Genetic association between intronic variants in AS3MT and arsenic methylation efficiency is focused on a large linkage disequilibrium cluster in chromosome 10
Differences in arsenic metabolism are known to play a role in individual variability in arsenic‐induced disease susceptibility. Genetic variants in genes relevant to arsenic metabolism are considered to be partially responsible for the variation in arsenic metabolism. Specifically, variants in arsen...
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Published in | Journal of applied toxicology Vol. 30; no. 3; pp. 260 - 270 |
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Main Authors | , , , |
Format | Journal Article |
Language | English |
Published |
Chichester, UK
John Wiley & Sons, Ltd
01.04.2010
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Subjects | |
Online Access | Get full text |
ISSN | 0260-437X 1099-1263 1099-1263 |
DOI | 10.1002/jat.1492 |
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Abstract | Differences in arsenic metabolism are known to play a role in individual variability in arsenic‐induced disease susceptibility. Genetic variants in genes relevant to arsenic metabolism are considered to be partially responsible for the variation in arsenic metabolism. Specifically, variants in arsenic (3+ oxidation state) methyltransferase (AS3MT), the key gene in the metabolism of arsenic, have been associated with increased arsenic methylation efficiency. Of particular interest is the fact that different studies have reported that several of the AS3MT single nucleotide polymorphisms (SNPs) are in strong linkage‐disequilibrium (LD), which also extends to a nearby gene, CYP17A1. In an effort to characterize the extent of the region in LD, we genotyped 46 SNPs in a 347000 base region of chromosome 10 that included AS3MT in arsenic‐exposed subjects from Mexico. Pairwise LD analysis showed strong LD for these polymorphisms, represented by a mean r2 of 0.82, spanning a region that includes five genes. Genetic association analysis with arsenic metabolism confirmed the previously observed association between AS3MT variants, including this large cluster of linked polymorphisms, and arsenic methylation efficiency. The existence of a large genomic region sharing strong LD with polymorphisms associated with arsenic metabolism presents a predicament because the observed phenotype cannot be unequivocally assigned to a single SNP or even a single gene. The results reported here should be carefully considered for future genomic association studies involving AS3MT and arsenic metabolism. Copyright © 2009 John Wiley & Sons, Ltd.
Several AS3MT single nucleotide polymorphisms (SNPs) that previously were associated with arsenic methylation efficiency have also shown strong linkage‐disequilibrium (LD) in the genomic region including AS3MT. To characterize the extent of LD in this region, 46 SNPs were genotyped in chromosome 10. Strong LD was observed spanning a region that includes AS3MT and four other genes. Genetic association analysis confirmed the association between this large cluster of linked polymorphisms and arsenic methylation efficiency. |
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AbstractList | Differences in arsenic metabolism are known to play a role in individual variability in arsenic-induced disease susceptibility. Genetic variants in genes relevant to arsenic metabolism are considered to be partially responsible for the variation in arsenic metabolism. Specifically, variants in arsenic (3+ oxidation state) methyltransferase (AS3MT), the key gene in the metabolism of arsenic, have been associated with increased arsenic methylation efficiency. Of particular interest is the fact that different studies have reported that several of the AS3MT single nucleotide polymorphisms (SNPs) are in strong linkage-disequilibrium (LD), which also extends to a nearby gene, CYP17A1. In an effort to characterize the extent of the region in LD, we genotyped 46 SNPs in a 347,000 base region of chromosome 10 that included AS3MT in arsenic-exposed subjects from Mexico. Pairwise LD analysis showed strong LD for these polymorphisms, represented by a mean r(2) of 0.82, spanning a region that includes five genes. Genetic association analysis with arsenic metabolism confirmed the previously observed association between AS3MT variants, including this large cluster of linked polymorphisms, and arsenic methylation efficiency. The existence of a large genomic region sharing strong LD with polymorphisms associated with arsenic metabolism presents a predicament because the observed phenotype cannot be unequivocally assigned to a single SNP or even a single gene. The results reported here should be carefully considered for future genomic association studies involving AS3MT and arsenic metabolism. Differences in arsenic metabolism are known to play a role in individual variability in arsenic-induced disease susceptibility. Genetic variants in genes relevant to arsenic metabolism are considered to be partially responsible for the variation in arsenic metabolism. Specifically, variants in arsenic (3+ oxidation state) methyltransferase (AS3MT), the key gene in the metabolism of arsenic, have been associated with increased arsenic methylation efficiency. Of particular interest is the fact that different studies have reported that several of the AS3MT single nucleotide polymorphisms (SNPs) are in strong linkage-disequilibrium (LD), which also extends to a nearby gene, CYP17A1. In an effort to characterize the extent of the region in LD, we genotyped 46 SNPs in a 347,000 base region of chromosome 10 that included AS3MT in arsenic-exposed subjects from Mexico. Pairwise LD analysis showed strong LD for these polymorphisms, represented by a mean r(2) of 0.82, spanning a region that includes five genes. Genetic association analysis with arsenic metabolism confirmed the previously observed association between AS3MT variants, including this large cluster of linked polymorphisms, and arsenic methylation efficiency. The existence of a large genomic region sharing strong LD with polymorphisms associated with arsenic metabolism presents a predicament because the observed phenotype cannot be unequivocally assigned to a single SNP or even a single gene. The results reported here should be carefully considered for future genomic association studies involving AS3MT and arsenic metabolism.Differences in arsenic metabolism are known to play a role in individual variability in arsenic-induced disease susceptibility. Genetic variants in genes relevant to arsenic metabolism are considered to be partially responsible for the variation in arsenic metabolism. Specifically, variants in arsenic (3+ oxidation state) methyltransferase (AS3MT), the key gene in the metabolism of arsenic, have been associated with increased arsenic methylation efficiency. Of particular interest is the fact that different studies have reported that several of the AS3MT single nucleotide polymorphisms (SNPs) are in strong linkage-disequilibrium (LD), which also extends to a nearby gene, CYP17A1. In an effort to characterize the extent of the region in LD, we genotyped 46 SNPs in a 347,000 base region of chromosome 10 that included AS3MT in arsenic-exposed subjects from Mexico. Pairwise LD analysis showed strong LD for these polymorphisms, represented by a mean r(2) of 0.82, spanning a region that includes five genes. Genetic association analysis with arsenic metabolism confirmed the previously observed association between AS3MT variants, including this large cluster of linked polymorphisms, and arsenic methylation efficiency. The existence of a large genomic region sharing strong LD with polymorphisms associated with arsenic metabolism presents a predicament because the observed phenotype cannot be unequivocally assigned to a single SNP or even a single gene. The results reported here should be carefully considered for future genomic association studies involving AS3MT and arsenic metabolism. Differences in arsenic metabolism are known to play a role in individual variability in arsenic-induced disease susceptibility. Genetic variants in genes relevant to arsenic metabolism are considered to be partially responsible for the variation in arsenic metabolism. Specifically, variants in arsenic (3+ oxidation state) methyltransferase (AS3MT), the key gene in the metabolism of arsenic, have been associated with increased arsenic methylation efficiency. Of particular interest is the fact that different studies have reported that several of the AS3MT single nucleotide polymorphisms (SNPs) are in strong linkage-disequilibrium (LD), which also extends to a nearby gene, CYP17A1. In an effort to characterize the extent of the region in LD, we genotyped 46 SNPs in a 347000 base region of chromosome 10 that included AS3MT in arsenic-exposed subjects from Mexico. Pairwise LD analysis showed strong LD for these polymorphisms, represented by a mean r2 of 0.82, spanning a region that includes five genes. Genetic association analysis with arsenic metabolism confirmed the previously observed association between AS3MT variants, including this large cluster of linked polymorphisms, and arsenic methylation efficiency. The existence of a large genomic region sharing strong LD with polymorphisms associated with arsenic metabolism presents a predicament because the observed phenotype cannot be unequivocally assigned to a single SNP or even a single gene. The results reported here should be carefully considered for future genomic association studies involving AS3MT and arsenic metabolism. Differences in arsenic metabolism are known to play a role in individual variability in arsenic‐induced disease susceptibility. Genetic variants in genes relevant to arsenic metabolism are considered to be partially responsible for the variation in arsenic metabolism. Specifically, variants in arsenic (3+ oxidation state) methyltransferase (AS3MT), the key gene in the metabolism of arsenic, have been associated with increased arsenic methylation efficiency. Of particular interest is the fact that different studies have reported that several of the AS3MT single nucleotide polymorphisms (SNPs) are in strong linkage‐disequilibrium (LD), which also extends to a nearby gene, CYP17A1. In an effort to characterize the extent of the region in LD, we genotyped 46 SNPs in a 347000 base region of chromosome 10 that included AS3MT in arsenic‐exposed subjects from Mexico. Pairwise LD analysis showed strong LD for these polymorphisms, represented by a mean r2 of 0.82, spanning a region that includes five genes. Genetic association analysis with arsenic metabolism confirmed the previously observed association between AS3MT variants, including this large cluster of linked polymorphisms, and arsenic methylation efficiency. The existence of a large genomic region sharing strong LD with polymorphisms associated with arsenic metabolism presents a predicament because the observed phenotype cannot be unequivocally assigned to a single SNP or even a single gene. The results reported here should be carefully considered for future genomic association studies involving AS3MT and arsenic metabolism. Copyright © 2009 John Wiley & Sons, Ltd. Several AS3MT single nucleotide polymorphisms (SNPs) that previously were associated with arsenic methylation efficiency have also shown strong linkage‐disequilibrium (LD) in the genomic region including AS3MT. To characterize the extent of LD in this region, 46 SNPs were genotyped in chromosome 10. Strong LD was observed spanning a region that includes AS3MT and four other genes. Genetic association analysis confirmed the association between this large cluster of linked polymorphisms and arsenic methylation efficiency. Differences in arsenic metabolism are known to play a role in individual variability in arsenic-induced disease susceptibility. Genetic variants in genes relevant to arsenic metabolism are considered to be partially responsible for the variation in arsenic metabolism. Specifically, variants in arsenic (3+ oxidation state) methyltransferase (AS3MT), the key gene in the metabolism of arsenic, have been associated with increased arsenic methylation efficiency. Of particular interest is the fact that different studies have reported that several of the AS3MT single nucleotide polymorphisms (SNPs) are in strong linkage-disequilibrium (LD), which also extends to a nearby gene, CYP17A1. In an effort to characterize the extent of the region in LD, we genotyped 46 SNPs in a 347,000 base region of chromosome 10 that included AS3MT in arsenic-exposed subjects from Mexico. Pairwise LD analysis showed strong LD for these polymorphisms, represented by a mean r 2 of 0.82, spanning a region that includes 5 genes. Genetic association analysis with arsenic metabolism confirmed the previously observed association between AS3MT variants, including this large cluster of linked polymorphisms, and arsenic methylation efficiency. The existence of a large genomic region sharing strong LD with polymorphisms associated with arsenic metabolism presents a predicament because the observed phenotype cannot be unequivocally assigned to a single SNP or even a single gene. The results reported here should be carefully considered for future genomic association studies involving AS3MT and arsenic metabolism. Differences in arsenic metabolism are known to play a role in individual variability in arsenic‐induced disease susceptibility. Genetic variants in genes relevant to arsenic metabolism are considered to be partially responsible for the variation in arsenic metabolism. Specifically, variants in arsenic (3+ oxidation state) methyltransferase (AS3MT), the key gene in the metabolism of arsenic, have been associated with increased arsenic methylation efficiency. Of particular interest is the fact that different studies have reported that several of the AS3MT single nucleotide polymorphisms (SNPs) are in strong linkage‐disequilibrium (LD), which also extends to a nearby gene, CYP17A1. In an effort to characterize the extent of the region in LD, we genotyped 46 SNPs in a 347000 base region of chromosome 10 that included AS3MT in arsenic‐exposed subjects from Mexico. Pairwise LD analysis showed strong LD for these polymorphisms, represented by a mean r 2 of 0.82, spanning a region that includes five genes. Genetic association analysis with arsenic metabolism confirmed the previously observed association between AS3MT variants, including this large cluster of linked polymorphisms, and arsenic methylation efficiency. The existence of a large genomic region sharing strong LD with polymorphisms associated with arsenic metabolism presents a predicament because the observed phenotype cannot be unequivocally assigned to a single SNP or even a single gene. The results reported here should be carefully considered for future genomic association studies involving AS3MT and arsenic metabolism. Copyright © 2009 John Wiley & Sons, Ltd. Several AS3MT single nucleotide polymorphisms (SNPs) that previously were associated with arsenic methylation efficiency have also shown strong linkage‐disequilibrium (LD) in the genomic region including AS3MT. To characterize the extent of LD in this region, 46 SNPs were genotyped in chromosome 10. Strong LD was observed spanning a region that includes AS3MT and four other genes. Genetic association analysis confirmed the association between this large cluster of linked polymorphisms and arsenic methylation efficiency. Differences in arsenic metabolism are known to play a role in individual variability in arsenic-induced disease susceptibility. Genetic variants in genes relevant to arsenic metabolism are considered to be partially responsible for the variation in arsenic metabolism. Specifically, variants in arsenic (3+ oxidation state) methyltransferase (AS3MT), the key gene in the metabolism of arsenic, have been associated with increased arsenic methylation efficiency. Of particular interest is the fact that different studies have reported that several of the AS3MT single nucleotide polymorphisms (SNPs) are in strong linkage-disequilibrium (LD), which also extends to a nearby gene, CYP17A1. In an effort to characterize the extent of the region in LD, we genotyped 46 SNPs in a 347000 base region of chromosome 10 that included AS3MT in arsenic-exposed subjects from Mexico. Pairwise LD analysis showed strong LD for these polymorphisms, represented by a mean r super(2) of 0.82, spanning a region that includes five genes. Genetic association analysis with arsenic metabolism confirmed the previously observed association between AS3MT variants, including this large cluster of linked polymorphisms, and arsenic methylation efficiency. The existence of a large genomic region sharing strong LD with polymorphisms associated with arsenic metabolism presents a predicament because the observed phenotype cannot be unequivocally assigned to a single SNP or even a single gene. The results reported here should be carefully considered for future genomic association studies involving AS3MT and arsenic metabolism. |
Author | Meza-Montenegro, Maria M. Gomez-Rubio, Paulina Cantu-Soto, Ernesto Klimecki, Walter T. |
AuthorAffiliation | 1 Department of Pharmacology and Toxicology, University of Arizona 2 Department of Environmental Sciences, Instituto Tecnologico de Sonora |
AuthorAffiliation_xml | – name: 2 Department of Environmental Sciences, Instituto Tecnologico de Sonora – name: 1 Department of Pharmacology and Toxicology, University of Arizona |
Author_xml | – sequence: 1 givenname: Paulina surname: Gomez-Rubio fullname: Gomez-Rubio, Paulina organization: Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona, USA – sequence: 2 givenname: Maria M. surname: Meza-Montenegro fullname: Meza-Montenegro, Maria M. organization: Department of Environmental Science, Instituto Technologico de Sonora, Ciudad Obregon, Sonora, Mexico – sequence: 3 givenname: Ernesto surname: Cantu-Soto fullname: Cantu-Soto, Ernesto organization: Department of Environmental Science, Instituto Technologico de Sonora, Ciudad Obregon, Sonora, Mexico – sequence: 4 givenname: Walter T. surname: Klimecki fullname: Klimecki, Walter T. email: klimecki@pharmacy.arizona.edu organization: Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona, USA |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/20014157$$D View this record in MEDLINE/PubMed |
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Keywords | AS3MT polymorphism Arsenic SNP Linkage Disequilibrium |
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Lindberg AL, Kumar R, Goessler W, Thirumaran R, Gurzau E, Koppova K, Rudnai P, Leonardi G, Fletcher T, Vahter M. 2007. Metabolism of low-dose inorganic arsenic in a central European population: influence of sex and genetic polymorphisms. Environ. Health Perspect. 115: 1081-1086. Petrick JS, Ayala-Fierro F, Cullen WR, Carter DE, Vasken Aposhian H. 2000. Monomethylarsonous acid (MMA(III)) is more toxic than arsenite in Chang human hepatocytes. Toxicol. Appl. Pharmacol. 163: 203-207. Schläwicke Engström K, Broberg K, Concha G, Nermell B, Warholm M, Vahter M. 2007. Genetic polymorphisms influencing arsenic metabolism: evidence from Argentina. Environ. Health Perspect. 115: 599-605. Morales KH, Ryan L, Kuo TL, Wu MM, Chen CJ. 2000. Risk of internal cancers from arsenic in drinking water. Environ. Health Perspect. 108: 655-661. Schläwicke Engström K, Nermell B, Concha G, Strömberg U, Vahter M, Broberg K. 2009. 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Health 70: 42-47. 2005; 113 2008; 19 1995; 55 2002; 133 2002; 77 1994; 88 2005; 21 2006; 19 2005 2007; 95 1996; 104 2009; 239 2008; 70 2003; 111 1998; 44 2005; 47 2007; 28 2007; 115 2004; 198 2007; 218 2009; 31 2004; 14 2007; 232 2000; 108 2000; 74 2006; 26 2006; 48 2008; 659 2008; 637 2005; 206 2003; 4 2000; 163 2007; 81 2005; 76 2007; 85 2001; 11 2009; 107 2001; 78 2005; 79 2003; 45 2009; 667 Chiou HY (e_1_2_1_4_1) 1995; 55 e_1_2_1_42_1 e_1_2_1_20_1 e_1_2_1_41_1 e_1_2_1_40_1 e_1_2_1_23_1 Nahar N (e_1_2_1_24_1) 2008; 70 e_1_2_1_46_1 e_1_2_1_45_1 e_1_2_1_21_1 e_1_2_1_44_1 e_1_2_1_22_1 e_1_2_1_43_1 e_1_2_1_27_1 e_1_2_1_28_1 e_1_2_1_25_1 e_1_2_1_26_1 e_1_2_1_29_1 Thomas DJ (e_1_2_1_39_1) 2007; 232 e_1_2_1_7_1 Jurinke C (e_1_2_1_19_1) 2002; 77 e_1_2_1_31_1 e_1_2_1_8_1 e_1_2_1_30_1 e_1_2_1_5_1 e_1_2_1_6_1 e_1_2_1_3_1 e_1_2_1_12_1 e_1_2_1_35_1 e_1_2_1_13_1 e_1_2_1_34_1 e_1_2_1_10_1 e_1_2_1_2_1 e_1_2_1_11_1 e_1_2_1_32_1 e_1_2_1_16_1 Singh N (e_1_2_1_33_1) 2007; 28 e_1_2_1_17_1 e_1_2_1_38_1 e_1_2_1_14_1 e_1_2_1_37_1 e_1_2_1_15_1 e_1_2_1_36_1 e_1_2_1_9_1 e_1_2_1_18_1 |
References_xml | – reference: Pu YS, Yang SM, Huang YK, Chung CJ, Huang SK, Chiu AW, Yang MH, Chen CJ, Hsueh YM. 2007. Urinary arsenic profile affects the risk of urothelial carcinoma even at low arsenic exposure. Toxicol. Appl. Pharmacol. 218: 99-106. – reference: Goldstein DB, Weale ME. 2001. Population genomics: linkage disequilibrium holds the key. Curr. Biol. 11: 576-579. – reference: Schläwicke Engström K, Nermell B, Concha G, Strömberg U, Vahter M, Broberg K. 2009. Arsenic metabolism is influenced by polymorphisms in genes involved in one-carbon metabolism and reduction reactions. Mutat. Res. 667: 4-14. – reference: Wigginton JE, Cutler DJ, Abecasis GR. 2005. A note on exact tests of Hardy-Weinberg equilibrium. Am. J. Hum. Genet. 76: 887-893. – reference: Barrett JC, Fry B, Maller J, Daly MJ. 2005. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 21: 263-265. – reference: Trinklein ND, Aldred SF, Hartman SJ, Schroeder DI, Otillar RP, Myers RM. 2004. An abundance of bidirectional promoters in the human genome. Genome Res. 14: 62-66. – reference: Chen YC, Guo YL, Su HJ, Hsueh YM, Smith TJ, Ryan LM, Lee MS, Chao SC, Lee JY, Christiani DC. 2003. Arsenic methylation and skin cancer risk in southwestern Taiwan. J. Occup. Environ. Med. 45: 241-248. – reference: Petrick JS, Ayala-Fierro F, Cullen WR, Carter DE, Vasken Aposhian H. 2000. Monomethylarsonous acid (MMA(III)) is more toxic than arsenite in Chang human hepatocytes. Toxicol. Appl. Pharmacol. 163: 203-207. – reference: Wall JD, Pritchard JK. 2003. Haplotype blocks and linkage disequilibrium in the human genome. Nat. Rev. Genet. 4: 587-597. – reference: Lieberman S, Warne PA. 2001. 17-Hydroxylase: an evaluation of the present view of its catalytic role in steroidogenesis. J. Steroid Biochem. Mol. 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Snippet | Differences in arsenic metabolism are known to play a role in individual variability in arsenic‐induced disease susceptibility. Genetic variants in genes... Differences in arsenic metabolism are known to play a role in individual variability in arsenic-induced disease susceptibility. Genetic variants in genes... |
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SubjectTerms | 5'-Nucleotidase - genetics Arsenic Arsenic - metabolism Arsenic - urine Arsenic Poisoning - genetics Arsenic Poisoning - urine Arsenicals - urine AS3MT Chromosomes Chromosomes, Human, Pair 10 - genetics Clusters Female Genes Genetic Association Studies Genetics Humans Introns - genetics Linkage Disequilibrium Male Metabolism Methylation Methyltransferases - genetics Mexico Mouth Mucosa - metabolism Multigene Family Polymorphism Polymorphism, Single Nucleotide SNP Steroid 17-alpha-Hydroxylase - genetics |
Title | Genetic association between intronic variants in AS3MT and arsenic methylation efficiency is focused on a large linkage disequilibrium cluster in chromosome 10 |
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