Association studies of candidate genes and cleft lip and palate taking into consideration geographical origin
Lace B, Kempa I, Piekuse L, Grinfelde I, Klovins J, Pliss L, Krumina A, Vieira AR. Association studies of candidate genes and cleft lip and palate taking into consideration geographical origin. Eur J Oral Sci 2011; 119: 413–417. © 2011 Eur J Oral Sci Isolated cleft lip and/or palate (CL/CLP) is a...
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| Published in | European journal of oral sciences Vol. 119; no. 6; pp. 413 - 417 |
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| Main Authors | , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Oxford, UK
Blackwell Publishing Ltd
01.12.2011
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| Subjects | |
| Online Access | Get full text |
| ISSN | 0909-8836 1600-0722 1600-0722 |
| DOI | 10.1111/j.1600-0722.2011.00877.x |
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| Abstract | Lace B, Kempa I, Piekuse L, Grinfelde I, Klovins J, Pliss L, Krumina A, Vieira AR. Association studies of candidate genes and cleft lip and palate taking into consideration geographical origin.
Eur J Oral Sci 2011; 119: 413–417. © 2011 Eur J Oral Sci
Isolated cleft lip and/or palate (CL/CLP) is a complex congenital anomaly with many contributing factors. There are several genes involved in the aetiology of CL/CLP, they are different in selected populations. In a previous study, the mitochondrial haplotypes of Latvian subjects with CL/CLP were characterized. Latvian subjects with CL/CLP have mostly mitochondrial haplogroups U4/U5 compared with the ethnic population of Latvia. The aim of this study was to stratify the results of genotyping based on European mitochondrial DNA (mtDNA) haplotypes. DNA samples from 108 patients with CL/CLP and from 182 unrelated and unaffected individuals selected randomly in Latvia (used as controls) were obtained for investigation. In this study, we analysed the data taking into consideration mitochondrial haplogroups and found that gene associations depended on the genetic origin of the population. The phenotype of patients with non‐U haplotypes was associated with markers in wingless‐type MMTV integration site family, member 3 (WNT3), collagen, type XI, alpha 2 (COL11A2), and fibroblast growth factor receptor 1 (FGFR1), whereas patients with U4 and U5 haplotypes showed significant association with WNT3 and COL11A2. It is unlikely that mtDNA variants play a direct role in the development of CL/CLP; rather, they may be a surrogate for population substructure and provide a tool to increase homogeneity and statistical power. |
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| AbstractList | Isolated cleft lip and/or palate (CL/CLP) is a complex congenital anomaly with many contributing factors. There are several genes involved in the aetiology of CL/CLP, they are different in selected populations. In a previous study, the mitochondrial haplotypes of Latvian subjects with CL/CLP were characterized. Latvian subjects with CL/CLP have mostly mitochondrial haplogroups U4/U5 compared with the ethnic population of Latvia. The aim of this study was to stratify the results of genotyping based on European mitochondrial DNA (mtDNA) haplotypes. DNA samples from 108 patients with CL/CLP and from 182 unrelated and unaffected individuals selected randomly in Latvia (used as controls) were obtained for investigation. In this study, we analysed the data taking into consideration mitochondrial haplogroups and found that gene associations depended on the genetic origin of the population. The phenotype of patients with non-U haplotypes was associated with markers in wingless-type MMTV integration site family, member 3 (WNT3), collagen, type XI, alpha 2 (COL11A2), and fibroblast growth factor receptor 1 (FGFR1), whereas patients with U4 and U5 haplotypes showed significant association with WNT3 and COL11A2. It is unlikely that mtDNA variants play a direct role in the development of CL/CLP; rather, they may be a surrogate for population substructure and provide a tool to increase homogeneity and statistical power.Isolated cleft lip and/or palate (CL/CLP) is a complex congenital anomaly with many contributing factors. There are several genes involved in the aetiology of CL/CLP, they are different in selected populations. In a previous study, the mitochondrial haplotypes of Latvian subjects with CL/CLP were characterized. Latvian subjects with CL/CLP have mostly mitochondrial haplogroups U4/U5 compared with the ethnic population of Latvia. The aim of this study was to stratify the results of genotyping based on European mitochondrial DNA (mtDNA) haplotypes. DNA samples from 108 patients with CL/CLP and from 182 unrelated and unaffected individuals selected randomly in Latvia (used as controls) were obtained for investigation. In this study, we analysed the data taking into consideration mitochondrial haplogroups and found that gene associations depended on the genetic origin of the population. The phenotype of patients with non-U haplotypes was associated with markers in wingless-type MMTV integration site family, member 3 (WNT3), collagen, type XI, alpha 2 (COL11A2), and fibroblast growth factor receptor 1 (FGFR1), whereas patients with U4 and U5 haplotypes showed significant association with WNT3 and COL11A2. It is unlikely that mtDNA variants play a direct role in the development of CL/CLP; rather, they may be a surrogate for population substructure and provide a tool to increase homogeneity and statistical power. Lace B, Kempa I, Piekuse L, Grinfelde I, Klovins J, Pliss L, Krumina A, Vieira AR. Association studies of candidate genes and cleft lip and palate taking into consideration geographical origin. Eur J Oral Sci 2011; 119: 413–417. © 2011 Eur J Oral Sci Isolated cleft lip and/or palate (CL/CLP) is a complex congenital anomaly with many contributing factors. There are several genes involved in the aetiology of CL/CLP, they are different in selected populations. In a previous study, the mitochondrial haplotypes of Latvian subjects with CL/CLP were characterized. Latvian subjects with CL/CLP have mostly mitochondrial haplogroups U4/U5 compared with the ethnic population of Latvia. The aim of this study was to stratify the results of genotyping based on European mitochondrial DNA (mtDNA) haplotypes. DNA samples from 108 patients with CL/CLP and from 182 unrelated and unaffected individuals selected randomly in Latvia (used as controls) were obtained for investigation. In this study, we analysed the data taking into consideration mitochondrial haplogroups and found that gene associations depended on the genetic origin of the population. The phenotype of patients with non‐U haplotypes was associated with markers in wingless‐type MMTV integration site family, member 3 (WNT3), collagen, type XI, alpha 2 (COL11A2), and fibroblast growth factor receptor 1 (FGFR1), whereas patients with U4 and U5 haplotypes showed significant association with WNT3 and COL11A2. It is unlikely that mtDNA variants play a direct role in the development of CL/CLP; rather, they may be a surrogate for population substructure and provide a tool to increase homogeneity and statistical power. Isolated cleft lip and/or palate (CL/CLP) is a complex congenital anomaly with many contributing factors. There are several genes involved in the aetiology of CL/CLP, they are different in selected populations. In a previous study, the mitochondrial haplotypes of Latvian subjects with CL/CLP were characterized. Latvian subjects with CL/CLP have mostly mitochondrial haplogroups U4/U5 compared with the ethnic population of Latvia. The aim of this study was to stratify the results of genotyping based on European mitochondrial DNA (mtDNA) haplotypes. DNA samples from 108 patients with CL/CLP and from 182 unrelated and unaffected individuals selected randomly in Latvia (used as controls) were obtained for investigation. In this study, we analysed the data taking into consideration mitochondrial haplogroups and found that gene associations depended on the genetic origin of the population. The phenotype of patients with non-U haplotypes was associated with markers in wingless-type MMTV integration site family, member 3 (WNT3), collagen, type XI, alpha 2 (COL11A2), and fibroblast growth factor receptor 1 (FGFR1), whereas patients with U4 and U5 haplotypes showed significant association with WNT3 and COL11A2. It is unlikely that mtDNA variants play a direct role in the development of CL/CLP; rather, they may be a surrogate for population substructure and provide a tool to increase homogeneity and statistical power. |
| Author | Vieira, Alexandre R. Krumina, Astrida Pliss, Liana Grinfelde, Ieva Klovins, Janis Lace, Baiba Piekuse, Linda Kempa, Inga |
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| References | Simon DK, Pankratz N, Kissell DK, Pauciulo MW, Halter CA, Rudolph A, Pfeiffer RF, Nichols WC, Foroud T. Maternal inheritance and mitochondrial DNA variants in familial Parkinson's disease. BMC Med Genet 2010; 11: 53. Schliekelman P, Slatkin M. Multiplex relative risk and estimation of the number of loci underlying an inherited disease. Am J Hum Genet 2002; 71: 1369-1385. Wolf E, Gramer B, Müller-Myhsok F, Pasutto B, Wissinger N, Weisschuh N. Mitochondrial haplogroup u is associated with a reduced risk to develop exfoliation glaucoma in the German population. BMC Genet 2010; 11: 8. Vieira AR, Pliss L, Pelnena I, Krumina A, Baumanis V, Lace B. Mitochondrial DNA origins of the Latvian clefting population. Mitochondrion 2010; 11: 357-359. Riley BM, Mansilla MA, Ma J, Daack-Hirsch S, Maher BS, Raffensperger LM, Russo ET, Vieira AR, Dodé C, Mohammadi M, Marazita ML, Murray JC. Impaired FGF signaling contributes to cleft lip and palate. Proc Natl Acad Sci U S A 2007; 13: 104. Latsoudis H, Spanaki C, Chlouverakis G, Plaitakis A. Mitochondrial DNA polymorphisms and haplogroups in Parkinson's disease and control individuals with a similar genetic background. J Hum Genet 2008; 53: 349-356. Brandstätter A, Sänger T, Lutz-Bonengel S, Parson W, Béraud-Colomb E, Wen B, Kong QP, Bravi CM, Bandelt HJ. Phantom mutation hotspots in human mitochondrial DNA. Electrophoresis 2005; 26: 3414-3429. Krjutskov K, Andreson R, Mägi R, Nikopensius T, Khrunin A, Mihailov E, Tammekivi V, Sork H, Remm M, Metspalu A. Development of a single tube 640-plex genotyping method for detection of nucleic acid variations on microarrays. Nucleic Acids Res 2008; 36: e75. Sambrook J, Firtsch EF, Maniatis T, Fritsch EF, Maniatis T. Molecular cloning: a laboratory manual. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 1989; 6.4. Niemann S, Zhao C, Pascu F, Stahl U, Aulepp U, Niswander L, Weber JL, Müller U. Homozygous WNT3 mutation causes tetra-amelia in a large consanguineous family. Am J Hum Genet 2004; 74: 558-563. Menezes R, Letra A, Ruff J, Granjeiro JM, Vieira AR. Studies of genes in the FGF signaling pathway and oral clefts with or without dental anomalies. Am J Med Genet A 2008; 146A: 1614-1617. Santoro A, Balbi V, Balducci E, Pirazzini C, Rosini F, Tavano F, Achilli A, Siviero P, Minicuci N, Bellavista E, Mishto M, Salvioli S, Marchegiani F, Cardelli M, Olivieri F, Nacmias B, Chiamenti AM, Benussi L, Ghidoni R, Rose G, Gabelli C, Binetti G, Sorbi S, Crepaldi G, Passarino G, Torroni A, Franceschi C. Evidence for sub-haplogroup h5 of mitochondrial dna as a risk factor for late onset Alzheimer's disease. PLoS ONE 2010; 5: e12037. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, De Bakker PI, Daly MJ, Sham PC. PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 2007; 81: 559-575. Vieira AR, Cooper ME, Marazita ML, Castilla EE, Orioli IM. Reduced folate carrier 1 (RFC1) is associated with cleft of the lip only. Braz J Med Biol Res 2008; 41: 689-693. Chiquet BT, Blanton SH, Burt A, Ma D, Stal S, Mulliken JB, Hecht JT. Variation in WNT genes is associated with non-syndromic cleft lip with or without cleft palate. Hum Mol Genet 2008; 17: 2212-2218. Vieira AR, Cooper ME, Marazita ML, Orioli IM, Castilla EE. Interferon regulatory factor 6 (IRF6) is associated with oral-facial cleft in individuals that originate in South America. Am J Med Genet A 2007; 143A: 2075-2078. Vieira AR. Unraveling human cleft lip and palate research. J Dent Res 2008; 87: 119-125. Nikopenius T, Kempa I, Ambrozaityte L, Jagomagi T, Saag M, Matuleviciene A, Utkus A, Krjutskov K, Tammekivi V, Piekuse L, Akota I, Barkane B, Krumina A, Klovins J, Lace B, Kucinskas V, Metspalu A. Variation in FGF1, FOXE1, and TIMP2 genes is associated with nonsyndromic cleft lip with or without cleft palate. Birth Defects Res A Clin Mol Teratol 2011; 91: 218-225. Vieira AR, Karras JC, Orioli IM, Castilla EE, Murray JC. Genetic origins of a South American clefting population. Clin Genet 2002; 62: 458-463. Yao T, Yang L, Li PQ, Wu H, Xie HB, Shen X, Xie XD. Association of Wnt3A gene variants with non-syndromic cleft lip with or without cleft palate in Chinese population. Arch Oral Biol 2010; 56: 73-78. Torroni A, Huoponen K, Francalacci P, Petrozzi M, Morelli L, Scozzari R, Obinu D, Savantous ML, Wallace DC. Classification of European mtDNAs from an analysis of three European populations. Genetics 1996; 144: 1835-1850. Menezes R, Letra A, Kim AH, Küchler EC, Day A, Tannure PN, Gomes Da Motta L, Paiva KB, Granjeiro JM, Vieira AR. Studies with Wnt genes and nonsyndromic cleft lip and palate. Birth Defects Res A Clin Mol Teratol 2008; 88: 995-1000. 2010; 56 2010; 11 2004; 74 2011; 91 2002; 62 2008; 17 2008; 36 2007; 81 2008; 146A 2008; 87 1996; 144 2002; 71 2008; 88 2008; 41 2008; 53 2002 2005; 26 2007; 143A 2010; 5 2007; 13 1989 |
| References_xml | – reference: Simon DK, Pankratz N, Kissell DK, Pauciulo MW, Halter CA, Rudolph A, Pfeiffer RF, Nichols WC, Foroud T. Maternal inheritance and mitochondrial DNA variants in familial Parkinson's disease. BMC Med Genet 2010; 11: 53. – reference: Menezes R, Letra A, Kim AH, Küchler EC, Day A, Tannure PN, Gomes Da Motta L, Paiva KB, Granjeiro JM, Vieira AR. Studies with Wnt genes and nonsyndromic cleft lip and palate. Birth Defects Res A Clin Mol Teratol 2008; 88: 995-1000. – reference: Santoro A, Balbi V, Balducci E, Pirazzini C, Rosini F, Tavano F, Achilli A, Siviero P, Minicuci N, Bellavista E, Mishto M, Salvioli S, Marchegiani F, Cardelli M, Olivieri F, Nacmias B, Chiamenti AM, Benussi L, Ghidoni R, Rose G, Gabelli C, Binetti G, Sorbi S, Crepaldi G, Passarino G, Torroni A, Franceschi C. Evidence for sub-haplogroup h5 of mitochondrial dna as a risk factor for late onset Alzheimer's disease. PLoS ONE 2010; 5: e12037. – reference: Krjutskov K, Andreson R, Mägi R, Nikopensius T, Khrunin A, Mihailov E, Tammekivi V, Sork H, Remm M, Metspalu A. Development of a single tube 640-plex genotyping method for detection of nucleic acid variations on microarrays. Nucleic Acids Res 2008; 36: e75. – reference: Torroni A, Huoponen K, Francalacci P, Petrozzi M, Morelli L, Scozzari R, Obinu D, Savantous ML, Wallace DC. Classification of European mtDNAs from an analysis of three European populations. Genetics 1996; 144: 1835-1850. – reference: Vieira AR, Pliss L, Pelnena I, Krumina A, Baumanis V, Lace B. Mitochondrial DNA origins of the Latvian clefting population. Mitochondrion 2010; 11: 357-359. – reference: Vieira AR, Cooper ME, Marazita ML, Orioli IM, Castilla EE. Interferon regulatory factor 6 (IRF6) is associated with oral-facial cleft in individuals that originate in South America. Am J Med Genet A 2007; 143A: 2075-2078. – reference: Yao T, Yang L, Li PQ, Wu H, Xie HB, Shen X, Xie XD. Association of Wnt3A gene variants with non-syndromic cleft lip with or without cleft palate in Chinese population. Arch Oral Biol 2010; 56: 73-78. – reference: Schliekelman P, Slatkin M. Multiplex relative risk and estimation of the number of loci underlying an inherited disease. Am J Hum Genet 2002; 71: 1369-1385. – reference: Vieira AR. Unraveling human cleft lip and palate research. J Dent Res 2008; 87: 119-125. – reference: Riley BM, Mansilla MA, Ma J, Daack-Hirsch S, Maher BS, Raffensperger LM, Russo ET, Vieira AR, Dodé C, Mohammadi M, Marazita ML, Murray JC. Impaired FGF signaling contributes to cleft lip and palate. Proc Natl Acad Sci U S A 2007; 13: 104. – reference: Nikopenius T, Kempa I, Ambrozaityte L, Jagomagi T, Saag M, Matuleviciene A, Utkus A, Krjutskov K, Tammekivi V, Piekuse L, Akota I, Barkane B, Krumina A, Klovins J, Lace B, Kucinskas V, Metspalu A. Variation in FGF1, FOXE1, and TIMP2 genes is associated with nonsyndromic cleft lip with or without cleft palate. Birth Defects Res A Clin Mol Teratol 2011; 91: 218-225. – reference: Brandstätter A, Sänger T, Lutz-Bonengel S, Parson W, Béraud-Colomb E, Wen B, Kong QP, Bravi CM, Bandelt HJ. Phantom mutation hotspots in human mitochondrial DNA. Electrophoresis 2005; 26: 3414-3429. – reference: Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, De Bakker PI, Daly MJ, Sham PC. PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 2007; 81: 559-575. – reference: Niemann S, Zhao C, Pascu F, Stahl U, Aulepp U, Niswander L, Weber JL, Müller U. Homozygous WNT3 mutation causes tetra-amelia in a large consanguineous family. Am J Hum Genet 2004; 74: 558-563. – reference: Latsoudis H, Spanaki C, Chlouverakis G, Plaitakis A. Mitochondrial DNA polymorphisms and haplogroups in Parkinson's disease and control individuals with a similar genetic background. J Hum Genet 2008; 53: 349-356. – reference: Vieira AR, Cooper ME, Marazita ML, Castilla EE, Orioli IM. Reduced folate carrier 1 (RFC1) is associated with cleft of the lip only. Braz J Med Biol Res 2008; 41: 689-693. – reference: Wolf E, Gramer B, Müller-Myhsok F, Pasutto B, Wissinger N, Weisschuh N. Mitochondrial haplogroup u is associated with a reduced risk to develop exfoliation glaucoma in the German population. BMC Genet 2010; 11: 8. – reference: Sambrook J, Firtsch EF, Maniatis T, Fritsch EF, Maniatis T. Molecular cloning: a laboratory manual. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 1989; 6.4. – reference: Menezes R, Letra A, Ruff J, Granjeiro JM, Vieira AR. Studies of genes in the FGF signaling pathway and oral clefts with or without dental anomalies. Am J Med Genet A 2008; 146A: 1614-1617. – reference: Chiquet BT, Blanton SH, Burt A, Ma D, Stal S, Mulliken JB, Hecht JT. Variation in WNT genes is associated with non-syndromic cleft lip with or without cleft palate. Hum Mol Genet 2008; 17: 2212-2218. – reference: Vieira AR, Karras JC, Orioli IM, Castilla EE, Murray JC. Genetic origins of a South American clefting population. 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| Snippet | Lace B, Kempa I, Piekuse L, Grinfelde I, Klovins J, Pliss L, Krumina A, Vieira AR. Association studies of candidate genes and cleft lip and palate taking into... Isolated cleft lip and/or palate (CL/CLP) is a complex congenital anomaly with many contributing factors. There are several genes involved in the aetiology of... |
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| SubjectTerms | alpha 2 Case-Control Studies Cleft Lip - ethnology Cleft Lip - genetics Cleft Palate - ethnology Cleft Palate - genetics collagen Collagen Type XI - genetics collagen, type XI, alpha 2 Databases, Genetic DNA, Mitochondrial - genetics Ethnic Groups - genetics Female fibroblast growth factor receptor 1 Genetic Association Studies Haplotypes - genetics Humans Latvia - ethnology Latvian population Male Reference Values type XI WNT3 Wnt3 Protein - genetics |
| Title | Association studies of candidate genes and cleft lip and palate taking into consideration geographical origin |
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