Rare variant modifier analysis identifies variants in SEC24D associated with orofacial cleft subtypes

Amidei RL, Hamman RF, Kassebaum DK, Marshall JA (1994) Birth prevalence of cleft lip and palate in Colorado by sex distribution, seasonality, race/ethnicity, and geographic variation. Spec Care Dentist 14:233–240. https://doi.org/10.1111/j.1754-4505.1994.tb01072.x

Article  CAS  PubMed  Google Scholar 

Attanasio C, Nord AS, Zhu Y, Blow MJ, Li Z, Liberton DK, Morrison H, Plajzer-Frick I, Holt A, Hosseini R, Phouanenavong S, Akiyama JA, Shoukry M, Afzal V, Rubin EM, FitzPatrick DR, Ren B, Hallgrimsson B, Pennacchio LA, Visel A (2013) Fine tuning of craniofacial morphology by distant-acting enhancers. Science 342:1241006. https://doi.org/10.1126/science.1241006

Article  CAS  PubMed  PubMed Central  Google Scholar 

Baines AC, Adams EJ, Zhang B, Ginsburg D (2013) Disruption of the Sec24d gene results in early embryonic lethality in the mouse. PLoS ONE 8:e61114. https://doi.org/10.1371/journal.pone.0061114

Article  CAS  PubMed  PubMed Central  Google Scholar 

Beaty TH, Murray JC, Marazita ML, Munger RG, Ruczinski I, Hetmanski JB, Liang KY, Wu T, Murray T, Fallin MD, Redett RA, Raymond G, Schwender H, Jin SC, Cooper ME, Dunnwald M, Mansilla MA, Leslie E, Bullard S, Lidral AC, Moreno LM, Menezes R, Vieira AR, Petrin A, Wilcox AJ, Lie RT, Jabs EW, Wu-Chou YH, Chen PK, Wang H, Ye X, Huang S, Yeow V, Chong SS, Jee SH, Shi B, Christensen K, Melbye M, Doheny KF, Pugh EW, Ling H, Castilla EE, Czeizel AE, Ma L, Field LL, Brody L, Pangilinan F, Mills JL, Molloy AM, Kirke PN, Scott JM, Arcos-Burgos M, Scott AF (2010) A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4. Nat Genet 42:525–529. https://doi.org/10.1038/ng.580

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bell JC, Raynes-Greenow C, Turner RM, Bower C, Nassar N, O’Leary CM (2014) Maternal alcohol consumption during pregnancy and the risk of orofacial clefts in infants: a systematic review and meta-analysis. Paediatr Perinat Epidemiol 28:322–332. https://doi.org/10.1111/ppe.12131

Article  PubMed  Google Scholar 

Birnbaum S, Ludwig KU, Reutter H, Herms S, de Assis NA, Diaz-Lacava A, Barth S, Lauster C, Schmidt G, Scheer M, Saffar M, Martini M, Reich RH, Schiefke F, Hemprich A, Potzsch S, Potzsch B, Wienker TF, Hoffmann P, Knapp M, Kramer FJ, Nothen MM, Mangold E (2009a) IRF6 gene variants in Central European patients with non-syndromic cleft lip with or without cleft palate. Eur J Oral Sci 117:766–769. https://doi.org/10.1111/j.1600-0722.2009.00680.x

Article  PubMed  Google Scholar 

Birnbaum S, Ludwig KU, Reutter H, Herms S, Steffens M, Rubini M, Baluardo C, Ferrian M, Almeida de Assis N, Alblas MA, Barth S, Freudenberg J, Lauster C, Schmidt G, Scheer M, Braumann B, Berge SJ, Reich RH, Schiefke F, Hemprich A, Potzsch S, Steegers-Theunissen RP, Potzsch B, Moebus S, Horsthemke B, Kramer FJ, Wienker TF, Mossey PA, Propping P, Cichon S, Hoffmann P, Knapp M, Nothen MM, Mangold E (2009b) Key susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24. Nat Genet 41:473–477. https://doi.org/10.1038/ng.333

Article  CAS  PubMed  Google Scholar 

Bishop MR, Diaz Perez KK, Sun M, Ho S, Chopra P, Mukhopadhyay N, Hetmanski JB, Taub MA, Moreno-Uribe LM, Valencia-Ramirez LC, Restrepo Muneton CP, Wehby G, Hecht JT, Deleyiannis F, Weinberg SM, Wu-Chou YH, Chen PK, Brand H, Epstein MP, Ruczinski I, Murray JC, Beaty TH, Feingold E, Lipinski RJ, Cutler DJ, Marazita ML, Leslie EJ (2020) Genome-wide enrichment of de novo coding mutations in orofacial cleft trios. Am J Hum Genet 107:124–136. https://doi.org/10.1016/j.ajhg.2020.05.018

Article  CAS  PubMed  PubMed Central  Google Scholar 

Candotto V, Oberti L, Gabrione F, Greco G, Rossi D, Romano M, Mummolo S (2019) Current concepts on cleft lip and palate etiology. J Biol Regul Homeost Agents 33:145–151

CAS  PubMed  Google Scholar 

Carlson JC, Standley J, Petrin A, Shaffer JR, Butali A, Buxo CJ, Castilla E, Christensen K, Deleyiannis FW, Hecht JT, Field LL, Garidkhuu A, Moreno Uribe LM, Nagato N, Orioli IM, Padilla C, Poletta F, Suzuki S, Vieira AR, Wehby GL, Weinberg SM, Beaty TH, Feingold E, Murray JC, Marazita ML, Leslie EJ (2017a) Identification of 16q21 as a modifier of nonsyndromic orofacial cleft phenotypes. Genet Epidemiol 41:887–897. https://doi.org/10.1002/gepi.22090

Article  PubMed  PubMed Central  Google Scholar 

Carlson JC, Taub MA, Feingold E, Beaty TH, Murray JC, Marazita ML, Leslie EJ (2017b) Identifying genetic sources of phenotypic heterogeneity in orofacial clefts by targeted sequencing. Birth Defects Res 109:1030–1038. https://doi.org/10.1002/bdr2.23605

Article  CAS  PubMed  PubMed Central  Google Scholar 

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 (2019) A systematic genetic analysis and visualization of phenotypic heterogeneity among orofacial cleft GWAS signals. Genet Epidemiol 43:704–716. https://doi.org/10.1002/gepi.22214

Article  PubMed  PubMed Central  Google Scholar 

Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ (2015) Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4:7. https://doi.org/10.1186/s13742-015-0047-8

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cheng HM, Chern Y, Chen IH, Liu CR, Li SH, Chun SJ, Rigo F, Bennett CF, Deng N, Feng Y, Lin CS, Yan YT, Cohen SN, Cheng TH (2015) Effects on murine behavior and lifespan of selectively decreasing expression of mutant huntingtin allele by supt4h knockdown. PLoS Genet 11:e15043. https://doi.org/10.1371/journal.pgen.1005043

Article  CAS  Google Scholar 

Ciminello FS, Morin RJ, Nguyen TJ, Wolfe SA (2009) Cleft lip and palate: review. Compr Ther 35:37–43

PubMed  Google Scholar 

Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P, Genomes P (2011) Variation in genome-wide mutation rates within and between human families. Nat Genet 43:712–714. https://doi.org/10.1038/ng.862

Article  CAS  PubMed  PubMed Central  Google Scholar 

Curtis SW, Chang D, Lee MK, Shaffer JR, Indencleef K, Epstein MP, Cutler DJ, Murray JC, Feingold E, Beaty TH, Claes P, Weinberg SM, Marazita ML, Carlson JC, Leslie EJ (2021a) The PAX1 locus at 20p11 is a potential genetic modifier for bilateral cleft lip. HGG Adv. https://doi.org/10.1016/j.xhgg.2021.100025

Article  PubMed  PubMed Central  Google Scholar 

Curtis SW, Chang D, Sun MR, Epstein MP, Murray JC, Feingold E, Beaty TH, Weinberg SM, Marazita ML, Lipinski RJ, Carlson JC, Leslie EJ (2021b) FAT4 identified as a potential modifier of orofacial cleft laterality. Genet Epidemiol 45:721–735. https://doi.org/10.1002/gepi.22420

Article  CAS  PubMed  PubMed Central  Google Scholar 

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, Genomes Project Analysis G (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158. https://doi.org/10.1093/bioinformatics/btr330

Article  CAS  PubMed  PubMed Central  Google Scholar 

D’Arcangelo JG, Stahmer KR, Miller EA (2013) Vesicle-mediated export from the ER: COPII coat function and regulation. Biochim Biophys Acta 1833:2464–2472. https://doi.org/10.1016/j.bbamcr.2013.02.003

Article  CAS  PubMed  PubMed Central  Google Scholar 

DeRoo LA, Wilcox AJ, Lie RT, Romitti PA, Pedersen DA, Munger RG, Moreno Uribe LM, Wehby GL (2016) Maternal alcohol binge-drinking in the first trimester and the risk of orofacial clefts in offspring: a large population-based pooling study. Eur J Epidemiol 31:1021–1034. https://doi.org/10.1007/s10654-016-0171-5

Article  PubMed  PubMed Central  Google Scholar 

Dixon MJ, Marazita ML, Beaty TH, Murray JC (2011) Cleft lip and palate: understanding genetic and environmental influences. Nat Rev Genet 12:167–178. https://doi.org/10.1038/nrg2933

Article  CAS  PubMed  PubMed Central  Google Scholar 

Duan S, Shi J, Shi B, Jia Z (2020) Association analysis of GWAS hits and non-syndromic cleft lip with/without palate with cleft alveolar in Han population of western China. Int J Clin Exp Pathol 13:2576–2585

CAS  PubMed  PubMed Central  Google Scholar 

Edgar R, Domrachev M, Lash AE (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207–210. https://doi.org/10.1093/nar/30.1.207

Article  CAS  PubMed  PubMed Central  Google Scholar 

Garbes L, Kim K, Riess A, Hoyer-Kuhn H, Beleggia F, Bevot A, Kim MJ, Huh YH, Kweon HS, Savarirayan R, Amor D, Kakadia PM, Lindig T, Kagan KO, Becker J, Boyadjiev SA, Wollnik B, Semler O, Bohlander SK, Kim J, Netzer C (2015) Mutations in SEC24D, encoding a component of the COPII machinery, cause a syndromic form of osteogenesis imperfecta. Am J Hum Genet 96:432–439. https://doi.org/10.1016/j.ajhg.2015.01.002

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gogarten SM, Sofer T, Chen H, Yu C, Brody JA, Thornton TA, Rice KM, Conomos MP (2019) Genetic association testing using the GENESIS R/Bioconductor package. Bioinformatics 35:5346–5348. https://doi.org/10.1093/bioinformatics/btz567

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gundlach KK, Maus C (2006) Epidemiological studies on the frequency of clefts in Europe and world-wide. J Craniomaxillofac Surg 34(Suppl 2):1–2. https://doi.org/10.1016/S1010-5182(06)60001-2

Article  PubMed  Google Scholar 

Hameed O, Amin N, Haria P, Patel B, Hay N (2019) Orthodontic burden of care for patients with a cleft lip and/or palate. J Orthod 46:63–67. https://doi.org/10.1177/1465312518823010

Article  PubMed  Google Scholar 

Hao J, Gao R, Wu W, Hua L, Chen Y, Li F, Liu J, Luo D, Han J, Wang H (2018) Association between BMP4 gene polymorphisms and cleft lip with or without cleft palate in a population from South China. Arch Oral Biol 93:95–99. https://doi.org/10.1016/j.archoralbio.2018.05.015

Article 

Comments (0)

No login
gif