile of GSE42589 were identified from Gene Expression Omnibus (GEO) database. Co-differentially expressed lncRNAs (co-DElncRNAs) were used to predict the microRNAs that may bind to them. Co-differentially expressed mRNAs (co-DEmRNAs) were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The hub genes were screened using the cytohubba plug-in in Cytoscape. A ceRNA network was built to investigate the molecular mechanism underlying the etiology of NSCL/P. The expression levels of lncRNAs, miRNAs, and mRNAs in the network were assessed by quantitative real-time polymerase chain reaction (qRT-PCR). Results We found 116 DElncRNAs and 2955 DEmRNAs from the GSE42589 dataset, and 2626 DElncRNAs and 2771 DEmRNAs from the Human Clariom D gene chip. A network of co-DEmRNAs containing 3712 edges and 621 nodes were identified by PPI analysis. A ceRNA regulatory network comprising lncRNA USP17L6P, hsa-miR-449c-5p, and MYC was established. qRT-PCR results revealed significantly lower expression levels of lncRNA USP17L6P and c-Myc in NSCL/P tissues, while the expression level of hsa-miR-449c-5p was higher as compared to control samples (p < 0.05). Conclusion The identified lncRNAs and the established ceRNA regulatory network provide novel insight into the pathogenesis of NSCL/P, therefore hold great promise in NSCL/P management in clinical practice.
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Affiliation(s)
- Xiangpu Wang
- Department of Oral and Maxillofacial Plastic and Trauma Surgery, Center of Cleft Lip and Palate Treatment, Beijing Stomatological Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Siyuan Guo
- Department of Oral and Maxillofacial Plastic and Trauma Surgery, Center of Cleft Lip and Palate Treatment, Beijing Stomatological Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Xinli Zhou
- Department of Oral and Maxillofacial Plastic and Trauma Surgery, Center of Cleft Lip and Palate Treatment, Beijing Stomatological Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Yupei Wang
- Department of Oral and Maxillofacial Plastic and Trauma Surgery, Center of Cleft Lip and Palate Treatment, Beijing Stomatological Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Ting Zhang
- Department of Oral and Maxillofacial Plastic and Trauma Surgery, Center of Cleft Lip and Palate Treatment, Beijing Stomatological Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Renji Chen
- Department of Oral and Maxillofacial Plastic and Trauma Surgery, Center of Cleft Lip and Palate Treatment, Beijing Stomatological Hospital, Capital Medical University, Beijing, People's Republic of China
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18
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Leslie EJ. Genetic models and approaches to study orofacial clefts. Oral Dis 2021; 28:1327-1338. [PMID: 34923716 DOI: 10.1111/odi.14109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/08/2021] [Accepted: 12/16/2021] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Orofacial clefts (OFCs) are common craniofacial birth defects with heterogeneous phenotype and etiology. Geneticists have applied nearly every available method and technology to further our understanding of the genetic architectures of OFCs. OBJECTIVE This review describes the evidence for a genetic etiology in OFCs, statistical genetic approaches employed to identify genetic causes, and how the results have shaped our current understanding of the genetic architectures of syndromic and nonsyndromic OFCs. CONCLUSION There has been rapid progress towards elucidating the genetic architectures of OFCs due to the availability of large collections of DNA samples from cases, controls, and families with OFCs and the consistent adoption of new methodologies and novel statistical approaches as they are developed. Genetic studies have identified rare and common variants influencing risk of OFCs in both Mendelian and complex forms of OFCs, blurring the distinctions traditional categories used in genetic studies and clinical medicine.
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19
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Avasthi KK, Muthuswamy S, Asim A, Agarwal A, Agarwal S. Identification of Novel Genomic Variations in Susceptibility to Nonsyndromic Cleft Lip and Palate Patients. Pediatr Rep 2021; 13:650-657. [PMID: 34941638 PMCID: PMC8703930 DOI: 10.3390/pediatric13040077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/27/2021] [Accepted: 12/01/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Nonsyndromic cleft lip with or without palate (NSCL/P) is a multifactorial and common birth malformation caused by genetic and environmental factors, as well as by teratogens. Genome-wide association studies found genetic variations with modulatory effects of NSCL/P formation in Chinese and Iranian populations. We aimed to identify the susceptibility of single-nucleotide polymorphisms (SNPs) to nonsyndromic cleft lip with or without palate in the Indian population. MATERIAL AND METHODS The present study was conducted on NSCL/P cases and controls. Genomic DNA was extracted from peripheral blood and Axiom- Precision Medicine Research Array (PMRA) was performed. The Axiom-PMRA covers 902,527 markers and several thousand novel risk variants. Quality control-passed samples were included for candidate genetic variation identification, gene functional enrichment, and pathway and network analysis. RESULTS The genome-wide association study identified fourteen novel candidate gene SNPs that showed the most significant association with the risk of NSCL/P, and eight were predicted to have regulatory sequences. CONCLUSION The GWAS study showed novel candidate genetic variations in NSCL/P formations. These findings contribute to the understanding of genetic predisposition to nonsyndromic cleft lip with or without palate.
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Affiliation(s)
- Kapil Kumar Avasthi
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow 226014, India; (K.K.A.); (A.A.)
| | - Srinivasan Muthuswamy
- Department of Life Sciences, National Institute of Technology, Rourkela 769001, Odisha, India;
| | - Ambreen Asim
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow 226014, India; (K.K.A.); (A.A.)
| | - Amit Agarwal
- Department of Burn and Plastic Surgery, Vivekananda Polyclinic and Institute of Medical Sciences, Lucknow 226007, India;
| | - Sarita Agarwal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow 226014, India; (K.K.A.); (A.A.)
- Correspondence: ; Tel.: +91-0522-2494356
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20
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Knol MJ, Pawlak MA, Lamballais S, Terzikhan N, Hofer E, Xiong Z, Klaver CCW, Pirpamer L, Vernooij MW, Ikram MA, Schmidt R, Kayser M, Evans TE, Adams HHH. Genetic architecture of orbital telorism. Hum Mol Genet 2021; 31:1531-1543. [PMID: 34791242 PMCID: PMC9071440 DOI: 10.1093/hmg/ddab334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 11/19/2022] Open
Abstract
The interocular distance, or orbital telorism, is a distinctive craniofacial trait that also serves as a clinically informative measure. While its extremes, hypo- and hypertelorism, have been linked to monogenic disorders and are often syndromic, little is known about the genetic determinants of interocular distance within the general population. We derived orbital telorism measures from cranial magnetic resonance imaging by calculating the distance between the eyeballs’ centre of gravity, which showed a good reproducibility with an intraclass correlation coefficient of 0.991 (95% confidence interval 0.985–0.994). Heritability estimates were 76% (standard error = 12%) with a family-based method (N = 364) and 39% (standard error = 2.4%) with a single nucleotide polymorphism-based method (N = 34 130) and were unaffected by adjustment for height (model II) and intracranial volume (model III) or head width (model IV). Genome-wide association studies in 34 130 European individuals identified 56 significantly associated genomic loci (P < 5 × 10−8) across four different models of which 46 were novel for facial morphology, and overall these findings replicated in an independent sample (N = 10 115) with telorism-related horizontal facial distance measures. Genes located nearby these 56 identified genetic loci were 4.9-fold enriched for Mendelian hypotelorism and hypertelorism genes, underlining their biological relevance. This study provides novel insights into the genetic architecture underlying interocular distance in particular, and the face in general, and explores its potential for applications in a clinical setting.
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Affiliation(s)
- Maria J Knol
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - Mikolaj A Pawlak
- Department of Neurology and Cerebrovascular Disorders, Poznan University of Medical Sciences, Poznan, Poland.,Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - Sander Lamballais
- Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - Natalie Terzikhan
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - Edith Hofer
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University Graz, Auenbruggerplatz 22, 8036 Graz, Austria.,Institute of Medical Informatics, Statistics and Documentation, Medical University Graz, Auenbruggerplatz 22, 8036 Graz, Austria
| | - Ziyi Xiong
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands.,Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - Caroline C W Klaver
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands.,Department of Ophthalmology, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - Lukas Pirpamer
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University Graz, Auenbruggerplatz 22, 8036 Graz, Austria
| | - Meike W Vernooij
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands.,Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - Reinhold Schmidt
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University Graz, Auenbruggerplatz 22, 8036 Graz, Austria
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - Tavia E Evans
- Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands.,Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
| | - Hieab H H Adams
- Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands.,Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3015 CE, the Netherlands
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21
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Nguyen DM, Suzuki S, Imura H, Niimi T, Furukawa H, Ta TV, Tong SM, Nguyen TT, Pham LNG, Tran DL, Natsume N. Family based and case-control designs reveal an association of TFAP2A in nonsyndromic cleft lip only among Vietnamese population. Mol Genet Genomic Med 2021; 9:e1754. [PMID: 34310873 PMCID: PMC8457689 DOI: 10.1002/mgg3.1754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/08/2021] [Indexed: 12/19/2022] Open
Abstract
Aims Dozens of causative genes and their mechanisms of nonsyndromic cleft lip with or without cleft palate (NSCL/P) were revealed through genome‐wide association and linkage studies. Results were, however, not always replicated in different populations or methodologies. This study used case–control and family based approaches to investigate the etiology of NSCL/P and its two subtypes: nonsyndromic cleft lip only (NSCLO) and nonsyndromic cleft lip and palate (NSCLP) among the Vietnamese population. Methods Two hundred and seventeen NSCL/P case‐parent trios (one affected child and two parents), including 105 NSCLO and 112 NSCLP were involved for a family based design; and 273 ethnic and region‐matched healthy controls with no cleft history in their families were recruited for a case–control design. Three SNPs consisting of TFAP2A (rs1675414 and rs303048) and 8q24 (rs987525) were genotyped using the TaqMan SNP genotyping assay. Results TFAP2A rs1675414 was associated with NSCLO, replicated by both case‐control and family based tests. Other SNPs yielded no evidence of susceptibility to NSCL/P or two subtypes. Conclusion The current investigation suggests an intriguing role of TFAP2A in the etiology of NSCLO among the Vietnamese population. This study used case‐control and family‐based approaches to investigate the etiology of NSCL/P and its two subtypes: nonsyndromic cleft lip only (NSCLO), nonsyndromic cleft lip and palate (NSCLP) among Vietnamese population. TFAP2A rs1675414 was associated with NSCLO, replicated by both case‐control and family‐based tests.
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Affiliation(s)
- Duc Minh Nguyen
- Division of Research and Treatment for Oral Maxillofacial Congenital Anomalies, Aichi Gakuin University, Nagoya, Japan.,School of Odonto-stomatology, Hanoi Medical University, Hanoi, Vietnam
| | - Satoshi Suzuki
- Division of Research and Treatment for Oral Maxillofacial Congenital Anomalies, Aichi Gakuin University, Nagoya, Japan
| | - Hideto Imura
- Division of Research and Treatment for Oral Maxillofacial Congenital Anomalies, Aichi Gakuin University, Nagoya, Japan.,Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, Nagoya, Japan.,Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, Nagoya, Japan
| | - Teruyuki Niimi
- Division of Research and Treatment for Oral Maxillofacial Congenital Anomalies, Aichi Gakuin University, Nagoya, Japan.,Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, Nagoya, Japan.,Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, Nagoya, Japan
| | - Hiroo Furukawa
- Division of Research and Treatment for Oral Maxillofacial Congenital Anomalies, Aichi Gakuin University, Nagoya, Japan.,Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, Nagoya, Japan.,Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, Nagoya, Japan
| | - Thanh-Van Ta
- Center for Gene and Protein Research, Hanoi Medical University, Hanoi, Vietnam
| | - Son Minh Tong
- School of Odonto-stomatology, Hanoi Medical University, Hanoi, Vietnam
| | - Tra Thu Nguyen
- School of Odonto-stomatology, Hanoi Medical University, Hanoi, Vietnam.,Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Loc Nguyen Gia Pham
- Division of Research and Treatment for Oral Maxillofacial Congenital Anomalies, Aichi Gakuin University, Nagoya, Japan.,Odonto - Maxillo Facial Hospital of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Duy Le Tran
- Nguyen Dinh Chieu General Hopsital, Ben Tre, Vietnam
| | - Nagato Natsume
- Division of Research and Treatment for Oral Maxillofacial Congenital Anomalies, Aichi Gakuin University, Nagoya, Japan.,Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, Nagoya, Japan.,Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, Nagoya, Japan
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22
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Sun JL, Shi JY, Yin B, Lin YS, Shi B, Jia ZL. Association analysis of SNPs in GRHL3, FAF1, and KCNJ2 with NSCPO sub-phenotypes in Han Chinese. Oral Dis 2021; 28:2204-2214. [PMID: 34255421 DOI: 10.1111/odi.13961] [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: 02/22/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 02/05/2023]
Abstract
OBJECTIVES Non-syndromic cleft palate only (NSCPO) is a common congenital deformity with complex etiologies. GRHL3, FAF1, and KCNJ2 have been reported to be involved in the pathogenesis of NSCPO. Up till now, there have been no replication studies based on large Han Chinese. Therefore, this study aimed to investigate associations between GRHL3, FAF1, KCNJ2, and NSCPO sub-phenotypes patients in Han Chinese. MATERIALS AND METHODS Firstly, we selected 2 SNPs based on previous literatures: FAF1 (rs3827730) and GRHL3 (rs41268753). Also, we selected 8 tagSNPs in GRHL3 (rs557811, rs609352, rs10903078, rs6659209, rs12401714, rs12568599, rs3887581, rs12024148) and 2 tagSNPs in KCNJ2 (rs75855040 and rs236514). Afterward, we evaluated these SNPs among 1668 NSCPO patients and 1811 normal controls from Han Chinese. Following data were analyzed by PLINK and Haploview program. RESULTS Association analysis under additive model showed that allele A at rs12568599 in GRHL3 gene is significantly associated with NSCPO (p = 0.0034, OR = 1.38 and 95%CI: 1.11-1.72) and its sub-phenotype incomplete cleft palate (ICP) (p = 0.0039, OR = 1.4 and 95%CI: 1.11-1.75), and it could increase the risk of both NSCPO and ICP. CONCLUSIONS This study firstly found that rs12568599 in GRHL3 is associated with NSCPO and ICP in Han Chinese, indicating that sub-phenotypes of NSCPO have different etiologies.
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Affiliation(s)
- Jia-Lin Sun
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jia-Yu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, California, USA
| | - Bin Yin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yan-Song Lin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhong-Lin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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23
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Welzenbach J, Hammond NL, Nikolić M, Thieme F, Ishorst N, Leslie EJ, Weinberg SM, Beaty TH, Marazita ML, Mangold E, Knapp M, Cotney J, Rada-Iglesias A, Dixon MJ, Ludwig KU. Integrative approaches generate insights into the architecture of non-syndromic cleft lip with or without cleft palate. HGG ADVANCES 2021; 2:100038. [PMID: 35047836 PMCID: PMC8756534 DOI: 10.1016/j.xhgg.2021.100038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/27/2021] [Indexed: 12/15/2022] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (nsCL/P) is a common congenital facial malformation with a multifactorial etiology. Genome-wide association studies (GWASs) have identified multiple genetic risk loci. However, functional interpretation of these loci is hampered by the underrepresentation in public resources of systematic functional maps representative of human embryonic facial development. To generate novel insights into the etiology of nsCL/P, we leveraged published GWAS data on nsCL/P as well as available chromatin modification and expression data on mid-facial development. Our analyses identified five novel risk loci, prioritized candidate target genes within associated regions, and highlighted distinct pathways. Furthermore, the results suggest the presence of distinct regulatory effects of nsCL/P risk variants throughout mid-facial development and shed light on its regulatory architecture. Our integrated data provide a platform to advance hypothesis-driven molecular investigations of nsCL/P and other human facial defects.
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Affiliation(s)
- Julia Welzenbach
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Nigel L. Hammond
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, UK
| | - Miloš Nikolić
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Frederic Thieme
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Nina Ishorst
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Elizabeth J. Leslie
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Psychiatry and Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Elisabeth Mangold
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics, and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Justin Cotney
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, Cantabria, Spain
| | - Michael J. Dixon
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, UK
| | - Kerstin U. Ludwig
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
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24
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Curtis SW, Chang D, Sun MR, Epstein MP, Murray JC, Feingold E, Beaty TH, Weinberg SM, Marazita ML, Lipinski RJ, Carlson JC, Leslie EJ. FAT4 identified as a potential modifier of orofacial cleft laterality. Genet Epidemiol 2021; 45:721-735. [PMID: 34130359 DOI: 10.1002/gepi.22420] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/04/2021] [Accepted: 05/24/2021] [Indexed: 01/02/2023]
Abstract
Orofacial clefts (OFCs) are common (1 in 700 births) congenital malformations that include a cleft lip (CL) and cleft lip and palate (CLP). These OFC subtypes are also heterogeneous themselves, with the CL occurring on the left, right, or both sides of the upper lip. Unilateral CL and CLP have a 2:1 bias towards left-sided clefts, suggesting a nonrandom process. Here, we performed a study of left- and right-sided clefts within the CL and CLP subtypes to better understand the genetic factors controlling cleft laterality. We conducted genome-wide modifier analyses by comparing cases that had right unilateral CL (RCL; N = 130), left unilateral CL (LCL; N = 216), right unilateral CLP (RCLP; N = 416), or left unilateral CLP (LCLP; N = 638), and identified a candidate region on 4q28, 400 kb downstream from FAT4, that approached genome-wide significance for LCL versus RCL (p = 8.4 × 10-8 ). Consistent with its potential involvement as a genetic modifier of CL, we found that Fat4 exhibits a specific domain of expression in the mesenchyme of the medial nasal processes that form the median upper lip. Overall, these results suggest that the epidemiological similarities in left- to right-sided clefts in CL and CLP are not reflected in the genetic association results.
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Affiliation(s)
- Sarah W Curtis
- Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | - Daniel Chang
- Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | - Miranda R Sun
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Seth M Weinberg
- Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mary L Marazita
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Robert J Lipinski
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jenna C Carlson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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25
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Steiper ME, Grube NT, Gagnon CM. Elevated diversity in loci linked to facial morphology is consistent with the hypothesis that individual facial recognition is important across hominoids. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 174:785-791. [PMID: 33454958 DOI: 10.1002/ajpa.24233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 12/31/2020] [Accepted: 01/04/2021] [Indexed: 11/05/2022]
Abstract
OBJECTIVES The ability to use visual signals to identify individuals is an important feature of primate social groups, including humans. Sheehan and Nachman (2014) showed that loci linked to facial morphology had elevated levels of diversity and interpreted this as evidence that the human face is under frequency-dependent selection to enhance individual recognition (Nature Communications 5). In our study, we tested whether this pattern is found in non-human ape species, to help understand whether individual recognition might also play a role in species other than humans. MATERIALS AND METHODS We examined levels of genetic diversity in an available population genomic dataset of humans, chimpanzees, bonobos, gorillas, and orangutans for three sets of loci, (1) loci linked to facial morphology, (2) loci linked to height, and (3) neutrally evolving regions. We tested whether loci linked to facial morphology were more variable than loci linked to height or neutrally evolving loci in each of these species. RESULTS We found significantly elevated diversity in loci linked to facial morphology in chimpanzees, gorillas, and Sumatran and Bornean orangutans. DISCUSSION Our findings closely parallel those of Sheehan and Nachman and are consistent with the idea that selection for facial diversity and individual recognition has not only shaped the evolution of the human face, but it has similarly shaped the evolution of most of our closest primate relatives. We also discuss alternative hypotheses for this pattern.
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Affiliation(s)
- Michael E Steiper
- Department of Anthropology, Hunter College of the City University of New York (CUNY), New York, New York, USA.,Program in Anthropology, The Graduate Center of the City University of New York (CUNY), New York, New York, USA.,New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, USA
| | - Natalia T Grube
- Department of Biology, The Pennsylvania State University, State College, Pennsylvania, USA
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26
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Howe LJ, Hemani G, Lesseur C, Gaborieau V, Ludwig KU, Mangold E, Brennan P, Ness AR, St Pourcain B, Davey Smith G, Lewis SJ. Evaluating shared genetic influences on nonsyndromic cleft lip/palate and oropharyngeal neoplasms. Genet Epidemiol 2020; 44:924-933. [PMID: 32710482 PMCID: PMC8240308 DOI: 10.1002/gepi.22343] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 06/12/2020] [Accepted: 07/15/2020] [Indexed: 12/23/2022]
Abstract
It has been hypothesised that nonsyndromic cleft lip/palate (nsCL/P) and cancer may share aetiological risk factors. Population studies have found inconsistent evidence for increased incidence of cancer in nsCL/P cases, but several genes (e.g., CDH1, AXIN2) have been implicated in the aetiologies of both phenotypes. We aimed to evaluate shared genetic aetiology between nsCL/P and oral cavity/oropharyngeal cancers (OC/OPC), which affect similar anatomical regions. Using a primary sample of 5,048 OC/OPC cases and 5,450 controls of European ancestry and a replication sample of 750 cases and 336,319 controls from UK Biobank, we estimate genetic overlap using nsCL/P polygenic risk scores (PRS) with Mendelian randomization analyses performed to evaluate potential causal mechanisms. In the primary sample, we found strong evidence for an association between a nsCL/P PRS and increased odds of OC/OPC (per standard deviation increase in score, odds ratio [OR]: 1.09; 95% confidence interval [CI]: 1.04, 1.13; p = .000053). Although confidence intervals overlapped with the primary estimate, we did not find confirmatory evidence of an association between the PRS and OC/OPC in UK Biobank (OR 1.02; 95% CI: 0.95, 1.10; p = .55). Mendelian randomization analyses provided evidence that major nsCL/P risk variants are unlikely to influence OC/OPC. Our findings suggest possible shared genetic influences on nsCL/P and OC/OPC.
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Affiliation(s)
- Laurence J Howe
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, UK
- Institute of Cardiovascular Science, University College London, London, UK
- Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Gibran Hemani
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, UK
| | - Corina Lesseur
- Section of Genetics, International Agency for Research on Cancer, Lyon, France
| | - Valérie Gaborieau
- Section of Genetics, International Agency for Research on Cancer, Lyon, France
| | | | | | - Paul Brennan
- Section of Genetics, International Agency for Research on Cancer, Lyon, France
| | - Andy R Ness
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol, Bristol, UK
- Weston NHS Foundation Trust, University of Bristol, Bristol, UK
| | - Beate St Pourcain
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, UK
- Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, UK
| | - Sarah J Lewis
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, UK
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27
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Rafighdoost H, Poudineh A, Bahari G, Ghaffari H, Hashemi M. Association of Genetic Polymorphisms of GREM1 Gene with Susceptibility to Non-Syndromic Cleft Lip with or without Cleft Palate in an Iranian Population. Fetal Pediatr Pathol 2020; 39:409-421. [PMID: 31650875 DOI: 10.1080/15513815.2019.1666329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Background: Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is common congenital birth anomaly with multifactorial etiology. The GREM1 gene has been proposed to play a role in oral clefts development.Objective: The aim of the present study was to evaluate the correlation between GREM1 polymorphisms and the risk of NSCL/P in an Iranian population.Methods: Genotyping of rs7162202, rs12915554, rs3743105, rs1129456, and rs10318 polymorphisms of GREM1 gene in 150 NSCL/P and 152 healthy subjects was determined by the PCR-RFLP or T-ARMS-PCR.Results: The findings showed that the rs12915554 variant significantly increased the risk of NSCL/P in heterozygous (OR = 4.20, 95%CI = 2.46-7.11, p < 0.0001, AC vs AA), and allele (OR = 3.17, 95%CI = 2.00-5.08, p < 0.0001, C vs A) genetic models. The rs3743105 polymorphism was correlated with reduced risk of NSCL/P in heterozygous (OR = 0.49, 95%CI = 0.29-0.83, p = 0.008, AG vs GG) and dominant (OR = 0.54, 95%CI = 0.33-0.89, p = 0.018, GA + AA vs GG) genetic models. The rs1129456 variant was positively associated with the risk of NSCL/P in heterozygous (OR = 2.91, 95%CI = 1.12-7.38, p = 0.028, AT vs AA) and allele (OR = 2.80, 95%CI = 2.80-6.95, p = 0.031, T vs C). The rs10318 polymorphism significantly reduced NSCL/P risk in homozygous (OR = 0.20, 95%CI = 0.06-0.67, p = 0.013, TT vs CC), dominant (OR = 0.57, 95%CI = 0.36-0.91, p = 0.019, CT + CC vs CC), recessive (OR = 0.24, 95%CI = 0.07-0.76, p = 0.031, TT vs CT + CC), and allele (OR = 0.57, 95%CI = 0.38-0.84, p = 0.005, T vs C). No correlation was observed between rs7162202 polymorphism and NSCL/P.Conclusion: The findings support that GREM1 polymorphisms are involved in NSCL/P susceptibility in an Iranian population.
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Affiliation(s)
- Houshang Rafighdoost
- Department of Anatomy, Faculty of medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ali Poudineh
- Department of Anatomy, Faculty of medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Gholamreza Bahari
- Children and Adolescent Health Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Hamidreza Ghaffari
- Department of Anatomy, Faculty of Medicine, Zabol University of Medical Sciences, Zabol, Iran
| | - Mohammad Hashemi
- Department of Biochemistry, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
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28
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Yin B, Shi JY, Lin YS, Shi B, Jia ZL. SNPs at TP63 gene was specifically associated with right-side cleft lip in Han Chinese population. Oral Dis 2020; 27:559-566. [PMID: 32687624 DOI: 10.1111/odi.13566] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/05/2020] [Accepted: 07/15/2020] [Indexed: 02/05/2023]
Abstract
OBJECTIVES Non-syndromic cleft lip with or without palate is one of the most common birth malformations. TP63 and GREM1 were recently reported to be associated with NSCL/P. However, there were few studies focused on their associations in non-syndromic cleft lip only (NSCLO). DESIGN Initial screening and replication in large cohorts were used to locate the susceptible SNPs of TP63 and GREM1. Firstly, variations were screened among 192 NSCLO cases by the Sanger sequencing. Then, we selected five associated SNPs in initial screening phase and replicated among 1,006 NSCLO cases and 1,823 normal controls. RESULTS Initial chi-square test showed that rs7653848, rs7624324, rs6790167, and rs1345186 in TP63 and rs2280738 in GREM1 achieved statistical significance (p < .05); the subsequent replication analysis showed that rs1345186 was specifically significant in right-side cleft lip (RCL; p = .017, OR = 1.33, and 95% CI: 1.05-1.69). CONCLUSION This study firstly used the subphenotype of cleft lip samples to verify the association between TP63 and GREM1, which indicated that TP63 is a promising susceptible gene for RCL in Chinese population. And further confirmed the different etiology in the right-sided cleft lip, left-sided cleft lip, and bilateral cleft lip of NSCLO. This will give new reference for the future research and genetic counseling.
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Affiliation(s)
- Bin Yin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jia-Yu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, CA, USA
| | - Yan-Song Lin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhong-Lin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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29
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Reynolds K, Zhang S, Sun B, Garland MA, Ji Y, Zhou CJ. Genetics and signaling mechanisms of orofacial clefts. Birth Defects Res 2020; 112:1588-1634. [PMID: 32666711 DOI: 10.1002/bdr2.1754] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 12/31/2022]
Abstract
Craniofacial development involves several complex tissue movements including several fusion processes to form the frontonasal and maxillary structures, including the upper lip and palate. Each of these movements are controlled by many different factors that are tightly regulated by several integral morphogenetic signaling pathways. Subject to both genetic and environmental influences, interruption at nearly any stage can disrupt lip, nasal, or palate fusion and result in a cleft. Here, we discuss many of the genetic risk factors that may contribute to the presentation of orofacial clefts in patients, and several of the key signaling pathways and underlying cellular mechanisms that control lip and palate formation, as identified primarily through investigating equivalent processes in animal models, are examined.
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Affiliation(s)
- Kurt Reynolds
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children-Northern California; University of California Davis, School of Medicine, Sacramento, California, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, California, USA
| | - Shuwen Zhang
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children-Northern California; University of California Davis, School of Medicine, Sacramento, California, USA
| | - Bo Sun
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children-Northern California; University of California Davis, School of Medicine, Sacramento, California, USA
| | - Michael A Garland
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children-Northern California; University of California Davis, School of Medicine, Sacramento, California, USA
| | - Yu Ji
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children-Northern California; University of California Davis, School of Medicine, Sacramento, California, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, California, USA
| | - Chengji J Zhou
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children-Northern California; University of California Davis, School of Medicine, Sacramento, California, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, California, USA
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30
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Nakatomi M, Ludwig KU, Knapp M, Kist R, Lisgo S, Ohshima H, Mangold E, Peters H. Msx1 deficiency interacts with hypoxia and induces a morphogenetic regulation during mouse lip development. Development 2020; 147:dev189175. [PMID: 32467233 DOI: 10.1242/dev.189175] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/16/2020] [Indexed: 12/19/2022]
Abstract
Nonsyndromic clefts of the lip and palate are common birth defects resulting from gene-gene and gene-environment interactions. Mutations in human MSX1 have been linked to orofacial clefting and we show here that Msx1 deficiency causes a growth defect of the medial nasal process (Mnp) in mouse embryos. Although this defect alone does not disrupt lip formation, Msx1-deficient embryos develop a cleft lip when the mother is transiently exposed to reduced oxygen levels or to phenytoin, a drug known to cause embryonic hypoxia. In the absence of interacting environmental factors, the Mnp growth defect caused by Msx1 deficiency is modified by a Pax9-dependent 'morphogenetic regulation', which modulates Mnp shape, rescues lip formation and involves a localized abrogation of Bmp4-mediated repression of Pax9 Analyses of GWAS data revealed a genome-wide significant association of a Gene Ontology morphogenesis term (including assigned roles for MSX1, MSX2, PAX9, BMP4 and GREM1) specifically for nonsyndromic cleft lip with cleft palate. Our data indicate that MSX1 mutations could increase the risk for cleft lip formation by interacting with an impaired morphogenetic regulation that adjusts Mnp shape, or through interactions that inhibit Mnp growth.
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Affiliation(s)
- Mitsushiro Nakatomi
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne NE1 3BZ, UK
- Division of Anatomy, Department of Health Promotion, Kyushu Dental University, Kitakyushu 803-8580, Japan
| | - Kerstin U Ludwig
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, 53127 Bonn, Germany
| | - Ralf Kist
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne NE1 3BZ, UK
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4BW, UK
| | - Steven Lisgo
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne NE1 3BZ, UK
| | - Hayato Ohshima
- Division of Anatomy and Cell Biology of the Hard Tissue, Department of Tissue Regeneration and Reconstruction, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8514, Japan
| | - Elisabeth Mangold
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
| | - Heiko Peters
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne NE1 3BZ, UK
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31
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Saleem K, Zaib T, Sun W, Fu S. Assessment of candidate genes and genetic heterogeneity in human non syndromic orofacial clefts specifically non syndromic cleft lip with or without palate. Heliyon 2019; 5:e03019. [PMID: 31886431 PMCID: PMC6921104 DOI: 10.1016/j.heliyon.2019.e03019] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/25/2019] [Accepted: 12/06/2019] [Indexed: 12/26/2022] Open
Abstract
Non syndromic orofacial clefts specifically non-syndromic cleft lip/palate are one of the most common craniofacial malformation among birth defects in human having multifactorial etiology with an incidence of 1:700/1000. On the basis of association with other congenital malformations or their presence as isolated anomaly, OFC can be classified as syndromic (30%) and nonsyndromic (70%) respectively. The major cause of disease demonstrates complex interplay between genetic and environmental factors. The pathogenic mechanism of underlying factors have been provided by different genetic studies on large-scale with significant recent advances in genotyping technologies usually based on linkage or genome wide association studies (GWAS). On the basis of recent studies, new tools to identify causative genes involved in NSCL/P reported approximately more than 30 genetic risk loci that are responsible for pathogenesis of facial deformation. Despite these findings, it is still uncertain that how much of variance in NSCL/P predisposing factors can be explain by identified risk loci, as they all together accounts for only 20%-25% of NSCL/P heritability. So there is need of further findings about the problem of rare low frequency coding variants and other missing responsive factors or genetic modifiers. This review will described those potential genes and loci reported in different studies whose involvement in pathogenesis of nonsyndromic OFC has wide scientific evidence.
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Affiliation(s)
- Komal Saleem
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China.,Key Laboratory of Preservation of Human Genetics Resources and Disease Control in China (Harbin Medical University), Ministry of Education, China
| | - Tahir Zaib
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China.,Key Laboratory of Preservation of Human Genetics Resources and Disease Control in China (Harbin Medical University), Ministry of Education, China
| | - Wenjing Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China.,Key Laboratory of Preservation of Human Genetics Resources and Disease Control in China (Harbin Medical University), Ministry of Education, China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China.,Key Laboratory of Preservation of Human Genetics Resources and Disease Control in China (Harbin Medical University), Ministry of Education, China
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32
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van Rooij IALM, Ludwig KU, Welzenbach J, Ishorst N, Thonissen M, Galesloot TE, Ongkosuwito E, Bergé SJ, Aldhorae K, Rojas-Martinez A, Kiemeney LALM, Vermeesch JR, Brunner H, Roeleveld N, Devriendt K, Dormaar T, Hens G, Knapp M, Carels C, Mangold E. Non-Syndromic Cleft Lip with or without Cleft Palate: Genome-Wide Association Study in Europeans Identifies a Suggestive Risk Locus at 16p12.1 and Supports SH3PXD2A as a Clefting Susceptibility Gene. Genes (Basel) 2019; 10:genes10121023. [PMID: 31817908 PMCID: PMC6947597 DOI: 10.3390/genes10121023] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 01/16/2023] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (nsCL/P) ranks among the most common human congenital malformations, and has a multifactorial background in which both exogenous and genetic risk factors act in concert. The present report describes a genome-wide association study (GWAS) involving a total of 285 nsCL/P patients and 1212 controls from the Netherlands and Belgium. Twenty of the 40 previously reported nsC/LP susceptibility loci were replicated, which underlined the validity of this sample. SNV-based analysis of the data identified an as yet unreported suggestive locus at chromosome 16p12.1 (p-value of the lead SNV: 4.17 × 10-7). This association was replicated in two of three patient/control replication series (Central European and Yemeni). Gene analysis of the GWAS data prioritized SH3PXD2A at chromosome 10q24.33 as a candidate gene for nsCL/P. To date, support for this gene as a cleft gene has been restricted to data from zebrafish and a knockout mouse model. The present GWAS was the first to implicate SH3PXD2A in non-syndromic cleft formation in humans. In summary, although performed in a relatively small sample, the present GWAS generated novel insights into nsCL/P etiology.
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Affiliation(s)
- Iris ALM van Rooij
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center, 6500 HB Nijmegen, The Netherlands; (I.A.v.R.); (T.E.G.); (L.A.K.); (N.R.)
| | - Kerstin U Ludwig
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (K.U.L.); (J.W.); (N.I.)
| | - Julia Welzenbach
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (K.U.L.); (J.W.); (N.I.)
| | - Nina Ishorst
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (K.U.L.); (J.W.); (N.I.)
| | - Michelle Thonissen
- Department of Dentistry, Radboud Institute for Health Sciences, Section of Orthodontics and Craniofacial Biology, Radboud university medical center, 6500 HB Nijmegen, The Netherlands; (M.T.); (E.O.)
| | - Tessel E Galesloot
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center, 6500 HB Nijmegen, The Netherlands; (I.A.v.R.); (T.E.G.); (L.A.K.); (N.R.)
| | - Edwin Ongkosuwito
- Department of Dentistry, Radboud Institute for Health Sciences, Section of Orthodontics and Craniofacial Biology, Radboud university medical center, 6500 HB Nijmegen, The Netherlands; (M.T.); (E.O.)
| | - Stefaan J Bergé
- Department of Oral and Maxillofacial Surgery, Radboud university medical center, 6500 HB Nijmegen, The Netherlands;
| | - Khalid Aldhorae
- Orthodontic Department, College of Dentistry, Thamar University, Thamar, Yemen;
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, School of Medicine, and Universidad Autonoma de Nuevo Leon, Centro de Investigación y Desarrollo en Ciencias de la Salud, Monterrey 64460, Mexico;
| | - Lambertus ALM Kiemeney
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center, 6500 HB Nijmegen, The Netherlands; (I.A.v.R.); (T.E.G.); (L.A.K.); (N.R.)
- Department of Urology, Radboud Institute for Health Sciences, Radboud university medical center, 6500 HB Nijmegen, The Netherlands
| | | | - Han Brunner
- Department of Human Genetics, and Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6500 HB Nijmgen, The Netherlands;
- Department of Clinical Genetics, and GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, 6202 AZ Maastricht, The Netherlands
| | - Nel Roeleveld
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center, 6500 HB Nijmegen, The Netherlands; (I.A.v.R.); (T.E.G.); (L.A.K.); (N.R.)
| | - Koen Devriendt
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium;
| | - Titiaan Dormaar
- Department of Imaging and Pathology, KU Leuven, 3000 Leuven, Belgium;
- Oral and Maxillofacial Surgery, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Greet Hens
- Department of Neurosciences, Experimental Otorhinolaryngology, KU Leuven, 3000 Leuven, Belgium;
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, 53127 Bonn, Germany;
| | - Carine Carels
- Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium (C.C.)
- Department of Human Genetics, and Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6500 HB Nijmgen, The Netherlands;
- Orthodontics, University Hospitals KU Leuven, 3000 Leuven, Belgium
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (K.U.L.); (J.W.); (N.I.)
- Correspondence: ; Tel.: +49-228-28751008
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Demeer B, Revencu N, Helaers R, Gbaguidi C, Dakpe S, François G, Devauchelle B, Bayet B, Vikkula M. Likely Pathogenic Variants in One Third of Non-Syndromic Discontinuous Cleft Lip and Palate Patients. Genes (Basel) 2019; 10:genes10100833. [PMID: 31652620 PMCID: PMC6826364 DOI: 10.3390/genes10100833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/14/2019] [Accepted: 10/19/2019] [Indexed: 12/19/2022] Open
Abstract
Oral clefts are composed of cleft of the lip, cleft of the lip and palate, or cleft of the palate, and they are associated with a wide range of expression and severity. When cleft of the palate is associated with cleft of the lip with preservation of the primary palate, it defines an atypical phenotype called discontinuous cleft. Although this phenotype may represent 5% of clefts of the lip and/or palate (CLP), it is rarely specifically referred to and its pathophysiology is unknown. We conducted whole exome sequencing (WES) and apply a candidate gene approach to non-syndromic discontinuous CLP individuals in order to identify genes and deleterious variants that could underlie this phenotype. We discovered loss-of-function variants in two out of the seven individuals, implicating FGFR1 and DLG1 genes, which represents almost one third of this cohort. Whole exome sequencing of clinically well-defined subgroups of CLP, such as discontinuous cleft, is a relevant approach to study CLP etiopathogenesis. It could facilitate more accurate clinical, epidemiological and fundamental research, ultimately resulting in better diagnosis and care of CLP patients. Non-syndromic discontinuous cleft lip and palate seems to have a strong genetic basis.
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Affiliation(s)
- Bénédicte Demeer
- Human Molecular Genetics, de Duve Institute, University of Louvain, 1200 Brussels, Belgium.
- Center for Human Genetics, CLAD Nord de France, CHU Amiens-Picardie, 80054 Amiens, France.
- Université Picardie Jules Verne, EA CHIMERE, EA 7516, 80054 Amiens, France.
- Facing Faces Institute, 80054 Amiens, France.
| | - Nicole Revencu
- Human Molecular Genetics, de Duve Institute, University of Louvain, 1200 Brussels, Belgium.
- Center for Human Genetics, Cliniques universitaires Saint-Luc, University of Louvain, 1200 Brussels, Belgium.
| | - Raphael Helaers
- Human Molecular Genetics, de Duve Institute, University of Louvain, 1200 Brussels, Belgium.
| | - Cica Gbaguidi
- Department of Maxillofacial Surgery and Stomatology, Centre de Compétence Fentes et Malformations Faciales (MAFACE), CHU Amiens-Picardie, 80054 Amiens, France.
| | - Stéphanie Dakpe
- Université Picardie Jules Verne, EA CHIMERE, EA 7516, 80054 Amiens, France.
- Facing Faces Institute, 80054 Amiens, France.
- Department of Maxillofacial Surgery and Stomatology, Centre de Compétence Fentes et Malformations Faciales (MAFACE), CHU Amiens-Picardie, 80054 Amiens, France.
| | - Geneviève François
- Department of Pediatrics, Cliniques Universitaires Saint-Luc, University of Louvain, 1200 Brussels, Belgium.
| | - Bernard Devauchelle
- Université Picardie Jules Verne, EA CHIMERE, EA 7516, 80054 Amiens, France.
- Facing Faces Institute, 80054 Amiens, France.
- Department of Maxillofacial Surgery and Stomatology, Centre de Compétence Fentes et Malformations Faciales (MAFACE), CHU Amiens-Picardie, 80054 Amiens, France.
| | - Bénédicte Bayet
- Centre Labiopalatin, Division of Plastic Surgery, Cliniques Universitaires Saint-Luc, University of Louvain, 1200 Brussels, Belgium.
| | - Miikka Vikkula
- Human Molecular Genetics, de Duve Institute, University of Louvain, 1200 Brussels, Belgium.
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Wilderman A, VanOudenhove J, Kron J, Noonan JP, Cotney J. High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development. Cell Rep 2019; 23:1581-1597. [PMID: 29719267 PMCID: PMC5965702 DOI: 10.1016/j.celrep.2018.03.129] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/05/2017] [Accepted: 03/28/2018] [Indexed: 11/29/2022] Open
Abstract
Defects in patterning during human embryonic development frequently result in craniofacial abnormalities. The gene regulatory programs that build the craniofacial complex are likely controlled by information located between genes and within intronic sequences. However, systematic identification of regulatory sequences important for forming the human face has not been performed. Here, we describe comprehensive epigenomic annotations from human embryonic craniofacial tissues and systematic comparisons with multiple tissues and cell types. We identified thousands of tissue-specific craniofacial regulatory sequences and likely causal regions for rare craniofacial abnormalities. We demonstrate significant enrichment of common variants associated with orofacial clefting in enhancers active early in embryonic development, while those associated with normal facial variation are enriched near the end of the embryonic period. These data are provided in easily accessible formats for both craniofacial researchers and clinicians to aid future experimental design and interpretation of noncoding variation in those affected by craniofacial abnormalities.
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Affiliation(s)
- Andrea Wilderman
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington, CT 06030, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
| | | | - Jeffrey Kron
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
| | - James P Noonan
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Kavli Institute for Neuroscience, Yale University, New Haven, CT 06520, USA
| | - Justin Cotney
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
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Carlson JC, Anand D, Butali A, Buxo CJ, Christensen K, Deleyiannis F, Hecht JT, Moreno LM, Orioli IM, Padilla C, Shaffer JR, Vieira AR, Wehby GL, Weinberg SM, Murray JC, Beaty TH, Saadi I, Lachke SA, Marazita ML, Feingold E, Leslie EJ. A systematic genetic analysis and visualization of phenotypic heterogeneity among orofacial cleft GWAS signals. Genet Epidemiol 2019; 43:704-716. [PMID: 31172578 PMCID: PMC6687557 DOI: 10.1002/gepi.22214] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 03/29/2019] [Accepted: 04/17/2019] [Indexed: 12/17/2022]
Abstract
Phenotypic heterogeneity is a hallmark of complex traits, and genetic studies of such traits may focus on them as a single diagnostic entity or by analyzing specific components. For example, in orofacial clefting (OFC), three subtypes-cleft lip (CL), cleft lip and palate (CLP), and cleft palate (CP) have been studied separately and in combination. To further dissect the genetic architecture of OFCs and how a given associated locus may be contributing to distinct subtypes of a trait we developed a framework for quantifying and interpreting evidence of subtype-specific or shared genetic effects in complex traits. We applied this technique to create a "cleft map" of the association of 30 genetic loci with three OFC subtypes. In addition to new associations, we found loci with subtype-specific effects (e.g., GRHL3 [CP], WNT5A [CLP]), as well as loci associated with two or all three subtypes. We cross-referenced these results with mouse craniofacial gene expression datasets, which identified additional promising candidate genes. However, we found no strong correlation between OFC subtypes and expression patterns. In aggregate, the cleft map revealed that neither subtype-specific nor shared genetic effects operate in isolation in OFC architecture. Our approach can be easily applied to any complex trait with distinct phenotypic subgroups.
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Affiliation(s)
- Jenna C. Carlson
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, IA 52242, USA
| | - Carmen J. Buxo
- Dental and Craniofacial Genomics Core, School of Dental Medicine, University of Puerto Rico, San Juan, Puerto Rico, 00936, USA
| | - Kaare Christensen
- Department of Epidemiology, Institute of Public Health, University of Southern Denmark, Odense, DK-5230, Denmark
| | | | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical School and School of Dentistry UT Health at Houston, Houston, TX, 77030, USA
| | - Lina M. Moreno
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Ieda M. Orioli
- INAGEMP (National Institute of Population Medical Genetics), Porto Alegre, 91501-970, Brazil
- ECLAMC (Latin American Collaborative Study of Congenital Malformations) at Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Carmencita Padilla
- Department of Pediatrics, College of Medicine; Institute of Human Genetics, National Institutes of Health; University of the Philippines Manila, Manila, 1000, The Philippines
- Philippine Genome Center, University of the Philippines System, Quezon City, 1101, The Philippines
| | - John R. Shaffer
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh PA,15219, USA
| | - Alexandre R. Vieira
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh PA,15219, USA
| | - George L. Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA, 52242, USA
| | - Seth M. Weinberg
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh PA,15219, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, and Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa,52242, USA
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore MD, 21205, USA
| | - Irfan Saadi
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160 USA
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716 USA
| | - Mary L. Marazita
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh PA,15219, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, and Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Eleanor Feingold
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, and Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Elizabeth J. Leslie
- Department of Human Genetics, Emory University School of Medicine, Emory University, Atlanta, GA, 30322, USA
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Gaczkowska A, Biedziak B, Budner M, Zadurska M, Lasota A, Hozyasz KK, Dąbrowska J, Wójcicki P, Szponar-Żurowska A, Żukowski K, Jagodziński PP, Mostowska A. PAX7 nucleotide variants and the risk of non-syndromic orofacial clefts in the Polish population. Oral Dis 2019; 25:1608-1618. [PMID: 31173442 DOI: 10.1111/odi.13139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/16/2019] [Accepted: 06/03/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The etiology of non-syndromic cleft lip with or without cleft palate (nsCL/P) is multifactorial, heterogeneous, and still not completely understood. The aim of the present study was to examine the associations between common and rare PAX7 nucleotide variants and the risk of this common congenital anomaly in a Polish population. SUBJECTS AND METHODS Eight top nsCL/P-associated PAX7 variants identified in our cleft genome-wide association study (GWAS) were selected for replication analysis in an independent group of patients and controls (n = 247 and n = 445, respectively). In addition, mutation screening of the PAX7 protein-coding region was conducted. RESULTS Analysis of the pooled data from the GWAS and replication study confirmed that common PAX7 nucleotide variants are significantly associated with the increased risk of nsCL/P. The strongest individual variant was rs1339062 (c.586 + 15617T > C) with a p-value = 2.47E-05 (OR = 1.4, 95%CI: 1.20-1.64). Sequencing analysis identified a novel synonymous PAX7 substitution (c.87G > A, p.Val29Val) in a single patient with nsCLP. This transition located in the early exonic position was predicted to disrupt potential splice enhancer elements. CONCLUSION Our study confirmed that PAX7 is a strong candidate gene for nsCL/P. Nucleotide variants of this gene contribute to the etiology of nsCL/P in the homogenous Polish population.
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Affiliation(s)
- Agnieszka Gaczkowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Poznan, Poland
| | - Barbara Biedziak
- Clinic of Craniofacial Anomalies, Poznan University of Medical Sciences, Poznan, Poland
| | - Margareta Budner
- Eastern Poland Burn Treatment and Reconstructive Center, Leczna, Poland
| | | | - Agnieszka Lasota
- Department of Jaw Orthopedics, Medical University of Lublin, Lublin, Poland
| | - Kamil K Hozyasz
- Institute of Health Sciences, State School of Higher Education, Biala Podlaska, Poland
| | - Justyna Dąbrowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Poznan, Poland
| | - Piotr Wójcicki
- Plastic Surgery Clinic, Medical University in Wroclaw, Wroclaw, Poland
| | - Anna Szponar-Żurowska
- Clinic of Craniofacial Anomalies, Poznan University of Medical Sciences, Poznan, Poland
| | - Kacper Żukowski
- Department of Cattle Breeding, National Research Institute of Animal Production, Balice, Poland
| | - Paweł P Jagodziński
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Poznan, Poland
| | - Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Poznan, Poland
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37
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Mohamad Shah NS, Sulong S, Wan Sulaiman WA, Halim AS. Two novel genes TOX3 and COL21A1 in large extended Malay families with nonsyndromic cleft lip and/or palate. Mol Genet Genomic Med 2019; 7:e635. [PMID: 30924295 PMCID: PMC6503016 DOI: 10.1002/mgg3.635] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 01/09/2019] [Accepted: 02/11/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Nonsyndromic cleft lip and/or palate is one of the most common human birth defects worldwide that affects the lip and/or palate. The incidence of clefts varies among populations through ethnic, race, or geographical differences. The focus on Malay nonsyndromic cleft lip and/or palate (NSCL/P) is because of a scarce report on genetic study in relation to this deformity in Malaysia. We are interested to discuss about the genes that are susceptible to cause orofacial cleft formation in the family. METHODS Genome-wide linkage analysis was carried out on eight large extended families of NSCL/P with the total of 91 individuals among Malay population using microarray platform. Based on linkage analyses findings, copy number variation (CNV) of LPHN2, SATB2, PVRL3, COL21A1, and TOX3 were identified in four large extended families that showed linkage evidence using quantitative polymerase chain reaction (qPCR) as for a validation purpose. Copy number calculated (CNC) for each genes were determined with Applied Biosystems CopyCallerTM Software v2.0. Normal CNC of the target sequence expected was set at two. RESULTS Genome-wide linkage analysis had discovered several genes including TOX3 and COL21A1 in four different loci 4p15.2-p16.1, 6p11.2-p12.3, 14q13-q21, and 16q12.1. There was significant decreased, p < 0.05 of SATB2, COL21A1, and TOX3 copy number in extended families compared to the normal controls. CONCLUSION Novel linkage evidence and significant low copy number of COL21A1 and TOX3 in NSCLP family was confirmed. These genes increased the risks toward NSCLP formation in that family traits.
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Affiliation(s)
- Nurul Syazana Mohamad Shah
- Reconstructive Science Unit, School of Medical SciencesUniversiti Sains MalaysiaKubang KerianKelantanMalaysia
| | - Sarina Sulong
- Human Genome Centre, School of Medical SciencesUniversiti Sains MalaysiaKubang KerianKelantanMalaysia
| | - Wan Azman Wan Sulaiman
- Reconstructive Science Unit, School of Medical SciencesUniversiti Sains MalaysiaKubang KerianKelantanMalaysia
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38
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Butali A, Mossey PA, Adeyemo WL, Eshete MA, Gowans LJJ, Busch TD, Jain D, Yu W, Huan L, Laurie CA, Laurie CC, Nelson S, Li M, Sanchez-Lara PA, Magee WP, Magee KS, Auslander A, Brindopke F, Kay DM, Caggana M, Romitti PA, Mills JL, Audu R, Onwuamah C, Oseni GO, Owais A, James O, Olaitan PB, Aregbesola BS, Braimah RO, Oginni FO, Oladele AO, Bello SA, Rhodes J, Shiang R, Donkor P, Obiri-Yeboah S, Arthur FKN, Twumasi P, Agbenorku P, Plange-Rhule G, Oti AA, Ogunlewe OM, Oladega AA, Adekunle AA, Erinoso AO, Adamson OO, Elufowoju AA, Ayelomi OI, Hailu T, Hailu A, Demissie Y, Derebew M, Eliason S, Romero-Bustillous M, Lo C, Park J, Desai S, Mohammed M, Abate F, Abdur-Rahman LO, Anand D, Saadi I, Oladugba AV, Lachke SA, Amendt BA, Rotimi CN, Marazita ML, Cornell RA, Murray JC, Adeyemo AA. Genomic analyses in African populations identify novel risk loci for cleft palate. Hum Mol Genet 2019; 28:1038-1051. [PMID: 30452639 PMCID: PMC6400042 DOI: 10.1093/hmg/ddy402] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 11/07/2018] [Accepted: 11/11/2018] [Indexed: 12/13/2022] Open
Abstract
Orofacial clefts are common developmental disorders that pose significant clinical, economical and psychological problems. We conducted genome-wide association analyses for cleft palate only (CPO) and cleft lip with or without palate (CL/P) with ~17 million markers in sub-Saharan Africans. After replication and combined analyses, we identified novel loci for CPO at or near genome-wide significance on chromosomes 2 (near CTNNA2) and 19 (near SULT2A1). In situ hybridization of Sult2a1 in mice showed expression of SULT2A1 in mesenchymal cells in palate, palatal rugae and palatal epithelium in the fused palate. The previously reported 8q24 was the most significant locus for CL/P in our study, and we replicated several previously reported loci including PAX7 and VAX1.
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Affiliation(s)
- Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA,To whom correspondence should be addressed at: Azeez Butali, Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA 52242, USA. Tel:+319 3358980; Fax: 319-384-1169; ; or Adebowale A. Adeyemo, Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA. Tel: (301) 594-7501; Fax: (301) 451-5426;
| | - Peter A Mossey
- Department of Orthodontics, University of Dundee, Dundee, UK
| | - Wasiu L Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Mekonen A Eshete
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Lord J J Gowans
- Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | - Tamara D Busch
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - Deepti Jain
- Department of Biostatistics, Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Wenjie Yu
- Department of Anatomy and Cell Biology, University of Iowa, Iowa, IA, USA
| | - Liu Huan
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST, Ministry of Science and Technology) and Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Cecelia A Laurie
- Department of Biostatistics, Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Cathy C Laurie
- Department of Biostatistics, Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Sarah Nelson
- Department of Biostatistics, Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Mary Li
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - Pedro A Sanchez-Lara
- Department of Pediatrics, Cedars-Sinai Medical Center, David Geffen School of Medicine at University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - William P Magee
- Division of Plastic and Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Kathleen S Magee
- Operation Smile, 3641 Faculty Boulevard, Virginia Beach, VA, USA
| | - Allyn Auslander
- Division of Plastic and Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Frederick Brindopke
- Division of Plastic and Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Denise M Kay
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Michele Caggana
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Paul A Romitti
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa, IA, USA
| | - James L Mills
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Rosemary Audu
- Department of Virology, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Chika Onwuamah
- Department of Virology, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Ganiyu O Oseni
- Department of Plastic Surgery, Ladoke Akintola University of Science and Technology, Osogbo, Oyo, Nigeria
| | - Arwa Owais
- Department of Pediatric Dentistry, University of Iowa, Iowa, IA, USA
| | - Olutayo James
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Peter B Olaitan
- Department of Plastic Surgery, Ladoke Akintola University of Science and Technology, Osogbo, Oyo, Nigeria
| | - Babatunde S Aregbesola
- Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile-Ife, Osun, Nigeria
| | - Ramat O Braimah
- Department of Oral and Maxillofacial Surgery, Usmanu Danfodiyo University Teaching Hospital, Sokoto, Nigeria
| | - Fadekemi O Oginni
- Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile-Ife, Osun, Nigeria
| | - Ayodeji O Oladele
- Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile-Ife, Osun, Nigeria
| | | | - Jennifer Rhodes
- Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Rita Shiang
- Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Peter Donkor
- Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | | | | | - Peter Twumasi
- Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | - Pius Agbenorku
- Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | | | | | - Olugbenga M Ogunlewe
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Afisu A Oladega
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Adegbayi A Adekunle
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Akinwunmi O Erinoso
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Olatunbosun O Adamson
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Abosede A Elufowoju
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Oluwanifemi I Ayelomi
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Taiye Hailu
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abiye Hailu
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Yohannes Demissie
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Miliard Derebew
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Steve Eliason
- Department of Anatomy and Cell Biology, University of Iowa, Iowa, IA, USA
| | | | - Cynthia Lo
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - James Park
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - Shaan Desai
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - Muiawa Mohammed
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - Firke Abate
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Lukman O Abdur-Rahman
- Division of Pediatric Surgery, Department of Surgery, University of Ilorin, Ilorin, Kwara, Nigeria
| | - Deepti Anand
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Irfaan Saadi
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas, KS, USA
| | | | - Salil A Lachke
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Brad A Amendt
- Department of Anatomy and Cell Biology, University of Iowa, Iowa, IA, USA
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine; Department of Human Genetics, Graduate School of Public Health, and Clinical and Translational Sciences, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert A Cornell
- Department of Anatomy and Cell Biology, University of Iowa, Iowa, IA, USA
| | | | - Adebowale A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD, USA,To whom correspondence should be addressed at: Azeez Butali, Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA 52242, USA. Tel:+319 3358980; Fax: 319-384-1169; ; or Adebowale A. Adeyemo, Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA. Tel: (301) 594-7501; Fax: (301) 451-5426;
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Viena CS, Machado RA, Persuhn DC, Martelli-Júnior H, Medrado AP, Coletta RD, Reis SRA. Understanding the participation of GREM1 polymorphisms in nonsyndromic cleft lip with or without cleft palate in the Brazilian population. Birth Defects Res 2018; 111:16-25. [PMID: 30402937 DOI: 10.1002/bdr2.1405] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/15/2018] [Accepted: 09/04/2018] [Indexed: 01/06/2023]
Abstract
BACKGROUND GREM1, which encodes Gremlin 1, an antagonist of bone morphogenic proteins with effects on proliferation and apoptosis, has been considered a candidate gene for nonsyndromic cleft lip with or without cleft palate (NSCL±P). In this study, we investigated potential associations of single nucleotide polymorphisms (SNP) in GREM1 and NSCL±P risk in the Brazilian population. Additionally, SNP-SNP interactions of GREM1 with previously reported rs1880646 variant in NTN1 (netrin 1), a gene also responsible for apoptotic phenotypes were verified. METHODS Applying Taqman allelic discrimination assays, we evaluated the variants rs16969681, rs16969816, rs16969862, and rs1258763 in 325 case-parent trios and in 1,588 isolated samples in a case-control study. Allelic and genotypic analyses, as well as interaction tests assessing gene-environmental factor (GxE) and SNP-SNP interaction with rs1880646 variant in NTN1, were performed based on logistic regression analysis adjusted for the effects of gender and genomic ancestry proportions. RESULTS The risk alleles of all SNP were undertransmitted in NSCL±P trios, though the case-control analysis confirmed only the association with rs16969862 alleles (OR: 0.78, 95% CI: 0.63-0.96, p = .02). The GxE interaction analysis revealed a significant interaction between maternal environmental contact with agrotoxics and rs16969816 (OR: 0.25, 95% CI: 0.08-0.74, p = .01), and pairwise interaction test with NTN1 rs1880646 yielded significant p values in the 1,000 permutation test for rs16969681, rs16969816, and rs16969862. CONCLUSION The GREM1 is involved in the etiology of NSCL±P in the Brazilian population and reveal that the interaction between GREM1 and NTN1 may be related with the pathogenesis of this common craniofacial malformation.
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Affiliation(s)
- Camila Sane Viena
- Basic Science Department, Area of Oral Pathology, Bahiana School of Medicine and Public Health, Salvador, Bahia, Brazil
| | - Renato Assis Machado
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Darlene Camati Persuhn
- Molecular Biology Department, Federal University of Paraíba, João Pessoa, Paraíba, Brazil
| | - Hercílio Martelli-Júnior
- Stomatology Clinic, Dental School, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil.,Center for Rehabilitation of Craniofacial Anomalies, Dental School, University of José Rosário Vellano, Minas Gerais, Brazil
| | - Alena Peixoto Medrado
- Basic Science Department, Area of Oral Pathology, Bahiana School of Medicine and Public Health, Salvador, Bahia, Brazil
| | - Ricardo D Coletta
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Silvia R A Reis
- Basic Science Department, Area of Oral Pathology, Bahiana School of Medicine and Public Health, Salvador, Bahia, Brazil
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Alhayyan WA, Pan SC, AlQatami FM. Birth Prevalence of Orofacial Clefts in Kuwait From Hospital-Based Registration. Cleft Palate Craniofac J 2018; 55:1450-1455. [DOI: 10.1177/1055665618766059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Introduction: Cleft lip and palate (CLAP) are the most common craniofacial anomalies and birth defects globally. Despite the fact that a tertiary care registry of clefts has existed in Kuwait since 2008, to date there is no published data regarding the prevalence of orofacial clefts in this population. Objective: To tabulate the pattern of orofacial clefts from tertiary care center registration during 2009 through 2014 and to estimate the prevalence and trend using population-based records. Methodology: Data from all CLAP cases (born in Kuwait) registered in the central cleft center registry of the Al-Amiri hospital, Kuwait City, Kuwait, from January 2009 to December 2014 were obtained. Data regarding the type, severity, gender as well as nationality, parental consanguinity, and associated syndrome were obtained from medical records. Birth prevalence was tabulated against the population statistics for the period obtained from the central department of statistics. Result: A total of 202 CLAP patients were recorded in the study period with a mean birth prevalence of 0.57 per 1000 live births (95% confidence interval [CI] .57 ± .23). The registry recorded 108 (53.2%) males and 94 (47.8%) females. Children born to Kuwaitis represented 53.7% of cases while those born to non-Kuwaitis represented 45.3%. The most common oral cleft was CLAP (47.3%), followed by cleft palate (30.5%), cleft lip (20.2%), and other facial clefts (2%). Other congenital anomalies were recognized in 33% of all cases. There were no statistically significant differences in oral cleft prevalence across gender or nationality. Conclusion: The prevalence of oral cleft in Kuwait appears to be similar to those of other Middle Eastern populations.
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Affiliation(s)
- Wasmiya A. Alhayyan
- Riyadh College of Dentistry and Pharmacy (RCDP), Riyadh, Saudi Arabia
- Ministry of Health (MoH), Kuwait City, Kuwait
| | - Sharat C. Pan
- Riyadh College of Dentistry and Pharmacy (RCDP), Riyadh, Saudi Arabia
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Indencleef K, Roosenboom J, Hoskens H, White JD, Shriver MD, Richmond S, Peeters H, Feingold E, Marazita ML, Shaffer JR, Weinberg SM, Hens G, Claes P. Six NSCL/P Loci Show Associations With Normal-Range Craniofacial Variation. Front Genet 2018; 9:502. [PMID: 30410503 PMCID: PMC6210408 DOI: 10.3389/fgene.2018.00502] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/05/2018] [Indexed: 12/17/2022] Open
Abstract
Objectives: Orofacial clefting is one of the most prevalent craniofacial malformations. Previous research has demonstrated that unaffected relatives of patients with non-syndromic cleft lip with/without cleft palate (NSCL/P) show distinctive facial features, which can be an expression of underlying NSCL/P susceptibility genes. These results support the hypothesis that genes involved in the occurrence of a cleft also play a role in normal craniofacial development. In this study, we investigated the influence of genetic variants associated with NSCL/P on normal-range variation in facial shape. Methods: A literature review of genome wide association studies (GWAS) investigating the genetic etiology of NSCL/P was performed, resulting in a list of 75 single nucleotide polymorphisms (SNPs) located in 38 genetic loci. Genotype data were available for 65 of these selected SNPs in three datasets with a combined sample size of 7,418 participants of European ancestry, whose 3D facial images were also available. The effect of each SNP was tested using a multivariate canonical correlation analysis (CCA) against 63 hierarchically-constructed facial segments in each of the three datasets and meta-analyzed. This allowed for the investigation of associations between SNPs known to be involved in NSCL/P and normal-range facial shape variations in a global-to-local perspective, without preselecting specific facial shape features or characteristics. Results: Six NSCL/P SNPs showed significant associations with variation in normal-range facial morphology. rs6740960 showed significant effects in the chin area (p = 3.71 × 10−28). This SNP lies in a non-coding area. Another SNP, rs227731 near the NOG gene, showed a significant effect in the philtrum area (p = 1.96 × 10−16). Three SNPs showed significant effects on the shape of the nose. rs742071 (p = 8.71 × 10−14), rs34246903 (p = 6.87 × 10−12), and rs10512248 (p = 8.4 × 10−9). Respectively, these SNPs are annotated to PAX7, MSX1, and PTCH1. Finally, rs7590268, an intron variant of THADA, showed an effect in the shape of the supraorbital ridge (p = 3.84 × 10−7). Conclusions: This study provides additional evidence NSCL/P-associated genetic variants influence normal-range craniofacial morphology, with significant effects observed for the chin, the nose, the supraorbital ridges and the philtrum area.
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Affiliation(s)
- Karlijne Indencleef
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.,Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
| | - Jasmien Roosenboom
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Hanne Hoskens
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium.,Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Julie D White
- Department of Anthropology, The Pennsylvania State University, University Park, PA, United States
| | - Mark D Shriver
- Department of Anthropology, The Pennsylvania State University, University Park, PA, United States
| | - Stephen Richmond
- Applied Clinical Research and Public Health, School of Dentistry, Cardiff University, College of Biomedical and Life Sciences, Heath Park, Cardiff, United Kingdom
| | - Hilde Peeters
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Eleanor Feingold
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Mary L Marazita
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - John R Shaffer
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Seth M Weinberg
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Greet Hens
- Department of Otorhinolaryngology, University Hospitals Leuven, Leuven, Belgium
| | - Peter Claes
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.,Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
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42
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Zhou R, Wang M, Li W, Wang S, Zhou Z, Li J, Wu T, Zhu H, Beaty TH. Gene-Gene Interactions among SPRYs for Nonsyndromic Cleft Lip/Palate. J Dent Res 2018; 98:180-185. [PMID: 30273098 DOI: 10.1177/0022034518801537] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect with a complex genetic architecture. Gene-gene interactions have been increasingly regarded as contributing to the etiology of NSCL/P. A recent genome-wide association study revealed that a novel single-nucleotide polymorphism at SPRY1 in 4q28.1 showed a significant association with NSCL/P. In the current study, we explored the role of 3 SPRY genes in the etiology of NSCL/P by detecting gene-gene interactions: SPRY1, SPRY2, and SPRY4-with SPRY3 excluded due to its special location on the X chromosome. We selected markers in 3 SPRY genes to test for gene-gene interactions using 1,908 case-parent trios recruited from an international consortium established for a genome-wide association study of nonsyndromic oral clefts. As the trios came from populations with different ancestries, subgroup analyses were conducted among Europeans and Asians. Cordell's method based on conditional logistic regression models was applied to test for potential gene-gene interactions via the statistical package TRIO in R software. Gene-gene interaction analyses yielded 10 pairs of SNPs in Europeans and 6 pairs in Asians that achieved significance after Bonferroni correction. The significant interactions were confirmed in the 10,000-permutation tests (empirical P = 0.003 for the most significant interaction). The study identified gene-gene interactions among SPRY genes among 1,908 NSCL/P trios, which revealed the importance of potential gene-gene interactions for understanding the genetic architecture of NSCL/P. The evidence of gene-gene interactions in this study also provided clues for future biological studies to further investigate the mechanism of how SPRY genes participate in the development of NSCL/P.
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Affiliation(s)
- R Zhou
- 1 School of Public Health, Peking University, Beijing, China
| | - M Wang
- 1 School of Public Health, Peking University, Beijing, China
| | - W Li
- 1 School of Public Health, Peking University, Beijing, China
| | - S Wang
- 1 School of Public Health, Peking University, Beijing, China
| | - Z Zhou
- 2 School of Stomatology, Peking University, Beijing, China
| | - J Li
- 2 School of Stomatology, Peking University, Beijing, China
| | - T Wu
- 1 School of Public Health, Peking University, Beijing, China.,3 Key Laboratory of Reproductive Health, Ministry of Health, Beijing, China
| | - H Zhu
- 2 School of Stomatology, Peking University, Beijing, China
| | - T H Beaty
- 4 School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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43
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Howe LJ, Lee MK, Sharp GC, Davey Smith G, St Pourcain B, Shaffer JR, Ludwig KU, Mangold E, Marazita ML, Feingold E, Zhurov A, Stergiakouli E, Sandy J, Richmond S, Weinberg SM, Hemani G, Lewis SJ. Investigating the shared genetics of non-syndromic cleft lip/palate and facial morphology. PLoS Genet 2018; 14:e1007501. [PMID: 30067744 PMCID: PMC6089455 DOI: 10.1371/journal.pgen.1007501] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 08/13/2018] [Accepted: 06/19/2018] [Indexed: 01/06/2023] Open
Abstract
There is increasing evidence that genetic risk variants for non-syndromic cleft lip/palate (nsCL/P) are also associated with normal-range variation in facial morphology. However, previous analyses are mostly limited to candidate SNPs and findings have not been consistently replicated. Here, we used polygenic risk scores (PRS) to test for genetic overlap between nsCL/P and seven biologically relevant facial phenotypes. Where evidence was found of genetic overlap, we used bidirectional Mendelian randomization (MR) to test the hypothesis that genetic liability to nsCL/P is causally related to implicated facial phenotypes. Across 5,804 individuals of European ancestry from two studies, we found strong evidence, using PRS, of genetic overlap between nsCL/P and philtrum width; a 1 S.D. increase in nsCL/P PRS was associated with a 0.10 mm decrease in philtrum width (95% C.I. 0.054, 0.146; P = 2x10-5). Follow-up MR analyses supported a causal relationship; genetic variants for nsCL/P homogeneously cause decreased philtrum width. In addition to the primary analysis, we also identified two novel risk loci for philtrum width at 5q22.2 and 7p15.2 in our Genome-wide Association Study (GWAS) of 6,136 individuals. Our results support a liability threshold model of inheritance for nsCL/P, related to abnormalities in development of the philtrum.
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Affiliation(s)
- Laurence J. Howe
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
- Institute of Cardiovascular Science, University College London, London, United Kingdom
- * E-mail: (LJH); (SJL)
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Gemma C. Sharp
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
- Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Beate St Pourcain
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
- Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
| | - John R. Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | | | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alexei Zhurov
- Department of Applied Clinical Research and Public Health, School of Dentistry, University of Cardiff, Cardiff, United Kingdom
| | - Evie Stergiakouli
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
- Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Jonathan Sandy
- Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Stephen Richmond
- Department of Applied Clinical Research and Public Health, School of Dentistry, University of Cardiff, Cardiff, United Kingdom
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Gibran Hemani
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Sarah J. Lewis
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
- Bristol Dental School, University of Bristol, Bristol, United Kingdom
- * E-mail: (LJH); (SJL)
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Khan MFJ, Little J, Mossey PA, Steegers-Theunissen RPM, Bonsi M, Bassi Andreasi R, Rubini M. Association between a common missense variant in LOXL3 gene and the risk of non-syndromic cleft palate. Congenit Anom (Kyoto) 2018; 58:136-140. [PMID: 29802726 DOI: 10.1111/cga.12288] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 05/19/2018] [Accepted: 05/22/2018] [Indexed: 12/14/2022]
Abstract
To investigate possible association between functional common variants in the lysyl oxidase like 3 gene and non-syndromic cleft palate we selected a common missense variant p.Ile615Phe (rs17010021), which was predicted to have a probably damaging effect on the lysyl oxidase like 3 enzyme. We genotyped 258 non-syndromic cleft palate case-parent triads of European origin and tested genetic association using the transmission disequilibrium test and log-linear regression analyses of genotypic relative risks and of parent-of-origin effects. The observed genotype frequency in parents was in Hardy-Weinberg equilibrium. Compared with wild-type Ile/Ile homozygotes, the relative risks for Phe/Phe homozygote infants was 6.87 (P value 3.0 × 10-3 ), while that for Ile/Phe heterozygotes was not significant. Assuming an autosomal recessive model, the relative risks for Phe/Phe genotype resulted 10.54 (P value 2.9 × 10-5 ), with a 3.6% population attributable risk. No parent-of-origin effect was observed. The identification in lysyl oxidase like 3 of a missense variant which under a recessive model associates with 10-fold increased risk of non-syndromic cleft palate supports the hypothesis that the genetic etiology of this congenital anomaly includes relatively uncommon recessive variants with moderate penetrance and located in genes which are also involved in syndromes that include cleft palate as part of the phenotype. Our findings require functional validation and replication in a larger independent genetic association study.
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Affiliation(s)
- Mohammad Faisal J Khan
- Department of Biomedical and Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
| | - Julian Little
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Peter A Mossey
- Craniofacial Development at the World Health Organization-collaborating Centre for Oral and Craniofacial Research, Dental Hospital and School, University of Dundee, Dundee, Scotland
| | - Régine P M Steegers-Theunissen
- Department of Obstetrics and Gynaecology, Department of Pediatrics, Division Neonatology Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Martina Bonsi
- Department of Biomedical and Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
| | - Rita Bassi Andreasi
- Department of Biomedical and Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
| | - Michele Rubini
- Department of Biomedical and Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
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45
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Affiliation(s)
- Seth M. Weinberg
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Anthropology, University of Pittsburgh, Pittsburgh, Pennsylvania, United Staes of America
- * E-mail:
| | - Robert Cornell
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, United States America
| | - Elizabeth J. Leslie
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
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46
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da Silva HPV, Oliveira GHDM, Ururahy MAG, Bezerra JF, de Souza KSC, Bortolin RH, Luchessi AD, Silbiger VN, Lima VMGDM, Leite GCP, Brito MEF, Ribeiro EM, Gil-da-Silva-Lopes VL, de Rezende AA. Application of high-resolution array platform for genome-wide copy number variation analysis in patients with nonsyndromic cleft lip and palate. J Clin Lab Anal 2018; 32:e22428. [PMID: 29512191 DOI: 10.1002/jcla.22428] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/09/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Although more than 14 loci may be involved in the development of nonsyndromic cleft lip and palate (NSCLP), the etiology has not been fully elucidated due to genetic and environmental risk factor interactions. Despite advances in identifying genes associated with the NSCLP development using traditional genetic mapping strategies of candidate genes, genome-wide studies, and epidemiologic and linkage analysis, microarray techniques have become important complementary tools in the search for potential causative oral clefts genes in genetic studies. Microarray hybridization enables scanning of the whole genome and detecting copy number variants (CNVs). Although common benign CNVs are often smaller, with sizes smaller than 20 kb, here we reveal small exonic CNVs based on the importance of the encompassed genes in cleft lip and palate phenotype. METHODS Microarray hybridization analysis was performed in 15 individuals with NSCLP. RESULTS We identified 11 exonic CNVs affecting at least one exon of the candidate genes. Thirteen candidate genes (COL11A1-1p21; IRF6-1q32.3; MSX1-4p16.2; TERT-5p15.33; MIR4457-5p15.33; CLPTM1L-5p15.33; ESR1-6q25.1; GLI3-7p13; FGFR-8p11.23; TBX1-22q11.21; OFD-Xp22; PHF8-Xp11.22; and FLNA-Xq28) overlapped with the CNVs identified. CONCLUSIONS Considering the importance to NSCLP, the microdeletions that encompass MSX1, microduplications over TERT, MIR4457, CLPTM1L, and microduplication of PHF8 have been identified as small CNVs related to sequence variants associated with oral clefts susceptibility. Our findings represent a preliminary study on the clinical significance of small CNVs and their relationship with genes implicated in NSCLP.
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Affiliation(s)
| | | | | | - João Felipe Bezerra
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
| | | | - Raul Hernandes Bortolin
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
| | - André Ducati Luchessi
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Vivian Nogueira Silbiger
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
| | | | | | | | | | | | - Adriana Augusto de Rezende
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
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Ishorst N, Francheschelli P, Böhmer AC, Khan MFJ, Heilmann-Heimbach S, Fricker N, Little J, Steegers-Theunissen RPM, Peterlin B, Nowak S, Martini M, Kruse T, Dunsche A, Kreusch T, Gölz L, Aldhorae K, Halboub E, Reutter H, Mossey P, Nöthen MM, Rubini M, Ludwig KU, Knapp M, Mangold E. Nonsyndromic cleft palate: An association study at GWAS candidate loci in a multiethnic sample. Birth Defects Res 2018; 110:871-882. [PMID: 29498243 DOI: 10.1002/bdr2.1213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/19/2018] [Accepted: 02/07/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Nonsyndromic cleft palate only (nsCPO) is a common and multifactorial form of orofacial clefting. In contrast to successes achieved for the other common form of orofacial clefting, that is, nonsyndromic cleft lip with/without cleft palate (nsCL/P), genome wide association studies (GWAS) of nsCPO have identified only one genome wide significant locus. Aim of the present study was to investigate whether common variants contribute to nsCPO and, if so, to identify novel risk loci. METHODS We genotyped 33 SNPs at 27 candidate loci from 2 previously published nsCPO GWAS in an independent multiethnic sample. It included: (i) a family-based sample of European ancestry (n = 212); and (ii) two case/control samples of Central European (n = 94/339) and Arabian ancestry (n = 38/231), respectively. A separate association analysis was performed for each genotyped dataset, and meta-analyses were performed. RESULTS After association analysis and meta-analyses, none of the 33 SNPs showed genome-wide significance. Two variants showed nominally significant association in the imputed GWAS dataset and exhibited a further decrease in p-value in a European and an overall meta-analysis including imputed GWAS data, respectively (rs395572: PMetaEU = 3.16 × 10-4 ; rs6809420: PMetaAll = 2.80 × 10-4 ). CONCLUSION Our findings suggest that there is a limited contribution of common variants to nsCPO. However, the individual effect sizes might be too small for detection of further associations in the present sample sizes. Rare variants may play a more substantial role in nsCPO than in nsCL/P, for which GWAS of smaller sample sizes have identified genome-wide significant loci. Whole-exome/genome sequencing studies of nsCPO are now warranted.
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Affiliation(s)
- Nina Ishorst
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Paola Francheschelli
- Department of Biomedical and Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
| | - Anne C Böhmer
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Mohammad Faisal J Khan
- Department of Biomedical and Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
| | - Stefanie Heilmann-Heimbach
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Nadine Fricker
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Julian Little
- School of Epidemiology, Public Health and Preventive Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Regine P M Steegers-Theunissen
- Department of Obstetrics and Gynaecology, Department of Pediatrics, Division Neonatology Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Borut Peterlin
- Department of Obstetrics & Gynecology, Clinical Institute of Medical Genetics, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Stefanie Nowak
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Markus Martini
- Department of Oral and Maxillo-Facial-Plastic Surgery, University of Bonn, Bonn, Germany
| | - Teresa Kruse
- Department of Orthodontics, University of Cologne, Cologne, Germany
| | - Anton Dunsche
- Department of Oral and Maxillo-Facial Surgery, Clinics Karlsruhe, Karlsruhe, Germany
| | - Thomas Kreusch
- Department of Oral and Maxillofacial Surgery, Head and Neck Centre, Asklepios Klinik Nord-Heidberg, Hamburg, Germany
| | - Lina Gölz
- Department of Orthodontics, University of Bonn, Bonn, Germany
| | - Khalid Aldhorae
- Orthodontic Department, College of Dentistry, Thamar University, Thamar, Yemen
| | - Esam Halboub
- Department of Maxillofacial Surgery and Diagnostic Sciences, Devision of Oral Medicine and Diagnostic Sciences, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Neonatology, Children's Hospital, University of Bonn, Bonn, Germany
| | - Peter Mossey
- Dental Hospital, University of Dundee, Dundee, United Kingdom
| | - Markus M Nöthen
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Michele Rubini
- Department of Biomedical and Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
| | - Kerstin U Ludwig
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
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48
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Gowans LJJ, Oseni G, Mossey PA, Adeyemo WL, Eshete MA, Busch TD, Donkor P, Obiri-Yeboah S, Plange-Rhule G, Oti AA, Owais A, Olaitan PB, Aregbesola BS, Oginni FO, Bello SA, Audu R, Onwuamah C, Agbenorku P, Ogunlewe MO, Abdur-Rahman LO, Marazita ML, Adeyemo AA, Murray JC, Butali A. Novel GREM1 Variations in Sub-Saharan African Patients With Cleft Lip and/or Cleft Palate. Cleft Palate Craniofac J 2018; 55:736-742. [PMID: 29489415 DOI: 10.1177/1055665618754948] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE Cleft lip and/or cleft palate (CL/P) are congenital anomalies of the face and have multifactorial etiology, with both environmental and genetic risk factors playing crucial roles. Though at least 40 loci have attained genomewide significant association with nonsyndromic CL/P, these loci largely reside in noncoding regions of the human genome, and subsequent resequencing studies of neighboring candidate genes have revealed only a limited number of etiologic coding variants. The present study was conducted to identify etiologic coding variants in GREM1, a locus that has been shown to be largely associated with cleft of both lip and soft palate. PATIENTS AND METHOD We resequenced DNA from 397 sub-Saharan Africans with CL/P and 192 controls using Sanger sequencing. Following analyses of the sequence data, we observed 2 novel coding variants in GREM1. These variants were not found in the 192 African controls and have never been previously reported in any public genetic variant database that includes more than 5000 combined African and African American controls or from the CL/P literature. RESULTS The novel variants include p.Pro164Ser in an individual with soft palate cleft only and p.Gly61Asp in an individual with bilateral cleft lip and palate. The proband with the p.Gly61Asp GREM1 variant is a van der Woude (VWS) case who also has an etiologic variant in IRF6 gene. CONCLUSION Our study demonstrated that there is low number of etiologic coding variants in GREM1, confirming earlier suggestions that variants in regulatory elements may largely account for the association between this locus and CL/P.
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Affiliation(s)
- Lord Jephthah Joojo Gowans
- 1 Cleft Clinic, Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Ganiyu Oseni
- 2 Department of Plastic Surgery, Ladoke Akintola University of Science and Technology, Osogbo, Nigeria
| | - Peter A Mossey
- 3 Department of Orthodontics, University of Dundee, Dundee, United Kingdom
| | - Wasiu Lanre Adeyemo
- 4 Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - Mekonen A Eshete
- 5 Addis Ababa University, School of Public Health, Addis Ababa, Ethiopia
| | - Tamara D Busch
- 6 Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Peter Donkor
- 1 Cleft Clinic, Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Solomon Obiri-Yeboah
- 1 Cleft Clinic, Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Gyikua Plange-Rhule
- 1 Cleft Clinic, Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Alexander A Oti
- 1 Cleft Clinic, Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Arwa Owais
- 7 Department of Pediatric Dentistry, University of Iowa, Iowa City, IA, USA
| | - Peter B Olaitan
- 2 Department of Plastic Surgery, Ladoke Akintola University of Science and Technology, Osogbo, Nigeria
| | - Babatunde S Aregbesola
- 8 Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Fadekemi O Oginni
- 8 Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile-Ife, Nigeria
| | | | - Rosemary Audu
- 10 Department of Virology, Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Chika Onwuamah
- 10 Department of Virology, Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Pius Agbenorku
- 1 Cleft Clinic, Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Mobolanle O Ogunlewe
- 4 Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - Lukman O Abdur-Rahman
- 11 Division of Pediatric Surgery, Department of Surgery, University of Ilorin, Ilorin, Nigeria
| | - Mary L Marazita
- 12 Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA.,13 Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - A A Adeyemo
- 14 National Human Genome Research Institute, Bethesda, MD, USA
| | - Jeffrey C Murray
- 6 Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Azeez Butali
- 15 Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
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49
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Wang X, Song H, Jiao X, Hao Y, Zhang W, Gao Y, Li Y, Mi N, Yan J. Association between a single-nucleotide polymorphism in the GREM1 gene and non-syndromic orofacial cleft in the Chinese population. J Oral Pathol Med 2017; 47:206-210. [PMID: 29149498 DOI: 10.1111/jop.12662] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2017] [Indexed: 01/02/2023]
Abstract
BACKGROUND Non-syndromic orofacial cleft (NSOC) is a common craniofacial deformity among newborns. The GREM1 gene is correlated with orofacial development. The aim of our study was to investigate the association between a single-nucleotide polymorphism in the GREM1 gene and this malformation in the Chinese population. METHODS The SNaPshot mini-sequencing technique was used to genotype the locus rs1258763 of the GREM1 gene in 331 patients with NSOC and 271 individuals in a control group. RESULTS For GREM1 rs1258763, there was a significant difference between the NSOC case group and control group (P = .022). Children carrying GA and GA/AA genotypes had an increased risk of NSOC (OR=1.62, 95%CI: 1.15-2.30; OR=1.52, 95%CI: 1.09-2.12). In the cleft subgroup, we found that the GREM1 rs1258763 GA genotype might contribute to the elevated risk of the cleft lip with or without cleft palate (CL/P) (P = .029). Non-significant differences were found between the cleft palate only (CPO) and control groups (P = .077). CONCLUSION Our findings revealed that the GREM1 polymorphism was significantly associated with the risk of NSOC in the Chinese population.
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Affiliation(s)
- Xiaotong Wang
- Department of Oral Maxillofacial Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Hongquan Song
- Department of Oral Maxillofacial Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Xiaohui Jiao
- Department of Oral Maxillofacial Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yanru Hao
- Department of Stomatology, Plastic surgery hospital, Chinese Academy of Medical Science and Peking Union Medical College, Shijingshan District, Beijing
| | - Wei Zhang
- Department of Oral Maxillofacial Surgery, The Fourth Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yuwei Gao
- Department of Oral Maxillofacial Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yong Li
- Department of Oral Maxillofacial Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Na Mi
- Department of Oral Maxillofacial Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Jiaqun Yan
- Department of Stomatology, Tumor Hospital of Harbin Medical University, Harbin, China
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50
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Böhmer AC, Gölz L, Kreusch T, Kramer FJ, Pötzsch B, Nöthen MM, Jäger A, Mangold E, Knapp M, Ludwig KU. Investigation of dominant and recessive inheritance models in genome-wide association studies data of nonsyndromic cleft lip with or without cleft palate. Birth Defects Res 2017; 110:336-341. [PMID: 29134786 DOI: 10.1002/bdr2.1144] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 11/11/2022]
Abstract
Nonsyndromic cleft lip with or without cleft palate (nsCL/P) is one of the most common congenital malformation worldwide, and its etiology involves both genetic and environmental factors. Recent genome-wide and targeted genetic studies of nsCL/P have identified numerous genetic risk loci, under the hypothesis of a multiplicative mode of inheritance. The present study investigated whether novel nsCL/P risk loci could be identified by analyzing dominant/recessive genetic effects in single nucleotide polymorphism (SNP) data from genome-wide association studies. For this purpose, a genome-wide investigation of dominant/recessive common SNP effects was performed in our previously published meta-analysis data set. Twenty-four loci were identified as candidate regions. In a subsequent association analysis in an independent study cohort of 224 nsCL/P patients and 986 controls of European descent, none of the loci could be replicated. Therefore, our strategy of identifying novel loci by applying different genetic models did not yield any novel findings, suggesting that recessive/dominant common variation only make a limited contribution to nsCL/P in Europeans. However, we cannot rule out that such effects are present at some of the loci that have previously been identified, or are present in different populations.
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Affiliation(s)
- Anne C Böhmer
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Lina Gölz
- Department of Orthodontics, University of Bonn, Bonn, Germany
| | - Thomas Kreusch
- Department of Oral and Maxillofacial Surgery, Head and Neck Centre, Asklepios Klinik Nord, Heidberg, Hamburg, Germany
| | - Franz-Josef Kramer
- Department of Oral and Maxillofacial Surgery, University of Göttingen, Göttingen, Germany
| | - Bernd Pötzsch
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Andreas Jäger
- Department of Orthodontics, University of Bonn, Bonn, Germany
| | - Elisabeth Mangold
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Michael Knapp
- Department of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Kerstin U Ludwig
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
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