X-linked markers in the Duchenne muscular dystrophy gene associated with oral clefts

As part of an international consortium, case–parent trios were collected for a genome‐wide association study of isolated, non‐syndromic oral clefts, including cleft lip (CL), cleft palate (CP), and cleft lip and palate (CLP). Non‐syndromic oral clefts have a complex and heterogeneous etiology. Risk...

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Published in	European journal of oral sciences Vol. 121; no. 2; pp. 63 - 68
Main Authors	Patel, Poorav J., Beaty, Terri H., Ruczinski, Ingo, Murray, Jeffrey C., Marazita, Mary L., Munger, Ronald G., Hetmanski, Jacqueline B., Wu, Tao, Murray, Tanda, Rose, Margaret, Redett, Richard J., Jin, Sheng C., Lie, Rolv T., Wu-Chou, Yah-Huei, Wang, Hong, Ye, Xiaoqian, Yeow, Vincent, Chong, Samuel, Jee, Sun H., Shi, Bing, Scott, Alan F.
Format	Journal Article
Language	English
Published	England Blackwell Publishing Ltd 01.04.2013
Subjects	Adult Asian People - genetics case-parent trios Cleft Lip - genetics Cleft Palate - genetics Duchenne muscular dystrophy (DMD) family-based association Female Genes, X-Linked - physiology Genetic Markers Genome-Wide Association Study - methods Haplotypes - genetics Haplotypes - physiology Humans Male Muscular Dystrophy, Duchenne - genetics oral clefts Polymorphism, Single Nucleotide Principal Component Analysis Risk White People - genetics X-linked
Online Access	Get full text
ISSN	0909-8836 1600-0722 1600-0722
DOI	10.1111/eos.12025

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Abstract	As part of an international consortium, case–parent trios were collected for a genome‐wide association study of isolated, non‐syndromic oral clefts, including cleft lip (CL), cleft palate (CP), and cleft lip and palate (CLP). Non‐syndromic oral clefts have a complex and heterogeneous etiology. Risk is influenced by genes and environmental factors, and differs markedly by gender. Family‐based association tests (FBAT) were used on 14,486 single nucleotide polymorphisms (SNPs) spanning the X chromosome, stratified by type of cleft and racial group. Significant results, even after multiple‐comparisons correction, were obtained for the Duchenne muscular dystrophy (DMD) gene, the largest single gene in the human genome, among CL/P (i.e. both CL and CLP combined) trios. When stratified into groups of European and Asian ancestry, stronger signals were obtained for Asian subjects. Although conventional sliding‐window haplotype analysis showed no increase in significance, selected combinations of the 25 most significant SNPs in the DMD gene identified four SNPs together that attained genome‐wide significance among Asian CL/P trios, raising the possibility of interaction between distant SNPs within the DMD gene.
AbstractList	As part of an international consortium, case–parent trios were collected for a genome‐wide association study of isolated, non‐syndromic oral clefts, including cleft lip (CL), cleft palate (CP), and cleft lip and palate (CLP). Non‐syndromic oral clefts have a complex and heterogeneous etiology. Risk is influenced by genes and environmental factors, and differs markedly by gender. Family‐based association tests (FBAT) were used on 14,486 single nucleotide polymorphisms (SNPs) spanning the X chromosome, stratified by type of cleft and racial group. Significant results, even after multiple‐comparisons correction, were obtained for the Duchenne muscular dystrophy (DMD) gene, the largest single gene in the human genome, among CL/P (i.e. both CL and CLP combined) trios. When stratified into groups of European and Asian ancestry, stronger signals were obtained for Asian subjects. Although conventional sliding‐window haplotype analysis showed no increase in significance, selected combinations of the 25 most significant SNPs in the DMD gene identified four SNPs together that attained genome‐wide significance among Asian CL/P trios, raising the possibility of interaction between distant SNPs within the DMD gene. As part of an international consortium, case-parent trios were collected for a genome-wide association study of isolated, non-syndromic oral clefts, including cleft lip (CL), cleft palate (CP), and cleft lip and palate (CLP). Non-syndromic oral clefts have a complex and heterogeneous etiology. Risk is influenced by genes and environmental factors, and differs markedly by gender. Family-based association tests (FBAT) were used on 14,486 single nucleotide polymorphisms (SNPs) spanning the X chromosome, stratified by type of cleft and racial group. Significant results, even after multiple-comparisons correction, were obtained for the Duchenne muscular dystrophy (DMD) gene, the largest single gene in the human genome, among CL/P (i.e., both CL and CLP combined) trios. When stratified into groups of European and Asian ancestry, stronger signals were obtained for Asian subjects. Although conventional sliding-window haplotype analysis showed no increase in significance, selected combinations of the 25 most significant SNPs in the DMD gene identified four SNPs together that attained genome-wide significance among Asian CL/P trios, raising the possibility of interaction between distant SNPs within the DMD gene.As part of an international consortium, case-parent trios were collected for a genome-wide association study of isolated, non-syndromic oral clefts, including cleft lip (CL), cleft palate (CP), and cleft lip and palate (CLP). Non-syndromic oral clefts have a complex and heterogeneous etiology. Risk is influenced by genes and environmental factors, and differs markedly by gender. Family-based association tests (FBAT) were used on 14,486 single nucleotide polymorphisms (SNPs) spanning the X chromosome, stratified by type of cleft and racial group. Significant results, even after multiple-comparisons correction, were obtained for the Duchenne muscular dystrophy (DMD) gene, the largest single gene in the human genome, among CL/P (i.e., both CL and CLP combined) trios. When stratified into groups of European and Asian ancestry, stronger signals were obtained for Asian subjects. Although conventional sliding-window haplotype analysis showed no increase in significance, selected combinations of the 25 most significant SNPs in the DMD gene identified four SNPs together that attained genome-wide significance among Asian CL/P trios, raising the possibility of interaction between distant SNPs within the DMD gene.
Author	Yeow, Vincent Hetmanski, Jacqueline B. Redett, Richard J. Rose, Margaret Scott, Alan F. Patel, Poorav J. Ruczinski, Ingo Jin, Sheng C. Lie, Rolv T. Chong, Samuel Munger, Ronald G. Jee, Sun H. Wu, Tao Ye, Xiaoqian Murray, Jeffrey C. Beaty, Terri H. Murray, Tanda Wang, Hong Shi, Bing Wu-Chou, Yah-Huei Marazita, Mary L.
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References	Harville EW, Wilcox AJ, Lie RT, Vindenes H, Abyholm F. Cleft lip and palate versus cleft lip only: are they distinct defects? Am J Epidemiol 2005; 162: 182-190. Marçano ACB, Doudney K, Braybrook C, Squires R, Patton MA, Lees MM, Richieri-Costa A, Lidral AC, Murray JC, Moore GE, Stanier P. TBX22 mutations are a frequent cause of cleft palate. J Med Genet 2004; 41: 68-74. Laird NM, Horvath S, Xu X. Implementing a unified approach to family-based tests of association. Genet Epidemiol 2000; 19: S36-S42. Christensen K, Juel K, Herskind AM, Murray JC. Long term follow up study of survival associated with cleft lip and palate at birth. BMJ 2004; 328: 1405-1409. Braybrook C, Doudney K, Marcano ACB, Arnason A, Bjornsson A, Patton MA, Goodfellow PJ, Moore GE, Stanier P. The T-box transcription factor gene TBX22 is mutated in X-linked cleft palate and ankyloglossia. Nat Genet 2001; 29: 179-183. Mossey P, Little J, Munger RG, Dixon MJ, Shaw WC. Cleft lip and palate. Lancet 2009; 374: 1773-1785. Wehby GL, Pedersen DA, Murray JC, Christensen K. The effects of oral clefts on hospital use throughout the lifespan. BMC Health Service Res 2012; 12: 58-74. Suphapeetiporn K, Tongkobpetch S, Siriwan P, Shotelersuk V. TBX22 mutations are a frequent cause of non-syndromic cleft palate in the Thai population. Clin Genet 2007; 78: 478-483. Braybrook C, Lisgo S, Doudney K, Henderson D, Marçano ACB, Strachan T, Patton MA, Villard L, Moore GE, Stanier P, Lindsay S. Craniofacial expression of human and murine TBX22 correlates with the cleft palate and ankyloglossia phenotype observed in CPX patients. Hum Mol Genet 2002; 11: 2793-2804. Jugessur A, Murray JC. Orofacial clefting: recent insights into a complex trait. Curr Opin Genet Dev 2005; 15: 270-278. 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, Menzes 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. A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4. Nat Genet 2010; 42: 525-529. Laird NM, Lange C. Family-based designs in the age of large-scale gene-association studies. Nat Rev Genet 2006; 7: 385-394. Derijcke A, Eerens A, Carels C. The incidence of oral clefts: a review. Brit J Oral Maxillofac Surg 1996; 34: 488-494. Dudbridge F. Likelihood-based association analysis for nuclear families and unrelated subjects with missing genotype data. Hum Hered 2008; 66: 87-98. Goodacre T, Swan MC. Cleft lip and palate: current management. Paediatr Child Health 2008; 18: 283-292. Andreou AM, Pauws E, Jones MC, Singh MK, Bussen M, Doudney K, Moore GE, Kispert A, Brosens JJ, Stanier P. TBX22 Missense mutations found in patients with X-linked cleft palate affect DNA bnding, sumoylation, and transcriptional repression. Am J Hum Genet 2007; 81: 700-712. Jugessur A, Skare O, Lie RT, Wilcox AJ, Christensen K, Christinasen L, Nguyen TT, Murray JC, Gjessing HK. X-linked genes and risk of orofacial clefts: evidence from two population based studies in Scandinavia. PLoS ONE 2012; 7: e392340. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007; 81: 559-575. Dixon MJ, Marazita ML, Beaty TH, Murray JC. Cleft lip and palate: understanding genetic and environmental influences. Nat Rev Genet 2011; 11: 67-178. Vieira AR. Unraveling human cleft lip and palate research. J Dent Res 2008; 87: 119-125. Beaty TH, Ruczinski I, Murray JC, Marazita ML, Munger RG, Hetmanski JB, Murray T, Redett RJ, Fallin D, Liang KY, Wu T, Patel PJ, Jin SC, Zhang TX, Schwender H, Wu-Chou YH, Chen PK, Chong SS, Cheah F, Yeow V, Ye X, Wang H, Huang S, Jabs EW, Shi B, Wilcox AJ, Lie RT, Jee SH, Christensen K, Doheny KF, Pugh EW, Ling H, Scott AF. Evidence for gene-environment interaction in a genome wide study of nonsyndromic cleft palate. Genet Epidemiol 2011; 32: 469-478. 2004; 41 2010; 42 2005; 162 2000; 19 2008; 18 2002; 11 2009; 374 2006; 7 2011; 11 2007; 81 2011; 32 2008; 87 2008; 66 2001; 29 2005; 15 2004; 328 2012; 7 2012; 12 2007; 78 1996; 34
References_xml	– reference: Mossey P, Little J, Munger RG, Dixon MJ, Shaw WC. Cleft lip and palate. Lancet 2009; 374: 1773-1785. – reference: Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007; 81: 559-575. – reference: Laird NM, Lange C. Family-based designs in the age of large-scale gene-association studies. Nat Rev Genet 2006; 7: 385-394. – reference: Goodacre T, Swan MC. Cleft lip and palate: current management. Paediatr Child Health 2008; 18: 283-292. – reference: Braybrook C, Doudney K, Marcano ACB, Arnason A, Bjornsson A, Patton MA, Goodfellow PJ, Moore GE, Stanier P. The T-box transcription factor gene TBX22 is mutated in X-linked cleft palate and ankyloglossia. Nat Genet 2001; 29: 179-183. – reference: Christensen K, Juel K, Herskind AM, Murray JC. Long term follow up study of survival associated with cleft lip and palate at birth. BMJ 2004; 328: 1405-1409. – reference: Andreou AM, Pauws E, Jones MC, Singh MK, Bussen M, Doudney K, Moore GE, Kispert A, Brosens JJ, Stanier P. TBX22 Missense mutations found in patients with X-linked cleft palate affect DNA bnding, sumoylation, and transcriptional repression. Am J Hum Genet 2007; 81: 700-712. – reference: Jugessur A, Skare O, Lie RT, Wilcox AJ, Christensen K, Christinasen L, Nguyen TT, Murray JC, Gjessing HK. X-linked genes and risk of orofacial clefts: evidence from two population based studies in Scandinavia. PLoS ONE 2012; 7: e392340. – reference: Marçano ACB, Doudney K, Braybrook C, Squires R, Patton MA, Lees MM, Richieri-Costa A, Lidral AC, Murray JC, Moore GE, Stanier P. TBX22 mutations are a frequent cause of cleft palate. J Med Genet 2004; 41: 68-74. – reference: Harville EW, Wilcox AJ, Lie RT, Vindenes H, Abyholm F. Cleft lip and palate versus cleft lip only: are they distinct defects? Am J Epidemiol 2005; 162: 182-190. – reference: Vieira AR. Unraveling human cleft lip and palate research. J Dent Res 2008; 87: 119-125. – reference: Dudbridge F. Likelihood-based association analysis for nuclear families and unrelated subjects with missing genotype data. Hum Hered 2008; 66: 87-98. – reference: Derijcke A, Eerens A, Carels C. The incidence of oral clefts: a review. Brit J Oral Maxillofac Surg 1996; 34: 488-494. – reference: Beaty TH, Ruczinski I, Murray JC, Marazita ML, Munger RG, Hetmanski JB, Murray T, Redett RJ, Fallin D, Liang KY, Wu T, Patel PJ, Jin SC, Zhang TX, Schwender H, Wu-Chou YH, Chen PK, Chong SS, Cheah F, Yeow V, Ye X, Wang H, Huang S, Jabs EW, Shi B, Wilcox AJ, Lie RT, Jee SH, Christensen K, Doheny KF, Pugh EW, Ling H, Scott AF. Evidence for gene-environment interaction in a genome wide study of nonsyndromic cleft palate. Genet Epidemiol 2011; 32: 469-478. – reference: 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, Menzes 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. A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4. Nat Genet 2010; 42: 525-529. – reference: Dixon MJ, Marazita ML, Beaty TH, Murray JC. Cleft lip and palate: understanding genetic and environmental influences. Nat Rev Genet 2011; 11: 67-178. – reference: Braybrook C, Lisgo S, Doudney K, Henderson D, Marçano ACB, Strachan T, Patton MA, Villard L, Moore GE, Stanier P, Lindsay S. Craniofacial expression of human and murine TBX22 correlates with the cleft palate and ankyloglossia phenotype observed in CPX patients. Hum Mol Genet 2002; 11: 2793-2804. – reference: Laird NM, Horvath S, Xu X. Implementing a unified approach to family-based tests of association. Genet Epidemiol 2000; 19: S36-S42. – reference: Jugessur A, Murray JC. Orofacial clefting: recent insights into a complex trait. Curr Opin Genet Dev 2005; 15: 270-278. – reference: Suphapeetiporn K, Tongkobpetch S, Siriwan P, Shotelersuk V. TBX22 mutations are a frequent cause of non-syndromic cleft palate in the Thai population. Clin Genet 2007; 78: 478-483. – reference: Wehby GL, Pedersen DA, Murray JC, Christensen K. The effects of oral clefts on hospital use throughout the lifespan. 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Snippet	As part of an international consortium, case–parent trios were collected for a genome‐wide association study of isolated, non‐syndromic oral clefts, including... As part of an international consortium, case-parent trios were collected for a genome-wide association study of isolated, non-syndromic oral clefts, including...
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SubjectTerms	Adult Asian People - genetics case-parent trios Cleft Lip - genetics Cleft Palate - genetics Duchenne muscular dystrophy (DMD) family-based association Female Genes, X-Linked - physiology Genetic Markers Genome-Wide Association Study - methods Haplotypes - genetics Haplotypes - physiology Humans Male Muscular Dystrophy, Duchenne - genetics oral clefts Polymorphism, Single Nucleotide Principal Component Analysis Risk White People - genetics X-linked
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Title	X-linked markers in the Duchenne muscular dystrophy gene associated with oral clefts
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