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Morak M, Massdorf T, Sykora H, Kerscher M, Holinski-Feder E. First evidence for digenic inheritance in hereditary colorectal cancer by mutations in the base excision repair genes. Eur J Cancer 2010; 47:1046-55. [PMID: 21195604 DOI: 10.1016/j.ejca.2010.11.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 11/23/2010] [Indexed: 10/18/2022]
Abstract
Biallelic mutations in the base excision repair gene Mut Y homologue (MUTYH) are responsible for variable recessively inherited phenotypes of polyposis. Beside MUTYH, the proteins 8-oxo-guanine DNA glycosylase (OGG1) and MTH1 (or NUDT1) are also involved in the repair of 7,8-dihydro-8-oxoguanine (8-oxo-G), previous studies, however, only found missense mutations of unclear pathogenicity in either MTH1 or OGG1. To investigate the role of a defective 8-oxo-G repair we performed a germline mutation screening in the genes OGG1, MTH1 and MUTYH, in 81 patients with a clinical phenotype ranging from attenuated or atypical adenomatous polyposis coli including hyperplastic polyps to hereditary non-polyposis colorectal cancer (HNPCC) type X syndrome without mono- or biallelic mutations in either APC, MUTYH or the DNA mismatch repair genes. We describe here the first pathogenic germline mutation in OGG1, a splice site mutation affecting exon 1, which was inherited from the father, in combination with a maternal MUTYH missense mutation p.Ile223Val in a female patient with advanced synchronous colon cancer and adenomas at the age of 36 years pointing towards digenic inheritance for colorectal cancer (CRC) predisposition. Monoallelic missense mutations in MTH1 (3x), OGG1 (2x), or MUTYH (3x) were identified in 10 patients (12%), three of them were novel. Our findings indicate that mutations in other genes of the 8-oxo-G repair beside MUTYH are involved in CRC predisposition. Oligogenic inheritance affecting genes of a certain repair pathway might therefore be the missing link between monogenic and polygenic traits.
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Affiliation(s)
- Monika Morak
- University Hospital of the Ludwig-Maximilians-University, Campus Innenstadt, Ziemssenstr. 1, 80336 Munich, Germany
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2
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Dumontet C, Landi S, Reiman T, Perry T, Plesa A, Bellini I, Barale R, Pilarski LM, Troncy J, Tavtigian S, Gemignani F. Genetic polymorphisms associated with outcome in multiple myeloma patients receiving high-dose melphalan. Bone Marrow Transplant 2009; 45:1316-24. [PMID: 19966851 DOI: 10.1038/bmt.2009.335] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
High-dose melphalan (HDM) is an essential component in the treatment of patients with multiple myeloma (MM). Few data are available regarding genetic polymorphisms associated with patient outcome or toxicity in this setting. To identify such polymorphisms, we performed a retrospective analysis, genotyping single nucleotide polymorphisms (SNPs) with the arrayed primer extension (APEX) technology in 169 patients having received HDM for MM. We analyzed 209 SNPs in 95 genes involved in drug metabolism, DNA repair, cell cycle and apoptosis. SNPs in ABCB1, CYP3A4 and TP53BP2 were associated with response to VAD induction therapy (P<0.01). SNPs in ALDH2, GSTT2 and BRCA1 were associated with response to HDM (P<0.01). Polymorphisms in CYP1A1, RAD51 and PARP were associated with disease progression whereas polymorphisms in ALDH2 and CYP1A1 were correlated with OS. Polymorphisms in BRCA1, CDKN1A and XRCC1 were associated with the occurrence of severe mucositis after HDM. These results suggest that SNPs of genes involved in drug metabolism or DNA repair could be used to distinguish MM patient subgroups with different toxicity/efficacy profiles.
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Affiliation(s)
- C Dumontet
- LCMT, Hospices Civils de Lyon, Lyon, France.
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3
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Gemignani F, Neri M, Bottari F, Barale R, Canessa PA, Canzian F, Ceppi M, Spitaleri I, Cipollini M, Ivaldi GP, Mencoboni M, Scaruffi P, Tonini GP, Ugolini D, Mutti L, Bonassi S, Landi S. Risk of malignant pleural mesothelioma and polymorphisms in genes involved in the genome stability and xenobiotics metabolism. Mutat Res 2009; 671:76-83. [PMID: 19751749 DOI: 10.1016/j.mrfmmm.2009.09.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 09/01/2009] [Accepted: 09/04/2009] [Indexed: 10/20/2022]
Abstract
Malignant pleural mesothelioma (MPM) is a rare and aggressive cancer mostly attributable to asbestos exposure. Many polymorphic genes encoding for xenobiotic and oxidative metabolism enzymes (XME) or involved in genome stability (GS) can modulate individual MPM risk in exposed populations. An association study was carried out in a case-control setting including 119 MPM patients and two groups of referent subjects (104 with and 695 without documented asbestos exposure). Forty-eight polymorphisms in XME genes and 75 in GS-genes were evaluated. Statistical analysis revealed some significant associations of studied polymorphisms with MPM risk, but most of them disappeared after applying Bonferroni correction (new threshold for statistical significance: p=4.07 x 10(-4)). On the other hand, the nucleotidic change 282C>T within NAT2 held the statistical significance (OR=3.54; 95% CI 1.75-7.16; p=0.0002), reinforcing existing evidences that describe genetic polymorphisms of NAT2 possibly involved in the etiology of the MPM.
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Affiliation(s)
- Federica Gemignani
- Genetics - Department of Biology, University of Pisa, Via Derna, 1, 56100 Pisa, Italy
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4
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Canova C, Hashibe M, Simonato L, Nelis M, Metspalu A, Lagiou P, Trichopoulos D, Ahrens W, Pigeot I, Merletti F, Richiardi L, Talamini R, Barzan L, Macfarlane GJ, Macfarlane TV, Holcátová I, Bencko V, Benhamou S, Bouchardy C, Kjaerheim K, Lowry R, Agudo A, Castellsagué X, Conway DI, McKinney PA, Znaor A, McCartan BE, Healy CM, Marron M, Brennan P. Genetic associations of 115 polymorphisms with cancers of the upper aerodigestive tract across 10 European countries: the ARCAGE project. Cancer Res 2009; 69:2956-65. [PMID: 19339270 DOI: 10.1158/0008-5472.can-08-2604] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cancers of the upper aerodigestive tract (UADT) include malignant tumors of the oral cavity, pharynx, larynx, and esophagus and account for 6.4% of all new cancers in Europe. In the context of a multicenter case-control study conducted in 14 centers within 10 European countries and comprising 1,511 cases and 1,457 controls (ARCAGE study), 115 single nucleotide polymorphisms (SNP) from 62 a priori-selected genes were studied in relation to UADT cancer. We found 11 SNPs that were statistically associated with UADT cancers overall (5.75 expected). Considering the possibility of false-positive results, we focused on SNPs in CYP2A6, MDM2, tumor necrosis factor (TNF), and gene amplified in squamous cell carcinoma 1 (GASC1), for which low P values for trend (P trend<0.01) were observed in the main effects analyses of UADT cancer overall or by subsite. The rare variant of CYP2A6 -47A>C (rs28399433), a phase I metabolism gene, was associated with reduced UADT cancer risk (P trend=0.01). Three SNPs in the MDM2 gene, involved in cell cycle control, were associated with UADT cancer. MDM2 IVS5+1285A>G (rs3730536) showed a strong codominant effect (P trend=0.007). The rare variants of two SNPs in the TNF gene were associated with a decreased risk; for TNF IVS1+123G>A (rs1800610), the P trend was 0.007. Variants in two SNPs of GASC1 were found to be strongly associated with increased UADT cancer risk (for both, P trend=0.008). This study is the largest genetic epidemiologic study on UADT cancers in Europe. Our analysis points to potentially relevant genes in various pathways.
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Affiliation(s)
- Cristina Canova
- Department of Environmental Medicine and Public Health, University of Padova, Padova, Italy
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5
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Betti M, Neri M, Ferrante D, Landi S, Biava A, Gemignani F, Bertolotti M, Mirabelli D, Padoan M, Ugolini D, Botta M, Bonassi S, Magnani C, Dianzani I. Pooled analysis of NAT2 genotypes as risk factors for asbestos-related malignant mesothelioma. Int J Hyg Environ Health 2009; 212:322-9. [DOI: 10.1016/j.ijheh.2008.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Revised: 07/31/2008] [Accepted: 08/04/2008] [Indexed: 10/21/2022]
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6
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Alcohol-related cancers and genetic susceptibility in Europe: the ARCAGE project: study samples and data collection. Eur J Cancer Prev 2009; 18:76-84. [DOI: 10.1097/cej.0b013e32830c8dca] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Dumaual C, Miao X, Daly TM, Bruckner C, Njau R, Fu DJ, Close-Kirkwood S, Bauer N, Watanabe N, Hardenbol P, Hockett RD. Comprehensive assessment of metabolic enzyme and transporter genes using the Affymetrix Targeted Genotyping System. Pharmacogenomics 2007; 8:293-305. [PMID: 17324118 DOI: 10.2217/14622416.8.3.293] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The combined effects of multiple polymorphisms in several drug-metabolizing enzyme and transporter genes can contribute to considerable interindividual variation in drug disposition and response. Therefore, it has been of increasing interest to generate scalable, flexible and cost-effective technologies for large-scale genotyping of the drug-metabolizing enzyme and transporter genes. However, the number of drug-metabolizing enzyme and transporter gene variants exceeds the capacity of current technologies to comprehensively assess multiple polymorphisms in a single, multiplexed assay. The Targeted Genotyping System (Affymetrix, CA, USA) provides a solution to this challenge, by combining molecular inversion probe technology with universal microarrays to provide a method that is capable of analyzing thousands of variants in a single reaction, while remaining relatively insensitive to cross-reactivity between reaction components. This review will focus on the Targeted Genotyping System and how this technology was adapted to enable comprehensive analysis of drug-metabolizing enzyme and transporter gene polymorphisms.
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Affiliation(s)
- Carmen Dumaual
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
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8
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Landi S, Gemignani F, Neri M, Barale R, Bonassi S, Bottari F, Canessa PA, Canzian F, Ceppi M, Filiberti R, Ivaldi GP, Mencoboni M, Scaruffi P, Tonini GP, Mutti L, Puntoni R. Polymorphisms of glutathione-S-transferase M1 and manganese superoxide dismutase are associated with the risk of malignant pleural mesothelioma. Int J Cancer 2007; 120:2739-43. [PMID: 17290392 DOI: 10.1002/ijc.22590] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Individual response to oxidative stress, due to exposure to asbestos fibres plays a significant role in the malignant pleural mesothelioma (MPM) etiology. The differential impact on MPM risk of polymorphic alleles of glutathione-S-transferases (GSTs) and manganese superoxide dismutase (MnSOD/SOD2) genes involved in the defence against oxidative damage has been investigated. Ninety cases of MPM and 395 controls were genotyped using the arrayed-primer extension technique. Logistic regression analysis was applied to assess the predictive role of single nucleotide polymorphisms (SNPs) potentially involved in MPM carcinogenesis after adjustment for potential confounders. An increased risk of MPM was found in subjects bearing a GSTM1 null allele (OR = 1.69, 95% CI = 1.04-2.74; p = 0.034), and in those with the Ala/Ala genotypes at codon 16 within MnSOD (OR = 3.07, 95% CI = 1.55-6.05; p = 0.001). A stronger effect of MnSOD was observed among patients without a clear exposure to asbestos fibres. No effect was found for GSTA2, GSTA4, GSTM3, GSTP1 and GSTT1 genes. These findings, if replicated, contribute substantial evidence to the hypothesis that oxidative stress and cellular antireactive oxygen species systems are involved in the pathogenesis and in the natural history of MPM.
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Affiliation(s)
- Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
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9
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Landi S, Gemignani F, Canzian F, Gaborieau V, Barale R, Landi D, Szeszenia-Dabrowska N, Zaridze D, Lissowska J, Rudnai P, Fabianova E, Mates D, Foretova L, Janout V, Bencko V, Gioia-Patricola L, Hall J, Boffetta P, Hung RJ, Brennan P. DNA repair and cell cycle control genes and the risk of young-onset lung cancer. Cancer Res 2006; 66:11062-9. [PMID: 17108146 DOI: 10.1158/0008-5472.can-06-1039] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Exposure to tobacco smoke and to mutagenic xenobiotics can cause various types of DNA damage in lung cells, which, if not corrected by DNA repair systems, may lead to deregulation of the cell cycle and, ultimately, to cancer. Genetic variation could thus be an important factor in determining susceptibility to tobacco-induced lung cancer with genetic susceptibility playing a larger role in young-onset cases compared with that in the general population. We have therefore studied 102 single-nucleotide polymorphisms (SNP) in 34 key DNA repair and cell cycle control genes in 299 lung cancer cases diagnosed before the age of 50 years and 317 controls from six countries of Central and Eastern Europe. We have found no association of lung cancer risk with polymorphisms in genes related to cell cycle control, single-strand/double-strand break repair, or base excision repair. Significant associations (P < 0.05) were found with polymorphisms in genes involved in DNA damage sensing (ATM) and, interestingly, in four genes encoding proteins involved in mismatch repair (LIG1, LIG3, MLH1, and MSH6). The strongest associations were observed with heterozygote carriers of LIG1 -7C>T [odds ratio (OR), 1.73; 95% confidence interval (95% CI), 1.13-2.64] and homozygote carriers of LIG3 rs1052536 (OR, 2.05; 95% CI, 1.25-3.38). Consideration of the relatively large number of markers assessed diminishes the significance of these findings; thus, these SNPs should be considered promising candidates for further investigation in other independent populations.
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Affiliation(s)
- Stefano Landi
- Dip. Biologia-Genetics, University of Pisa, Pisa, Italy
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10
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Stankov K, Landi S, Gioia-Patricola L, Bonora E, Volante M, Papotti M, Romeo G. GSTT1 and M1 polymorphisms in Hürthle thyroid cancer patients. Cancer Lett 2006; 240:76-82. [PMID: 16427734 DOI: 10.1016/j.canlet.2005.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Revised: 08/25/2005] [Accepted: 08/31/2005] [Indexed: 10/25/2022]
Abstract
Glutathione S-transferases (GST) are an important part of cell defense against numerous genotoxic compounds and ROS. In order to test the possibility of association between the GSTT1 and M1 null allele variant, and the risk of TCO (thyroid carcinoma with cell oxyphilia), a case-control study was carried out. The rationale for our study was that according to the important roles of GST enzymes in cells and association of GST null genotypes with many types of tumors, inactivating polymorphisms may be genetic susceptibility factors in the etiology of oxyphilic thyroid tumors characterized by mitochondrial dysfunction, increased ROS production and resistance to chemio- and radio-therapy. We found the frequency of GSTT1 null genotype of 19.2% in cases and 15.7% in controls, with an adjusted odds ratio (OR) of 1.4 (95% confidence interval (CI), 0.70-2.81), and a frequency of GSTM1 null genotype of 59% in cases with oxyphilic tumors and of 55.6% in controls (OR 1.24; 95% CI, 0.62-2.48), indicating that the GSTT1 and M1 null genotypes do not increase the risk of development of oxyphilic tumors.
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Affiliation(s)
- Karmen Stankov
- Dipartimento di Medicina Interna, Cardioangiologia ed Epatologia, Unita' Operativa di Genetica Medica, Policlinico S. Orsola-Malpighi, Pad. 11, via Massarenti 9, 40138 Bologna, Italy
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11
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Moreno V, Gemignani F, Landi S, Gioia-Patricola L, Chabrier A, Blanco I, González S, Guino E, Capellà G, Canzian F. Polymorphisms in genes of nucleotide and base excision repair: risk and prognosis of colorectal cancer. Clin Cancer Res 2006; 12:2101-8. [PMID: 16609022 DOI: 10.1158/1078-0432.ccr-05-1363] [Citation(s) in RCA: 194] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVES We have undertaken a comprehensive study of common polymorphisms in genes of DNA repair, exploring both the risk of developing colorectal cancer and the prognosis of patients. METHODS Subjects from a case-control study (377 cases and 329 controls) designed to assess gene-environment interactions were genotyped by use of an oligonucleotide microarray and the arrayed primer extension technique. Twenty-eight single nucleotide polymorphisms in 15 DNA repair genes were included. The candidate genes belong to different DNA repair pathways: base excision repair (OGG1, LIG3, APEX, POLB, XRCC1, PCNA, and MUTYH), nucleotide excision repair (ERCC1, ERCC2, ERCC4, and ERCC5), double-strand breaks repair (XRCC2, XRCC3, and XRCC9), and reversion repair (MGMT) genes. RESULTS Polymorphism OGG1 S326C was associated with an increased risk of colorectal cancer [odds ratio (OR), 2.3; 95% confidence interval (95% CI), 1.1-5.0], the risk being higher in younger individuals. A haplotype of ERCC1 was associated with increased risk (OR, 2.3; 95% CI, 1.0-5.3). POLB P242R was also associated with decreased risk (OR, 0.23; 95% CI, 0.05-0.99), although the number of variant allele carriers was low. In the univariate analysis, adjusted for age, sex, and Dukes' stage, three polymorphisms were significantly associated with better prognosis: XRCC1 R399Q [hazard ratio (HR), 0.38; 95% CI, 0.17-0.85], XRCC3 T141M (HR, 0.66; 95% CI, 0.45-0.97), and MGMT L84F (HR, 0.14; 95% CI, 0.02-0.99). ERCC1 19007T>C was associated with worse prognosis (HR, 1.51; 95% CI, 1.01-2.27). In a multivariate analysis, only XRCC1 R399Q and ERCC1 19007T>C remained significant. These associations were stronger among patients receiving adjuvant chemotherapy. CONCLUSIONS Although the overall effect of DNA repair genes in colorectal cancer etiology seems limited, their influence in the response to chemotherapy and prognosis may be more relevant. This knowledge may help to clarify the utility of specific adjuvant treatments according to the individual genetic background.
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Affiliation(s)
- Victor Moreno
- Institut d'Investigació Biomèdica de Bellvitge, Institut Catala d'Oncologia, Hospitalet, Barcelona, Spain
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12
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Edvardsen H, Irene Grenaker Alnaes G, Tsalenko A, Mulcahy T, Yuryev A, Lindersson M, Lien S, Omholt S, Syvänen AC, Børresen-Dale AL, Kristensen VN. Experimental validation of data mined single nucleotide polymorphisms from several databases and consecutive dbSNP builds. Pharmacogenet Genomics 2006; 16:207-17. [PMID: 16495780 DOI: 10.1097/01.fpc.0000194422.12770.fb] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Rapid development in the annotation of human genetic variation has increased the numbers of single nucleotide polymorphisms (SNPs) in candidate genes by several orders of magnitude. The selection of both useful target SNPs for disease-gene association studies and SNPs associated with the treatment response is therefore an increasingly challenging task. We describe a workflow for selecting SNPs based on their putative function and frequency in candidate genes extracted from PubMed resources. The annotation of each SNP and its frequency in a Caucasian population was assessed in several databases. Approximately 4000 SNPs were identified from an initial 233 candidate genes. In a case study, we performed actual genotyping of 1030 of these SNPs in 213 genes and obtained 710 successfully genotyped SNPs. Using the flow-chart outlined here, only 87 SNPs were monomorphic (approximately 12%). This study reports the frequency of SNPs in a Caucasian population, selected in silico, using a candidate gene approach and validated by actually genotyping 193 individuals. The selected genotypes represent a valuable set of verified candidate SNPs for pharmacogenetic studies in Caucasian populations.
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Affiliation(s)
- Hege Edvardsen
- Department of Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Faculty Division of the University of Oslo, Oslo, Norway.
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13
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Zienolddiny S, Campa D, Lind H, Ryberg D, Skaug V, Stangeland L, Phillips DH, Canzian F, Haugen A. Polymorphisms of DNA repair genes and risk of non-small cell lung cancer. Carcinogenesis 2005; 27:560-7. [PMID: 16195237 DOI: 10.1093/carcin/bgi232] [Citation(s) in RCA: 302] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lung cancer is a leading cause of cancer mortality with an inter-individual difference in susceptibility to the disease. The inheritance of low-efficiency genotypes involved in DNA repair and replication may contribute to the difference in susceptibility. We investigated 44 single nucleotide polymorphisms (SNPs) in 20 DNA repair genes including nucleotide excision repair (NER) genes XPA, ERCC1, ERCC2/XPD, ERCC4/XPF and ERCC5/XPG; base excision repair (BER) genes APE1/APEX, OGG1, MPG, XRCC1, PCNA, POLB, POLiota, LIG3 and EXO1; double-strand break repair (DSB-R) genes XRCC2, XRCC3, XRCC9, NBS1 and ATR; and direct damage reversal (DR) gene MGMT/AGT. The study included 343 non-small cell lung cancer (NSCLC) cases and 413 controls from Norwegian general population. Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G>A), ERCC2/XPD (Lys751Gln) and ERCC5/XPD (His46His); the BER genes APE1/APEX (Ile64Val), OGG1 (Ser326Cys), PCNA (1876A>G) and XRCC1 (Arg194Trp, Arg280His, Arg399Gln); and the DSB-R genes ATR (Thr211Met), NBS1 (Glu185Gln), XRCC2 (Arg188His) and XRCC9 (Thr297Ile) modulate NSCLC risk. The level of polycyclic aromatic hydrocarbon-DNA (PAH-DNA) adducts in normal lung tissue from 211 patients was analysed. The variant alleles of XRCC1(Arg280His), XRCC1 (Arg399Gln), ERCC1(G8092T), ERCC5(His46His) and MGMT/AGT(Lys178Arg) were more frequent in patients with PAH-DNA adduct levels lower than the mean whereas the XRCC1(Arg194Trp) variant was more frequent in cases with higher adduct levels than the mean.
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Affiliation(s)
- Shanbeh Zienolddiny
- Department of Toxicology, National Institute of Occupational Health, Oslo, Norway
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14
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Landi S, Gemignani F, Monnier S, Canzian F. A database of single-nucleotide polymorphisms and a genotyping microarray for genetic epidemiology of lung cancer. Exp Lung Res 2005; 31:223-58. [PMID: 15824023 DOI: 10.1080/01902140490495624] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The authors set up a database of 105 genes potentially related to lung cancer susceptibility and 464 of their polymorphisms. The database is based on extensive literature searches, and includes genes likely to influence the internal dose of genotoxic compounds that reach the lungs, following exposure to environmental insults, such as tobacco smoke. The authors selected a subset of 250 single-nucleotide polymorphisms with appreciable frequency in at least one major ethnic group and/or a clear functional role, which represent the best candidates as lung cancer risk factors. They developed a microarray for genotyping these polymorphisms, based on arrayed primer extension (APEX).
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Affiliation(s)
- Stefano Landi
- Dipartimento di Scienze dell'Uomo e dell' Ambiente, Genome Research Group, University of Pisa, Pisa, Italy
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15
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Landi S, Gemignani F, Moreno V, Gioia-Patricola L, Chabrier A, Guino E, Navarro M, de Oca J, Capellà G, Canzian F. A comprehensive analysis of phase I and phase II metabolism gene polymorphisms and risk of colorectal cancer. Pharmacogenet Genomics 2005; 15:535-46. [PMID: 16006997 DOI: 10.1097/01.fpc.0000165904.48994.3d] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
OBJECTIVES Sporadic colorectal cancer (CRC) is considered a multifactorial disease where multiple exposures interact with the individual genetic background resulting in risk modulation. We performed an association study aimed to investigate the role of single nucleotide polymorphisms (SNPs) within genes of phase I (CYP1A1, CYP1A2, CYP1B1, CYP2A6, CYP2D6, CYP2E1, CYP2C9, CYP2C19, CYP3A4, ADH2, EPHX1) and phase II of the xenobiotic metabolism (ALDH2, COMT, GSTA2, GSTA4, GSTM1, GSTM3, GSTP1, GSTT2, MTHFR, NAT1, NAT2, NQO1, MnSOD2, SULT1A1, TPMT). METHODS We genotyped 377 cases and 326 controls, by use of an oligonucleotide micro-array and the arrayed primer extension technique (APEX). RESULTS N-acetyl-transferase 1 'rapid' phenotype and CYP1A2 -164C>A carriers were associated with increased risk of CRC, confirming data reported in previous studies. Interestingly, homozygotes for allele 48G within CYP1B1, a variant with an increased activity towards several substrates including sex hormones, were at increased risk (OR=2.81, 95% CI 1.32-5.99). Moreover, CYP1A1 SNPs T461N and -1738A>C were associated with a reduced risk of cancer (OR=0.52; 95% CI 0.31-0.88 and OR=0.69, 95% CI 0.50-0.94 for carriers, respectively). CONCLUSIONS The present data suggest a role for CYP1B1 and CYP1A1 as new candidate genes in the etiology of CRC and confirm the carcinogenic role of aromatic amines metabolism for colorectum.
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Affiliation(s)
- Stefano Landi
- Genetica, Dip. Scienze Uomo e Ambiente, University of Pisa, Italy
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Gemignani F, Landi S, Moreno V, Gioia-Patricola L, Chabrier A, Guino E, Navarro M, Cambray M, Capellà G, Canzian F. Polymorphisms of the Dopamine Receptor Gene DRD2 and Colorectal Cancer Risk. Cancer Epidemiol Biomarkers Prev 2005; 14:1633-8. [PMID: 16030094 DOI: 10.1158/1055-9965.epi-05-0057] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Sporadic colorectal cancer is considered a multifactorial disease in which multiple exposures interact with the individual genetic background resulting in risk modulation. Recent experimental data suggest a role of dopamine and dopamine receptors in the control of proliferation of the cells of colon and gastrointestinal tract. To investigate whether polymorphisms within dopamine receptors genes could have a role in modulating the risk of sporadic colorectal cancer, we did a case-control association study and genotyped 370 cases and 327 controls for seven single-nucleotide polymorphisms (SNP) of DRD2 (-141Cdel, 957T>C, TaqIB, TaqIA, 1412A>G, S311C, and 3208G>T) by a microarray-based technique. Three SNPs within DRD2 were associated with colorectal cancer, with a maximum odds ratio of 2.28 (95% confidence interval, 1.38-3.76) for carriers of the functional SNP -141Cdel. The haplotype which includes -141Cdel, together with the variants 957C and 1412G, shows an odds ratio of 2.86 (95% confidence interval, 1.58-5.18), as compared with the most frequent haplotype. The SNPs within DRD2 associated with colorectal cancer are known to be related to reduced levels of D2 dopamine receptor. Thus, our data point to a possible role of dopamine receptor DRD2 in modulating the risk of colorectal cancer. Future studies on dopamine receptor-mediated signal transduction may provide new insight into the mechanisms of colorectal cancer and suggest new therapeutic strategies.
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Abstract
The epidemiologic approach enables the systematic evaluation of potential improvements in the safety and efficacy of drug treatment which might result from targeting treatment on the basis of genomic information. The main epidemiologic designs are the randomized control trial, the cohort study, and the case-control study, and derivatives of these proposed for investigating gene-environment interactions. However, no one design is ideal for every situation, and methodological issues, notably selection bias, information bias, confounding and chance, all play a part in determining which study design is best for a given situation. There is also a need to employ a range of different designs to establish a portfolio of evidence about specific gene-drug interactions. In view of the complexity of gene-drug interactions, pooling of data across studies is likely to be needed in order to have adequate statistical power to test hypotheses. We suggest that there may be opportunities (i) to exploit samples from trials already completed to investigate possible gene-drug interactions; (ii) to consider the use of the case-only design nested within randomized controlled trials as a possible means of reducing genotyping costs when dichotomous outcomes are being investigated; and (iii) to make use of population-based disease registries that can be linked with tissue samples, treatment information and death records, to investigate gene-treatment interactions in survival.
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Affiliation(s)
- Julian Little
- Department of Epidemiology and Community Medicine, University of Ottawa, 451 Smyth Rd, Ottawa, Ontario K1H 8M5, Canada.
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de Castro F, Morón FJ, Montoro L, Galán JJ, Hernández DP, Padilla ESC, Ramírez-Lorca R, Real LM, Ruiz A. Human controlled ovarian hyperstimulation outcome is a polygenic trait. ACTA ACUST UNITED AC 2004; 14:285-93. [PMID: 15115914 DOI: 10.1097/00008571-200405000-00003] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
This study aimed to evaluate the association between follicle-stimulating hormone (FSH) hormone efficacy and FSHR, CYP19, ESR1 and ESR2 genes using single nucleotide polymorphism analyses. One hundred and seventy women with conserved ovarian function undergoing controlled ovarian stimulation (COS) with daily exogenous recombinant FSH administration. Women were categorized as poor responders to FSH (three or less ovarian follicles observed at the end of cycle) or normal responders (more than three follicles). The outcome is the number of normal/poor responders as defined by the number of follicles obtained during COS. The DNA markers studied are located in genes related to the FSH mechanism of action (FSH receptor, CYP19 aromatase and oestrogen receptors alpha and beta genes). We conducted an association study between the COS outcome and selected DNA markers using two-point and multi-locus genetic association studies. Genotype pattern tracking in extreme phenotypes and multi-locus analysis using Sumstat and PM algorithms provided significant evidences of genetic interaction between FSHR, ESR1 and ESR2 markers in relation to COS outcome (P = 0.0015). Our results support the hypothesis that a discrete set of genes, related to the FSH hormone mechanism of action, controls the ovarian response to FSH in humans. An oligogenic model including specific FSHR, ESR1 and ESR2 genotype patterns may partially explain the poor response to FSH hormone during controlled ovarian stimulation treatments. The existence of genetic heterogeneity is also suspected.
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Affiliation(s)
- Francisco de Castro
- Unidad de Reproducción Humana Asistida, Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Madrid, Allat Médica, Madrid and Departamento de Genómica Estructural. Neocodex, Sevilla, Spain
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