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Menashe I, Figueroa JD, Garcia-Closas M, Chatterjee N, Malats N, Picornell A, Maeder D, Yang Q, Prokunina-Olsson L, Wang Z, Real FX, Jacobs KB, Baris D, Thun M, Albanes D, Purdue MP, Kogevinas M, Hutchinson A, Fu YP, Tang W, Burdette L, Tardón A, Serra C, Carrato A, García-Closas R, Lloreta J, Johnson A, Schwenn M, Schned A, Andriole G, Black A, Jacobs EJ, Diver RW, Gapstur SM, Weinstein SJ, Virtamo J, Caporaso NE, Landi MT, Fraumeni JF, Chanock SJ, Silverman DT, Rothman N. Large-scale pathway-based analysis of bladder cancer genome-wide association data from five studies of European background. PLoS One 2012; 7:e29396. [PMID: 22238607 PMCID: PMC3251580 DOI: 10.1371/journal.pone.0029396] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 11/28/2011] [Indexed: 12/14/2022] Open
Abstract
Pathway analysis of genome-wide association studies (GWAS) offer a unique opportunity to collectively evaluate genetic variants with effects that are too small to be detected individually. We applied a pathway analysis to a bladder cancer GWAS containing data from 3,532 cases and 5,120 controls of European background (n = 5 studies). Thirteen hundred and ninety-nine pathways were drawn from five publicly available resources (Biocarta, Kegg, NCI-PID, HumanCyc, and Reactome), and we constructed 22 additional candidate pathways previously hypothesized to be related to bladder cancer. In total, 1421 pathways, 5647 genes and ∼90,000 SNPs were included in our study. Logistic regression model adjusting for age, sex, study, DNA source, and smoking status was used to assess the marginal trend effect of SNPs on bladder cancer risk. Two complementary pathway-based methods (gene-set enrichment analysis [GSEA], and adapted rank-truncated product [ARTP]) were used to assess the enrichment of association signals within each pathway. Eighteen pathways were detected by either GSEA or ARTP at P≤0.01. To minimize false positives, we used the I(2) statistic to identify SNPs displaying heterogeneous effects across the five studies. After removing these SNPs, seven pathways ('Aromatic amine metabolism' [P(GSEA) = 0.0100, P(ARTP) = 0.0020], 'NAD biosynthesis' [P(GSEA) = 0.0018, P(ARTP) = 0.0086], 'NAD salvage' [P(ARTP) = 0.0068], 'Clathrin derived vesicle budding' [P(ARTP) = 0.0018], 'Lysosome vesicle biogenesis' [P(GSEA) = 0.0023, P(ARTP)<0.00012], 'Retrograde neurotrophin signaling' [P(GSEA) = 0.00840], and 'Mitotic metaphase/anaphase transition' [P(GSEA) = 0.0040]) remained. These pathways seem to belong to three fundamental cellular processes (metabolic detoxification, mitosis, and clathrin-mediated vesicles). Identification of the aromatic amine metabolism pathway provides support for the ability of this approach to identify pathways with established relevance to bladder carcinogenesis.
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Affiliation(s)
- Idan Menashe
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America.
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Jin W, Xu S, Wang H, Yu Y, Shen Y, Wu B, Jin L. Genome-wide detection of natural selection in African Americans pre- and post-admixture. Genome Res 2011; 22:519-27. [PMID: 22128132 DOI: 10.1101/gr.124784.111] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
It is particularly meaningful to investigate natural selection in African Americans (AfA) due to the high mortality their African ancestry has experienced in history. In this study, we examined 491,526 autosomal single nucleotide polymorphisms (SNPs) genotyped in 5210 individuals and conducted a genome-wide search for selection signals in 1890 AfA. Several genomic regions showing an excess of African or European ancestry, which were considered the footprints of selection since population admixture, were detected based on a commonly used approach. However, we also developed a new strategy to detect natural selection both pre- and post-admixture by reconstructing an ancestral African population (AAF) from inferred African components of ancestry in AfA and comparing it with indigenous African populations (IAF). Interestingly, many selection-candidate genes identified by the new approach were associated with AfA-specific high-risk diseases such as prostate cancer and hypertension, suggesting an important role these disease-related genes might have played in adapting to a new environment. CD36 and HBB, whose mutations confer a degree of protection against malaria, were also located in the highly differentiated regions between AAF and IAF. Further analysis showed that the frequencies of alleles protecting against malaria in AAF were lower than those in IAF, which is consistent with the relaxed selection pressure of malaria in the New World. There is no overlap between the top candidate genes detected by the two approaches, indicating the different environmental pressures AfA experienced pre- and post-population admixture. We suggest that the new approach is reasonably powerful and can also be applied to other admixed populations such as Latinos and Uyghurs.
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Affiliation(s)
- Wenfei Jin
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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154
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Qiao L, Feng Y. Genetic variations of prostate stem cell antigen (PSCA) contribute to the risk of gastric cancer for Eastern Asians: a meta-analysis based on 16792 individuals. Gene 2011; 493:83-91. [PMID: 22155405 DOI: 10.1016/j.gene.2011.11.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 11/09/2011] [Accepted: 11/10/2011] [Indexed: 12/14/2022]
Abstract
The associations between polymorphisms of prostate stem cell antigen (PSCA-rs2294008C>T and -rs2976392G>A) and gastric cancer (GC) risk for Eastern Asians have been commonly studied, but the results were conflicting. The aim of the present study was to further assess the associations by the method of meta-analysis. The databases of Medline, Embase and CNKI (up to May 25th, 2011) were retrieved to identify eligible case-control studies. Odds ratio (OR) and 95% confidence interval (95%CI) were used to present the strength of the associations. In total, eight case-control studies in seven articles with 16792 individuals (9738 cases of GC and 7054 controls) were included in this meta-analysis. Through quantitative analyses, we found that T allele of rs2294008C>T and A allele of rs2976392G>A were significantly associated with increased GC risk [rs2294008C>T: OR (95%CI)=1.31 (1.22-1.42), P(z-test)<0.001, P(heterogeneity)=0.166 for TT vs. C carriers; rs2976392G>A: OR (95%CI)=1.36(1.24-1.50), P(z-test)=0.015, P(heterogeneity)=0.111 for AA vs. G carriers]. The results of subgroup analyses (according to histopathology, countries and sources of controls) indicated that T allele of rs2294008C>T and A allele rs2976392G>A were associated with increased risk of both intestinal- and diffuse-type GC, and associated with increased risk of GC for Chinese, Japanese, Koreans, PCC and HCC/PHCC. Furthermore, T allele of rs2294008C>T was also associated with increased risk of cardia and non-cardia GC, and associated with increased risk of GC for males and females. Besides those, this meta-analysis also indicated that the interactions between T allele of rs2294008C>T and A allele of rs2976392G>A was associated with increased risk of GC (A-T vs. G-T: OR=1.16, 95%CI=1.06-1.27, P(z-test)=0.001, P(heterogeneity)=0.835). Although modest limitations and potential bias cannot be eliminated, this meta-analysis suggests that PSCA -rs2294008C>T and -rs2976392G>A are potential factors of GC development for Eastern Asians, and future work may incorporate these findings and evaluate these variants as potential markers for screening and early diagnosis of GC.
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Affiliation(s)
- Lei Qiao
- Department of General Surgery, Shengjing Hospital of China Medical University, He Ping district, Shen Yang City, Liang Ning Province 110004, PR China
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155
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Rafnar T, Vermeulen SH, Sulem P, Thorleifsson G, Aben KK, Witjes JA, Grotenhuis AJ, Verhaegh GW, Hulsbergen-van de Kaa CA, Besenbacher S, Gudbjartsson D, Stacey SN, Gudmundsson J, Johannsdottir H, Bjarnason H, Zanon C, Helgadottir H, Jonasson JG, Tryggvadottir L, Jonsson E, Geirsson G, Nikulasson S, Petursdottir V, Bishop DT, Chung-Sak S, Choudhury A, Elliott F, Barrett JH, Knowles MA, de Verdier PJ, Ryk C, Lindblom A, Rudnai P, Gurzau E, Koppova K, Vineis P, Polidoro S, Guarrera S, Sacerdote C, Panadero A, Sanz-Velez JI, Sanchez M, Valdivia G, Garcia-Prats MD, Hengstler JG, Selinski S, Gerullis H, Ovsiannikov D, Khezri A, Aminsharifi A, Malekzadeh M, van den Berg LH, Ophoff RA, Veldink JH, Zeegers MP, Kellen E, Fostinelli J, Andreoli D, Arici C, Porru S, Buntinx F, Ghaderi A, Golka K, Mayordomo JI, Matullo G, Kumar R, Steineck G, Kiltie AE, Kong A, Thorsteinsdottir U, Stefansson K, Kiemeney LA. European genome-wide association study identifies SLC14A1 as a new urinary bladder cancer susceptibility gene. Hum Mol Genet 2011; 20:4268-81. [PMID: 21750109 PMCID: PMC3188988 DOI: 10.1093/hmg/ddr303] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 07/07/2011] [Indexed: 11/14/2022] Open
Abstract
Three genome-wide association studies in Europe and the USA have reported eight urinary bladder cancer (UBC) susceptibility loci. Using extended case and control series and 1000 Genomes imputations of 5 340 737 single-nucleotide polymorphisms (SNPs), we searched for additional loci in the European GWAS. The discovery sample set consisted of 1631 cases and 3822 controls from the Netherlands and 603 cases and 37 781 controls from Iceland. For follow-up, we used 3790 cases and 7507 controls from 13 sample sets of European and Iranian ancestry. Based on the discovery analysis, we followed up signals in the urea transporter (UT) gene SLC14A. The strongest signal at this locus was represented by a SNP in intron 3, rs17674580, that reached genome-wide significance in the overall analysis of the discovery and follow-up groups: odds ratio = 1.17, P = 7.6 × 10(-11). SLC14A1 codes for UTs that define the Kidd blood group and are crucial for the maintenance of a constant urea concentration gradient in the renal medulla and, through this, the kidney's ability to concentrate urine. It is speculated that rs17674580, or other sequence variants in LD with it, indirectly modifies UBC risk by affecting urine production. If confirmed, this would support the 'urogenous contact hypothesis' that urine production and voiding frequency modify the risk of UBC.
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Affiliation(s)
| | - Sita H. Vermeulen
- Department of Epidemiology, Biostatistics and HTA
- Department of Genetics
| | - Patrick Sulem
- deCODE Genetics, Sturlugata 8, 101 Reykjavik, Iceland
| | | | - Katja K. Aben
- Department of Epidemiology, Biostatistics and HTA
- Integraal Kankercentrum Nederland, PO Box 1281, 6501 BG Nijmegen, The Netherlands
| | | | | | | | | | - Soren Besenbacher
- Bioinformatics Research Center, Aarhus University, 8000 Aarhus C, Denmark
| | | | | | | | | | | | - Carlo Zanon
- deCODE Genetics, Sturlugata 8, 101 Reykjavik, Iceland
| | | | - Jon Gunnlaugur Jonasson
- Icelandic Cancer Registry, Skogarhlid 8, 105 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Laufey Tryggvadottir
- Icelandic Cancer Registry, Skogarhlid 8, 105 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | | | | | - Sigfus Nikulasson
- Department of Pathology, Landspitali-University Hospital, 101 Reykjavik, Iceland
| | - Vigdis Petursdottir
- Department of Pathology, Landspitali-University Hospital, 101 Reykjavik, Iceland
| | | | - Sei Chung-Sak
- Section of Experimental Oncology, Leeds Institute of Molecular Medicine, St James's University Hospital, Beckett Street, LS9 7TF Leeds, UK
| | - Ananya Choudhury
- Christie Hospital National Health Service Foundation Trust, Wilmslow Road, M20 4BX Manchester, UK
| | | | | | - Margaret A. Knowles
- Section of Experimental Oncology, Leeds Institute of Molecular Medicine, St James's University Hospital, Beckett Street, LS9 7TF Leeds, UK
| | | | - Charlotta Ryk
- Urology Laboratory M1:02, Department of Molecular Medicine and Surgery and
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery L1:00, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Peter Rudnai
- National Institute of Environmental Health, Josef Fodor Nation Center of Public Health, Nagyvarad ter 2, H-1450 Budapest, Hungary
| | - Eugene Gurzau
- Environmental Health Centre, Department of Health, Cetatti 23 A, 3400 Cluj-Napoca, Romania
| | - Kvetoslava Koppova
- State Health Institute, Cesta K. Nemocnici 1, SK-975 56 Banska Bystrica, Slovakia
| | - Paolo Vineis
- Human Genetics Foundation—HuGeF, Via Nizza 52, 10126 Torino, Italy
- Department of Epidemiology and Public Health, Imperial College, Norfolk Place W2 1PG, London, UK
| | - Silvia Polidoro
- Human Genetics Foundation—HuGeF, Via Nizza 52, 10126 Torino, Italy
| | | | - Carlotta Sacerdote
- Human Genetics Foundation—HuGeF, Via Nizza 52, 10126 Torino, Italy
- Centre for Cancer Epidemiology and Prevention (CPO Piemonte), Via Santena 19, 10126 Torino, Italy
| | - Angeles Panadero
- Ciudad de Coria Hospital, Avenida Cervantes 75, 10800 Coria, Spain
| | - José I. Sanz-Velez
- San Jorge University Hospital, Avenida Martínez de Velasco 36, 22004 Huesca, Spain
| | - Manuel Sanchez
- University of Zaragoza, Avenida San Juan Bosco 15, 50009 Zaragoza, Spain
| | - Gabriel Valdivia
- University of Zaragoza, Avenida San Juan Bosco 15, 50009 Zaragoza, Spain
| | | | - Jan G. Hengstler
- Leibniz Research Centre for Working Environment and Human Factors, Ardeystraße 67, D-44139 Dortmund, Germany
| | - Silvia Selinski
- Leibniz Research Centre for Working Environment and Human Factors, Ardeystraße 67, D-44139 Dortmund, Germany
| | - Holger Gerullis
- Department of Urology, Lukasklinik Neuss, Preussenstr. 64, D-41464 Neuss, Germany
| | - Daniel Ovsiannikov
- Department of Urology, St.-Josefs-Hospital Dortmund-Hörde, Wilhelm-Schmidt-Str. 4, D-44263 Dortmund, Germany
| | | | - Alireza Aminsharifi
- Department of Urology, Shiraz University of Medical Sciences, PO Box 71345–3119, Shiraz, Iran
| | | | | | - Roel A. Ophoff
- Department of Medical Genetics, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
- UCLA Center for Neurobehavioral Genetics, 90095-1761 Los Angeles, CA, USA
| | | | - Maurice P. Zeegers
- Department of Complex Genetics, Cluster of Genetics and Cell Biology, Nutrition and Toxicology Research Institute and
- Unit of Genetic Epidemiology, Department of Public Health and Epidemiology, University of Birmingham, B15 2TT Birmingham, UK
| | - Eliane Kellen
- Leuven University Centre for Cancer Prevention, Kapucijnenvoer 33, B3000 Leuven, Belgium
| | - Jacopo Fostinelli
- Section of Occupational Medicine and Industrial Hygiene, Department of Experimental and Applied Medicine, University of Brescia, 1-25125 Brescia, Italy
| | - Daniele Andreoli
- Section of Occupational Medicine and Industrial Hygiene, Department of Experimental and Applied Medicine, University of Brescia, 1-25125 Brescia, Italy
| | - Cecilia Arici
- Section of Occupational Medicine and Industrial Hygiene, Department of Experimental and Applied Medicine, University of Brescia, 1-25125 Brescia, Italy
| | - Stefano Porru
- Section of Occupational Medicine and Industrial Hygiene, Department of Experimental and Applied Medicine, University of Brescia, 1-25125 Brescia, Italy
| | - Frank Buntinx
- Department of General Practice, Maastricht University, 6200 MD, Maastricht, The Netherlands
- Department of General Practice, Catholic University of Leuven, Kapucijnenvoer 33, B3000 Leuven, Belgium
| | | | - Klaus Golka
- Leibniz Research Centre for Working Environment and Human Factors, Ardeystraße 67, D-44139 Dortmund, Germany
| | - José I. Mayordomo
- University of Zaragoza, Avenida San Juan Bosco 15, 50009 Zaragoza, Spain
| | - Giuseppe Matullo
- Human Genetics Foundation—HuGeF, Via Nizza 52, 10126 Torino, Italy
- Department of Genetics, Biology and Biochemistry, University of Torino, Via Santena 19, 10126 Torino, Italy
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Gunnar Steineck
- Division of Clinical Cancer Epidemiology, University of Gothenburg, Sahlgrenska University Hospital, SE - 413 45 Gothenburg, Sweden and
| | - Anne E. Kiltie
- Department of Oncology, Gray Institute for Radiation Oncology and Biology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, OX3 7DQ Oxford, UK
| | | | - Unnur Thorsteinsdottir
- deCODE Genetics, Sturlugata 8, 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Kari Stefansson
- deCODE Genetics, Sturlugata 8, 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Lambertus A. Kiemeney
- Department of Epidemiology, Biostatistics and HTA
- Department of Urology and
- Integraal Kankercentrum Nederland, PO Box 1281, 6501 BG Nijmegen, The Netherlands
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156
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Garcia-Closas M, Ye Y, Rothman N, Figueroa JD, Malats N, Dinney CP, Chatterjee N, Prokunina-Olsson L, Wang Z, Lin J, Real FX, Jacobs KB, Baris D, Thun M, De Vivo I, Albanes D, Purdue MP, Kogevinas M, Kamat AM, Lerner SP, Grossman HB, Gu J, Pu X, Hutchinson A, Fu YP, Burdett L, Yeager M, Tang W, Tardón A, Serra C, Carrato A, García-Closas R, Lloreta J, Johnson A, Schwenn M, Karagas MR, Schned A, Andriole G, Grubb R, Black A, Jacobs EJ, Diver WR, Gapstur SM, Weinstein SJ, Virtamo J, Hunter DJ, Caporaso N, Landi MT, Fraumeni JF, Silverman DT, Chanock SJ, Wu X. A genome-wide association study of bladder cancer identifies a new susceptibility locus within SLC14A1, a urea transporter gene on chromosome 18q12.3. Hum Mol Genet 2011; 20:4282-9. [PMID: 21824976 PMCID: PMC3188994 DOI: 10.1093/hmg/ddr342] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 08/01/2011] [Indexed: 11/13/2022] Open
Abstract
Genome-wide and candidate-gene association studies of bladder cancer have identified 10 susceptibility loci thus far. We conducted a meta-analysis of two previously published genome-wide scans (4501 cases and 6076 controls of European background) and followed up the most significant association signals [17 single nucleotide polymorphisms (SNPs) in 10 genomic regions] in 1382 cases and 2201 controls from four studies. A combined analysis adjusted for study center, age, sex, and smoking status identified a novel susceptibility locus that mapped to a region of 18q12.3, marked by rs7238033 (P = 8.7 × 10(-9); allelic odds ratio 1.20 with 95% CI: 1.13-1.28) and two highly correlated SNPs, rs10775480/rs10853535 (r(2)= 1.00; P = 8.9 × 10(-9); allelic odds ratio 1.16 with 95% CI: 1.10-1.22). The signal localizes to the solute carrier family 14 member 1 gene, SLC14A1, a urea transporter that regulates cellular osmotic pressure. In the kidney, SLC14A1 regulates urine volume and concentration whereas in erythrocytes it determines the Kidd blood groups. Our findings suggest that genetic variation in SLC14A1 could provide new etiological insights into bladder carcinogenesis.
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157
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Wu X, Scelo G, Purdue MP, Rothman N, Johansson M, Ye Y, Wang Z, Zelenika D, Moore LE, Wood CG, Prokhortchouk E, Gaborieau V, Jacobs KB, Chow WH, Toro JR, Zaridze D, Lin J, Lubinski J, Trubicka J, Szeszenia-Dabrowska N, Lissowska J, Rudnai P, Fabianova E, Mates D, Jinga V, Bencko V, Slamova A, Holcatova I, Navratilova M, Janout V, Boffetta P, Colt JS, Davis FG, Schwartz KL, Banks RE, Selby PJ, Harnden P, Berg CD, Hsing AW, Grubb RL, Boeing H, Vineis P, Clavel-Chapelon F, Palli D, Tumino R, Krogh V, Panico S, Duell EJ, Quirós JR, Sanchez MJ, Navarro C, Ardanaz E, Dorronsoro M, Khaw KT, Allen NE, Bueno-de-Mesquita HB, Peeters PHM, Trichopoulos D, Linseisen J, Ljungberg B, Overvad K, Tjønneland A, Romieu I, Riboli E, Stevens VL, Thun MJ, Diver WR, Gapstur SM, Pharoah PD, Easton DF, Albanes D, Virtamo J, Vatten L, Hveem K, Fletcher T, Koppova K, Cussenot O, Cancel-Tassin G, Benhamou S, Hildebrandt MA, Pu X, Foglio M, Lechner D, Hutchinson A, Yeager M, Fraumeni JF, Lathrop M, Skryabin KG, McKay JD, Gu J, Brennan P, Chanock SJ. A genome-wide association study identifies a novel susceptibility locus for renal cell carcinoma on 12p11.23. Hum Mol Genet 2011; 21:456-62. [PMID: 22010048 DOI: 10.1093/hmg/ddr479] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Renal cell carcinoma (RCC) is the most lethal urologic cancer. Only two common susceptibility loci for RCC have been confirmed to date. To identify additional RCC common susceptibility loci, we conducted an independent genome-wide association study (GWAS). We analyzed 533 191 single nucleotide polymorphisms (SNPs) for association with RCC in 894 cases and 1516 controls of European descent recruited from MD Anderson Cancer Center in the primary scan, and validated the top 500 SNPs in silico in 3772 cases and 8505 controls of European descent involved in the only published GWAS of RCC. We identified two common variants in linkage disequilibrium, rs718314 and rs1049380 (r(2) = 0.64, D ' = 0.84), in the inositol 1,4,5-triphosphate receptor, type 2 (ITPR2) gene on 12p11.23 as novel susceptibility loci for RCC (P = 8.89 × 10(-10) and P = 6.07 × 10(-9), respectively, in meta-analysis) with an allelic odds ratio of 1.19 [95% confidence interval (CI): 1.13-1.26] for rs718314 and 1.18 (95% CI: 1.12-1.25) for rs1049380. It has been recently identified that rs718314 in ITPR2 is associated with waist-hip ratio (WHR) phenotype. To our knowledge, this is the first genetic locus associated with both cancer risk and WHR.
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Affiliation(s)
- Xifeng Wu
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.
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158
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Fu YP, Kohaar I, Mumy A, Tang W, Muchmore B, Porter-Gill P, Liu L, Figueroa J, Garcia-Closas M, Baris D, Purdue M, Thun M, Albanes D, Malats N, Real FX, Kogevinas M, Johnson A, Schwenn M, Chanock S, Rothman N, Silverman D, Prokunina-Olsson L. A novel functional variant in 8q24 is associated with regulation of prostate stem cell antigen (PSCA) gene expression and bladder cancer risk. Genome Biol 2011. [DOI: 10.1186/1465-6906-12-s1-p4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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159
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Bhatia G, Patterson N, Pasaniuc B, Zaitlen N, Genovese G, Pollack S, Mallick S, Myers S, Tandon A, Spencer C, Palmer CD, Adeyemo AA, Akylbekova EL, Cupples LA, Divers J, Fornage M, Kao WHL, Lange L, Li M, Musani S, Mychaleckyj JC, Ogunniyi A, Papanicolaou G, Rotimi CN, Rotter JI, Ruczinski I, Salako B, Siscovick DS, Tayo BO, Yang Q, McCarroll S, Sabeti P, Lettre G, De Jager P, Hirschhorn J, Zhu X, Cooper R, Reich D, Wilson JG, Price AL. Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection. Am J Hum Genet 2011; 89:368-81. [PMID: 21907010 DOI: 10.1016/j.ajhg.2011.07.025] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 07/18/2011] [Accepted: 07/29/2011] [Indexed: 12/11/2022] Open
Abstract
The study of recent natural selection in human populations has important applications to human history and medicine. Positive natural selection drives the increase in beneficial alleles and plays a role in explaining diversity across human populations. By discovering traits subject to positive selection, we can better understand the population level response to environmental pressures including infectious disease. Our study examines unusual population differentiation between three large data sets to detect natural selection. The populations examined, African Americans, Nigerians, and Gambians, are genetically close to one another (F(ST) < 0.01 for all pairs), allowing us to detect selection even with moderate changes in allele frequency. We also develop a tree-based method to pinpoint the population in which selection occurred, incorporating information across populations. Our genome-wide significant results corroborate loci previously reported to be under selection in Africans including HBB and CD36. At the HLA locus on chromosome 6, results suggest the existence of multiple, independent targets of population-specific selective pressure. In addition, we report a genome-wide significant (p = 1.36 × 10(-11)) signal of selection in the prostate stem cell antigen (PSCA) gene. The most significantly differentiated marker in our analysis, rs2920283, is highly differentiated in both Africa and East Asia and has prior genome-wide significant associations to bladder and gastric cancers.
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Affiliation(s)
- Gaurav Bhatia
- Harvard- Massachusetts Institute of Technology (MIT) Division of Health, Science and Technology, Cambridge, USA.
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161
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Sala N, Muñoz X, Travier N, Agudo A, Duell EJ, Moreno V, Overvad K, Tjonneland A, Boutron-Ruault MC, Clavel-Chapelon F, Canzian F, Kaaks R, Boeing H, Meidtner K, Trichopoulos A, Tsiotas K, Zylis D, Vineis P, Panico S, Palli D, Krogh V, Tumino R, Lund E, Bueno-de-Mesquita HB, Numans ME, Peeters PHM, Quirós JR, Sánchez MJ, Navarro C, Ardanaz E, Dorronsoro M, Hallmans G, Stenling R, Manjer J, Allen NE, Travis RC, Khaw KT, Jenab M, Offerhaus GJA, Riboli E, González CA. Prostate stem-cell antigen gene is associated with diffuse and intestinal gastric cancer in Caucasians: results from the EPIC-EURGAST study. Int J Cancer 2011; 130:2417-27. [PMID: 21681742 DOI: 10.1002/ijc.26243] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 05/25/2011] [Indexed: 12/20/2022]
Abstract
A genome-wide study performed in a Japanese population identified a strong association between SNP rs2294008 (Met1Thr) in the Prostate Stem Cell Antigen gene (PSCA) and diffuse-type gastric cancer (GC). This association was validated in different Asian populations, and, very recently, a study has been published in Caucasians. In this study, we analyzed the association between PSCA variation and GC risk in Caucasians from the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort. Six tagSNPs covering the PSCA gene region were genotyped in 411 incident gastric adenocarcinoma cases and 1530 matched controls from a nested case-control study in the EPIC cohort. Associations were analyzed by unconditional logistic regression, adjusting for age, sex and country. The T allele of rs2294008 in PSCA was found to be a highly significant risk factor for GC (per allele OR = 1.42, 95% CI: 1.23-1.66, p-value = 6.5 × 10(-6) ), particularly of the noncardia-type (per allele OR = 1.47, 95% CI: 1.19-1.81, p-value = 3 × 10(-4) ). At contrast with previous studies, no significant differences were observed between the diffuse (per allele OR = 1.54, 95% CI: 1.20-1.96, p-value = 5 × 10(-4) ) and the intestinal (per allele OR = 1.52, 95% CI: 1.20-1.93, p-value = 5 × 10(-4) ) GC histological subtypes. Although rs12155758 and rs9297976 were also found associated with GC, this association appeared to be due to linkage disequilibrium with rs2294008. Haplotype analysis did not provide additional information. These results confirm the association between variation in the promoter region of PSCA and GC risk in Caucasians and also indicate that the rs2294008 variant is a similar risk factor for both the diffuse and intestinal-types of GC.
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Affiliation(s)
- Núria Sala
- Translational Research Laboratory, Catalan Institute of Oncology-IDIBELL, Barcelona, Spain.
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162
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Angstadt AY, Motsinger-Reif A, Thomas R, Kisseberth WC, Guillermo Couto C, Duval DL, Nielsen DM, Modiano JF, Breen M. Characterization of canine osteosarcoma by array comparative genomic hybridization and RT-qPCR: signatures of genomic imbalance in canine osteosarcoma parallel the human counterpart. Genes Chromosomes Cancer 2011; 50:859-74. [PMID: 21837709 DOI: 10.1002/gcc.20908] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 06/26/2011] [Indexed: 02/03/2023] Open
Abstract
Osteosarcoma (OS) is the most commonly diagnosed malignant bone tumor in humans and dogs, characterized in both species by extremely complex karyotypes exhibiting high frequencies of genomic imbalance. Evaluation of genomic signatures in human OS using array comparative genomic hybridization (aCGH) has assisted in uncovering genetic mechanisms that result in disease phenotype. Previous low-resolution (10-20 Mb) aCGH analysis of canine OS identified a wide range of recurrent DNA copy number aberrations, indicating extensive genomic instability. In this study, we profiled 123 canine OS tumors by 1 Mb-resolution aCGH to generate a dataset for direct comparison with current data for human OS, concluding that several high frequency aberrations in canine and human OS are orthologous. To ensure complete coverage of gene annotation, we identified the human refseq genes that map to these orthologous aberrant dog regions and found several candidate genes warranting evaluation for OS involvement. Specifically, subsequenct FISH and qRT-PCR analysis of RUNX2, TUSC3, and PTEN indicated that expression levels correlated with genomic copy number status, showcasing RUNX2 as an OS associated gene and TUSC3 as a possible tumor suppressor candidate. Together these data demonstrate the ability of genomic comparative oncology to identify genetic abberations which may be important for OS progression. Large scale screening of genomic imbalance in canine OS further validates the use of the dog as a suitable model for human cancers, supporting the idea that dysregulation discovered in canine cancers will provide an avenue for complementary study in human counterparts.
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Affiliation(s)
- Andrea Y Angstadt
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, USA
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163
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Xing J, Dinney CP, Shete S, Huang M, Hildebrandt MA, Chen Z, Gu J. Comprehensive pathway-based interrogation of genetic variations in the nucleotide excision DNA repair pathway and risk of bladder cancer. Cancer 2011; 118:205-15. [PMID: 21692063 DOI: 10.1002/cncr.26224] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 01/26/2011] [Accepted: 04/04/2011] [Indexed: 11/08/2022]
Abstract
BACKGROUND Growing evidence suggests that single nucleotide polymorphisms (SNPs) in nucleotide excision repair (NER) pathway genes play an important role in bladder cancer etiology. However, only a limited number of genes and variations in this pathway have been evaluated to date. METHODS In this study, the authors applied a comprehensive pathway-based approach to assess the effects of 207 tagging and potentially functional SNPs in 26 NER genes on bladder cancer risk using a large case-control study that included 803 bladder cancer cases and 803 controls. RESULTS In total, 17 SNPs were associated significantly with altered bladder cancer risk (P < .05), of which, 7 SNPs retained noteworthiness after they were assessed with a Bayesian approach for the probability of false discovery. The most noteworthy SNP was reference SNP 11132186 (rs11132186) in the inhibitor of growth family, member 2 (ING2) gene. Compared with the major allele-containing genotypes, the odds ratio was 0.52 (95% confidence interval, 0.32-0.83; P = .005) for the homozygous variant genotype. Three additional ING2 variants also exhibited significant associations with bladder cancer risk. Significant gene-smoking interactions were observed for 3 of the top 17 SNPs. Furthermore, through an exploratory classification and regression tree (CART) analysis, potential gene-gene interactions were identified. CONCLUSIONS In this a large association study of the NER pathway and the risk of bladder cancer, several novel predisposition variants were identified along with potential gene-gene and gene-environment interactions in modulating bladder cancer risk. The results reinforce the importance of a comprehensive, pathway-focused, and tagging SNP-based candidate gene approach to identify low-penetrance cancer susceptibility loci.
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Affiliation(s)
- Jinliang Xing
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center and Department of Cell Biology, Fourth Military Medical University, Xi'an, People's Republic of China
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164
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Joung JY, Lee YS, Park S, Yoon H, Lee SJ, Park WS, Seo HK, Chung J, Kim SY, Hong SH, Kim JS, Lee KH. Haplotype Analysis of Prostate Stem Cell Antigen and Association With Prostate Cancer Risk. J Urol 2011; 185:2112-8. [DOI: 10.1016/j.juro.2011.01.083] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Indexed: 11/16/2022]
Affiliation(s)
- Jae Young Joung
- Center for Prostate Cancer, National Cancer Center, Goyang, Republic of Korea
| | - Yeon-Su Lee
- Functional Genomics Branch, National Cancer Center, Goyang, Republic of Korea
| | - Sohee Park
- Cancer Biostatistics Branch, National Cancer Center, Goyang, Republic of Korea
| | - Hyekyoung Yoon
- Cancer Biostatistics Branch, National Cancer Center, Goyang, Republic of Korea
| | - Sang Jin Lee
- Genitourinary Cancer Branch, National Cancer Center, Goyang, Republic of Korea
| | - Weon Seo Park
- Center for Prostate Cancer, National Cancer Center, Goyang, Republic of Korea
| | - Ho Kyung Seo
- Center for Prostate Cancer, National Cancer Center, Goyang, Republic of Korea
| | - Jinsoo Chung
- Center for Prostate Cancer, National Cancer Center, Goyang, Republic of Korea
| | - Sook-young Kim
- Functional Genomics Branch, National Cancer Center, Goyang, Republic of Korea
| | - Seung-Hyun Hong
- Functional Genomics Branch, National Cancer Center, Goyang, Republic of Korea
| | - Jeong Seon Kim
- Cancer Epidemiology Branch, National Cancer Center, Goyang, Republic of Korea
| | - Kang Hyun Lee
- Center for Prostate Cancer, National Cancer Center, Goyang, Republic of Korea
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165
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Abstract
Bladder cancer comprises a heterogeneous group of tumors, the majority of which are non-muscle-invasive bladder cancer (NMIBC) at initial presentation. Low-risk bladder cancer--defined as pTa low-grade papillary tumors--is the type of NMIBC with the most favorable oncologic outcome. Although the risk of progression is less than 1% in 5 years, almost 15% will recur after 1 year, and 32% after 5 years. A complete transurethral resection, followed by an immediate single postoperative instillation of chemotherapy will reduce the risk of recurrence for the first 2 years. Follow-up cystoscopy is required to detect recurrence; in the vast majority of cases the recurrent tumor is of the same stage and grade as the primary tumor. The first follow-up visit, 3 months after surgery, is the most important in predicting risk of recurrence for the future. Recent developments in profiling urine and cancer tissue make it possible to better predict risk of progression and recurrence. In the future this profiling will play an important role in the timing and the choice of treatment, as well as guiding follow-up procedures.
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Affiliation(s)
- Johannes Falke
- Radboud University Nijmegen Medical Center, Department of Urology (659), PO Box 9101, 6500 HB Nijmegen, The Netherlands.
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166
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Abstract
Bladder cancer is an excellent model for studying genetic susceptibility and gene-environment interaction in cancer etiology. The candidate gene approach found NAT2 slow acetylator and GSTM1-null genotypes to be bladder cancer susceptibility loci and also demonstrated interactions between these two genotypes and smoking in modulating bladder cancer risk. Recent genome-wide association studies identified at least eight novel genetic susceptibility loci for bladder cancer. Genetic determinants of clinical outcomes have been inconclusive. The future directions are to identify more genetic susceptibility loci for bladder cancer risk and outcome through a genome-wide association study approach, identify the causal genes and variants, study the biological mechanisms underlying the association between the causal variants and bladder cancer risk, detect gene-environment interactions and incorporate genetic knowledge into clinically applicable risk prediction models to benefit patients and public health.
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Affiliation(s)
- Jian Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1155 Pressler Street, Houston, TX 77030, USA
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167
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Gu J, Chen M, Shete S, Amos CI, Kamat A, Ye Y, Lin J, Dinney CP, Wu X. A genome-wide association study identifies a locus on chromosome 14q21 as a predictor of leukocyte telomere length and as a marker of susceptibility for bladder cancer. Cancer Prev Res (Phila) 2011; 4:514-21. [PMID: 21460395 DOI: 10.1158/1940-6207.capr-11-0063] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Telomeres play a critical role in maintaining genome integrity. Telomere shortening is associated with the risk of many aging-related diseases. Classic twin studies have shown that genetic components may contribute up to 80% of the heritability of telomere length. In the study we report here that we used a multistage genome-wide association study to identify genetic determinants of telomere length. The mean telomere length in peripheral blood leukocytes was measured by quantitative real-time PCR. We first analyzed 300,000 single-nucleotide polymorphisms (SNPs) in 459 healthy controls, finding 15,120 SNPs associated with telomere length at P < 0.05. We then validated these SNPs in two independent populations comprising 890 and 270 healthy controls, respectively. Four SNPs, including rs398652 on 14q21, were associated with telomere length across all three populations (pooled P values of <10(-5)). The variant alleles of these SNPs were associated with longer telomere length. We then analyzed the association of these SNPs with the risk of bladder cancer in a large case-control study. The variant allele of rs398652 was associated with a significantly reduced risk of bladder cancer (odds ratio = 0.81; 95% confidence interval, 0.67-0.97; P = 0.025), consistent with the correlation of this variant allele with longer telomeres. We then conducted a mediation analysis to examine whether the association between rs398652 and reduced bladder cancer risk is mediated by telomere length, finding that telomere length was a significant mediator of the relationship between rs398652 and bladder cancer (P = 0.013), explaining 14% of the effect. In conclusion, we found that the SNP rs398652 on 14q21 was associated with longer telomere length and a reduced risk of bladder cancer and that a portion of the effect of this SNP on bladder cancer risk was mediated by telomere length.
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Affiliation(s)
- Jian Gu
- Department of Epidemiology, Unit 1340, The University of Texas MD Anderson Cancer Center, 1155 Pressler Blvd, Houston, TX 77030, USA
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168
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Wang M, Chu H, Yan F, Qin C, Li P, Yuan L, Yin C, Xu J, Zhang Z. Chromosome 4p16.3 variant modify bladder cancer risk in a Chinese population. Carcinogenesis 2011; 32:872-5. [PMID: 21459758 DOI: 10.1093/carcin/bgr060] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A recent genome-wide association study identified a common variant (rs798766) on 4p16.3 that confers susceptibility to bladder cancer. The aim of this study was to assess whether rs798766 is associated with risk of bladder cancer in a Chinese population as well. We genotyped this variant using TaqMan technology in a case-control study of 815 histologically confirmed bladder cancer patients and 1141 controls. Normal bladder tissues adjacent to tumors were used to evaluate the functionality of rs798766 using quantitative real-time reverse transcription-polymerase chain reaction. We found that rs798766 CT/TT genotypes were associated with a significantly increased risk of bladder cancer (odds ratio = 1.36, 95% confidence interval = 1.10-1.67), compared with the CC genotype. Furthermore, rs798766 was significantly associated with FGFR3 messenger RNA expression. However, no significant interaction between rs798766 and tobacco smoking on bladder cancer risk was observed (P(multiplicative) = 0.785). Our results suggest that rs798766 on 4p16.3 may contribute to bladder cancer susceptibility in a Chinese population and explains an additional 3.65% of population attributable risk for bladder cancer.
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Affiliation(s)
- Meilin Wang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Nanjing Medical University, Nanjing 210029, China
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169
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Abstract
The number of known mutations in human nuclear genes, underlying or associated with human inherited disease, has now exceeded 100,000 in more than 3700 different genes (Human Gene Mutation Database). However, for a variety of reasons, this figure is likely to represent only a small proportion of the clinically relevant genetic variants that remain to be identified in the human genome (the 'mutome'). With the advent of next-generation sequencing, we are currently witnessing a revolution in medical genetics. In particular, whole-genome sequencing (WGS) has the potential to identify all disease-causing or disease-associated DNA variants in a given individual. Here, we use examples of recent advances in our understanding of mutational/pathogenic mechanisms to guide our thinking about possible locations outwith gene-coding sequences for those disease-causing or disease-associated variants that are likely so often to have been overlooked because of the inadequacy of current mutation screening protocols. Such considerations are important not only for improving mutation-screening strategies but also for enhancing the interpretation of findings derived from genome-wide association studies, whole-exome sequencing and WGS. An improved understanding of the human mutome will not only lead to the development of improved diagnostic testing procedures but should also improve our understanding of human genome biology.
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Affiliation(s)
- J M Chen
- Etablissement Français du Sang (EFS) - Bretagne, Brest, France.
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170
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Golka K, Selinski S, Lehmann ML, Blaszkewicz M, Marchan R, Ickstadt K, Schwender H, Bolt HM, Hengstler JG. Genetic variants in urinary bladder cancer: collective power of the “wimp SNPs”. Arch Toxicol 2011; 85:539-54. [DOI: 10.1007/s00204-011-0676-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 02/09/2011] [Indexed: 02/07/2023]
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171
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Marsit CJ, Koestler DC, Christensen BC, Karagas MR, Houseman EA, Kelsey KT. DNA methylation array analysis identifies profiles of blood-derived DNA methylation associated with bladder cancer. J Clin Oncol 2011; 29:1133-9. [PMID: 21343564 DOI: 10.1200/jco.2010.31.3577] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Epigenetic alterations in tissues targeted for cancer play a causal role in carcinogenesis. Changes in DNA methylation in nontarget tissues, specifically peripheral blood, can also affect risk of malignant disease. We sought to identify specific profiles of DNA methylation in peripheral blood that are associated with bladder cancer risk and therefore serve as an epigenetic marker of disease susceptibility. METHODS We performed genome-wide DNA methylation profiling on participants involved in a population-based incident case-control study of bladder cancer. RESULTS In a training set of 112 cases and 118 controls, we identified a panel of 9 CpG loci whose profile of DNA methylation was significantly associated with bladder cancer in a masked, independent testing series of 111 cases and 119 controls (P < .0001). Membership in three of the most methylated classes was associated with a 5.2-fold increased risk of bladder cancer (95% CI, 2.8 to 9.7), and a model that included the methylation classification, participant age, sex, smoking status, and family history of bladder cancer was a significant predictor of bladder cancer (area under the curve, 0.76; 95% CI, 0.70 to 0.82). CpG loci associated with bladder cancer and aging had neighboring sequences enriched for transcription-factor binding sites related to immune modulation and forkhead family members. CONCLUSION These results indicate that profiles of epigenetic states in blood are associated with risk of bladder cancer and signal the potential utility of epigenetic profiles in peripheral blood as novel markers of susceptibility to this and other malignancies.
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Affiliation(s)
- Carmen J Marsit
- Pathology and Laboratory Medicine, Brown University, Providence, RI 02912, USA.
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172
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Zeng Z, Wu X, Chen F, Yu J, Xue L, Hao Y, Wang Y, Chen M, Sung JJY, Hu P. Polymorphisms in prostate stem cell antigen gene rs2294008 increase gastric cancer risk in Chinese. Mol Carcinog 2011; 50:353-8. [PMID: 21268123 DOI: 10.1002/mc.20718] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 11/02/2010] [Accepted: 11/03/2010] [Indexed: 11/09/2022]
Abstract
A recent genome-wide study identified a strong association between polymorphisms in the prostate stem cell antigen (PSCA) gene and the risk of diffuse-type of gastric cancer in Japanese and Korean population. In this case-control study, we aimed to investigate the possible association between PSCA rs2294008 C/T with clinicopathological features and the prognosis of gastric cancer in a Southern Chinese population. Genotypes of 460 gastric cancer patients and 549 controls were determined by PCR-restriction fragment length polymorphism (PCR-RFLP) and DNA sequencing. We found that individuals with at least one copy of the rs2294008T allele (CT or TT genotype) had an increased risk for gastric cancer compared with CC genotype (OR = 1.42, 95% CI = 1.10-1.82, P = 0.006). Further stratification analyses indicated that the effect of PSCA rs2294008T carriers was noteworthy in intestinal type (OR = 1.55, 95% CI = 1.18-2.04, P = 0.002), poorly differentiated (OR = 1.59, 95% CI = 1.19-2.13, P = 0.002), noncardia (OR = 1.55, 95% CI = 1.17-2.04, P = 0.002) subtypes of gastric cancer. Cox proportional hazards analyses demonstrated that TT genotype (HR = 2.12, 95% CI = 1.22-3.69, P = 0.008) as well as TNM staging were prognostic factors of gastric cancer patients. In conclusion, The T allele of PSCA rs2294008 is associated with increased risk of gastric cancer, especially intestinal type, poorly differentiated, early onset, and noncardia gastric cancer in Chinese population. TNM staging and TT genotype might be involved in the prognosis of gastric cancer patients.
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Affiliation(s)
- Zhirong Zeng
- Department of Gastroenterology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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173
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Grotenhuis AJ, Vermeulen SH, Kiemeney LA. Germline genetic markers for urinary bladder cancer risk, prognosis and treatment response. Future Oncol 2011; 6:1433-60. [PMID: 20919828 DOI: 10.2217/fon.10.109] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
After decades of research using a candidate gene approach, only NAT2 and GSTM1 have consistently been demonstrated to be germline genetic susceptibility markers for urinary bladder cancer (UBC). The recent shift to an agnostic genome-wide association approach led to the identification of several UBC susceptibility loci, and provided valuable leads for new mechanistic insights into UBC carcinogenesis. The markers do not have sufficient discriminatory ability yet to be applied for risk assessment in the population and the question is whether they ever will. Prognostic and predictive studies in UBC are still in their infancy compared with etiologic studies. In the future, focus on a genome-wide association approach possibly using whole-genome sequence data, consortia formation and meta-analyses, and blood and tumor tissue collection, preferably in the context of randomized controlled trials will stimulate well designed and sufficiently powered studies, and thereby enhance the elucidation of genetic prognostic and predictive markers.
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Affiliation(s)
- Anne J Grotenhuis
- Department of Epidemiology, Biostatistics & HTA, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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174
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Hosking FJ, Dobbins SE, Houlston RS. Genome-wide association studies for detecting cancer susceptibility. Br Med Bull 2011; 97:27-46. [PMID: 21247937 DOI: 10.1093/bmb/ldq038] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome-wide association (GWA) studies search for genetic variants, across the entire genome, which display differences in frequencies between cases and controls. Studies in PubMed using the keywords 'genomewide association' and 'cancer' are reported together with selected literature. Since 2007, GWA studies have successfully yielded risk loci for most common cancers. Findings have provided insights into the biological basis of cancer susceptibility implicating previously unsuspected genes in tumourogenesis. The variants identified typically account for only a small proportion of the familial risk of cancer and thus their application for individual risk prediction is poor. Furthermore, the genotyped variants are unlikely to be directly causal and identifying the causal basis is a major challenge. Methodological developments are desirable to fully utilize existing data sets and to enable more complex models of inherited predisposition to be investigated. Annotation of low frequency variation coupled with next-generation sequencing is making the search for rare disease-causing variants a realistic prospect.
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Affiliation(s)
- Fay J Hosking
- Section of Cancer Genetics, Institute of Cancer Research, Surrey, UK
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175
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Swartz MD, Peng B, Reyes-Gibby C, Shete S. Using Ascertainment for Targeted Resequencing to Increase Power to Identify Causal Variants. STATISTICS AND ITS INTERFACE 2011; 4:285-294. [PMID: 22468169 PMCID: PMC3316326 DOI: 10.4310/sii.2011.v4.n3.a3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Researchers continue to use genome-wide association studies (GWAS) to find the genetic markers associated with disease. Recent studies have added to the typical two-stage analysis a third stage that uses targeted resequencing on a randomly selected subset of the cases to detect the causal single-nucleotide polymorphism (SNP). We propose a design for targeted resequencing that increases the power to detect the causal variant. The design features an ascertainment scheme wherein only those cases with the presence of a risk allele are selected for targeted resequencing. We simulated a disease with a single causal SNP to evaluate our method versus a targeted resequencing design using randomly selected individuals. The simulation studies showed that ascertaining individuals for the targeted resequencing can substantially increase the power to detect a causal SNP, without increasing the false-positive rate.
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Affiliation(s)
- M. D. Swartz
- Division of Biostatistics, The University of Texas Health Science Center at Houston (UT Health), School of Public Health, Houston, TX 77030
| | - B. Peng
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
| | - C. Reyes-Gibby
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
| | - S. Shete
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
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176
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Wang M, Bai J, Tan Y, Wang S, Tian Y, Gong W, Zhou Y, Gao Y, Zhou J, Zhang Z. Genetic variant in PSCA predicts survival of diffuse-type gastric cancer in a Chinese population. Int J Cancer 2010; 129:1207-13. [PMID: 21064099 DOI: 10.1002/ijc.25740] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 10/12/2010] [Indexed: 12/21/2022]
Abstract
Recent genome-wide association study (GWAS) has identified that the prostate stem cell antigen (PSCA) rs2294008 is involving in regulating gastric epithelial-cell proliferation, influencing the risk of diffuse-type gastric cancer. We hypothesized that PSCA rs2294008 is also associated with gastric cancer survival. We genotyped PSCA rs2294008 using TaqMan method in 943 patients with surgically resected gastric cancer. Analyses of genotype association with survival outcomes were assessed by the Kaplan-Meier method, Cox proportional hazards models and the log-rank test. There was no significant association between rs2294008 and survival of gastric cancer (log-rank p=0.085 for CT/TT versus CC). However, in the stratification analysis of histology, we found that rs2294008 CT/TT genotypes were associated with significantly improved survival among diffuse-type gastric cancer (log-rank p=0.025, hazard ratio [HR]=0.75, 95% confidence interval [CI]=0.59-0.96), compared to the CC genotype. Moreover, this protective effect was more predominant for diffuse-type gastric cancer patients with tumor size >5 cm and distant metastasis. If validated in further studies, PSCA rs2294008 could be useful marker of survival assessment and individualized clinical therapy for gastric cancer, particularly among the diffuse-type gastric cancer.
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Affiliation(s)
- Meilin Wang
- Department of Molecular and Genetic Toxicology, School of Public Health, Cancer Center, Nanjing Medical University, Nanjing, China
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177
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Cortessis VK, Yuan JM, Van Den Berg D, Jiang X, Gago-Dominguez M, Stern MC, Castelao JE, Xiang YB, Gao YT, Pike MC, Conti DV. Risk of urinary bladder cancer is associated with 8q24 variant rs9642880[T] in multiple racial/ethnic groups: results from the Los Angeles-Shanghai case-control study. Cancer Epidemiol Biomarkers Prev 2010; 19:3150-6. [PMID: 21051319 PMCID: PMC3417222 DOI: 10.1158/1055-9965.epi-10-0763] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Multiple chromosome 8q24 genotypic variants are strongly implicated in several cancers. Recent genome-wide association studies of urinary bladder cancer report risk to be associated with the T allele of rs9642880 on 8q24 among individuals of European descent. METHODS We examined associations between bladder cancer risk and genotypes defined by rs9642880 and each of 8 additional 8q24 variants associated with risk of other cancers, in both high-risk non-Hispanic white and low-risk Chinese participants enrolled in a large population-based case-control study conducted in Los Angeles County and Shanghai. RESULTS We confirmed association of rs9642880 T with bladder cancer risk not only among non-Hispanic whites but also among Chinese participants [overall per-allele relative risk estimate 1.32 (95% CI, 1.16-1.50; P = 0.000024)]. Subgroup analyses suggested that effects of rs9642880 are largely confined to nonsmokers and former smokers, and may be particularly important in the etiology of noninvasive papillary tumors. There was little indication that 8q24 SNPs associated with other cancer types--rs7008482, rs7000448, rs6983561, rs6983267, rs13281615, rs13254738, or rs10090154--are associated with bladder cancer risk. CONCLUSIONS Bladder cancer risk is associated specifically with variation in the discrete 8q24 region containing rs9642880. Factors other than rs9642880 genotypes seem to underlie differences in bladder cancer risk between non-Hispanic whites and Chinese. IMPACT Characterization of functional consequences of genetic variation in the discrete region including rs9642880 is needed to understand biological basis of this bladder cancer-specific 8q24 association in these racial/ethnic groups characterized by both high and low risk of bladder cancer.
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Affiliation(s)
- Victoria K Cortessis
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, 1441 Eastlake Ave, MC-9175, Los Angeles, CA 90089, USA.
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Gu J, Ye Y, Spitz MR, Lin J, Kiemeney LA, Xing J, Hildebrandt MAT, Ki Hong W, Amos CI, Wu X. A genetic variant near the PMAIP1/Noxa gene is associated with increased bleomycin sensitivity. Hum Mol Genet 2010; 20:820-6. [PMID: 21106707 DOI: 10.1093/hmg/ddq509] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mutagen sensitivity, a measurement of chromatid breaks induced by various mutagens in short-term cultures of peripheral blood lymphocytes, is an established risk factor for a number of cancers and is highly heritable. The purpose of this study is to identify genetic predictors of mutagen sensitivity. Therefore, we conducted a multi-stage genome-wide association study. The primary scan analyzed 539,437 autosomal SNPs in 673 healthy individuals, followed by validations in two independent sets of 575 and 259 healthy individuals, respectively. One SNP, rs8093763, on chromosome 18q21 showed significant association with bleomycin (BLM) sensitivity (combined P = 2.64 × 10⁻⁸). We observed significantly lower BLM-induced chromotid breaks for genotypes containing wild-type allele compared with the homozygous variant genotype in the discovery set (0.71 versus 0.90, P= 3.77 × 10⁻⁵) and in replication phase 1 (0.61 versus 0.84, P= 7.00 × 10⁻⁵). The result of replication phase 2 was not statistically significant (0.65 versus 0.68, P= 0.44). This SNP is approximately 64 kb from PMAIP1/Noxa, which is a radiation-inducible gene and exhibits higher expression in BLM-sensitive lymphoblastoid cell lines than insensitive cell lines upon BLM treatment. In conclusion, we identified a biologically plausible genetic variant on 18q21 near the PMAIP1/Noxa gene that is associated with BLM sensitivity.
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Affiliation(s)
- Jian Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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179
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Gago-Dominguez M, Jiang X, Conti DV, Castelao JE, Stern MC, Cortessis VK, Pike MC, Xiang YB, Gao YT, Yuan JM, Van Den Berg DJ. Genetic variations on chromosomes 5p15 and 15q25 and bladder cancer risk: findings from the Los Angeles-Shanghai bladder case-control study. Carcinogenesis 2010; 32:197-202. [PMID: 21081471 DOI: 10.1093/carcin/bgq233] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies have associated common variations at chromosomes 5p15 and 15q25 with lung cancer risk. The 5p15 locus has also been associated with increased bladder cancer risk in a recent report. The 15q25 locus has been associated with nicotine dependence and self-reported number of cigarettes smoked per day in some studies and it was proposed that its association with lung cancer may be mediated through differences in smoking behavior. Here, we investigated the roles of variations at 5p15 (rs401681, rs402710, rs2736098 and rs2736100) and 15q25 (rs1051730 and rs8034191) in bladder cancer etiology in two case-control studies conducted separately in Los Angeles County, CA, USA (498 cases and 588 controls) and in Shanghai, China (506 cases and 530 controls). We replicated the association between the 5p15 locus and bladder cancer among non-Hispanic whites (NHW) in Los Angeles [for rs2736100, per C allele odds ratio (OR) = 1.23; 95% confidence interval (CI), 1.02-1.48; P = 0.029] and among Chinese in Shanghai (OR = 1.22; 95% CI, 1.02-1.47; P = 0.033). Both rs1051730 and rs8034191 at 15q25 were rare among Chinese. Among NHW, a significant association was found between rs8034191 and bladder cancer which persisted after adjustment for cigarette smoking status, number of cigarettes smoked per day and number of years of smoking (per C allele OR = 1.26; 95% CI, 1.04-1.54; P = 0.017). Our results support 5p15 and 15q25 as susceptibility regions for bladder cancer risk.
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Affiliation(s)
- Manuela Gago-Dominguez
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089-9175, USA.
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Lehmann ML, Selinski S, Blaszkewicz M, Orlich M, Ovsiannikov D, Moormann O, Guballa C, Kress A, Truss MC, Gerullis H, Otto T, Barski D, Niegisch G, Albers P, Frees S, Brenner W, Thüroff JW, Angeli-Greaves M, Seidel T, Roth G, Dietrich H, Ebbinghaus R, Prager HM, Bolt HM, Falkenstein M, Zimmermann A, Klein T, Reckwitz T, Roemer HC, Löhlein D, Weistenhöfer W, Schöps W, Beg AE, Aslam M, Bánfi G, Romics I, Ickstadt K, Schwender H, Winterpacht A, Hengstler JG, Golka K. Rs710521[A] on chromosome 3q28 close to TP63 is associated with increased urinary bladder cancer risk. Arch Toxicol 2010; 84:967-78. [DOI: 10.1007/s00204-010-0617-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 10/18/2010] [Indexed: 12/01/2022]
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181
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Rothman N, Garcia-Closas M, Chatterjee N, Malats N, Wu X, Figueroa J, Real FX, Van Den Berg D, Matullo G, Baris D, Thun M, Kiemeney LA, Vineis P, De Vivo I, Albanes D, Purdue MP, Rafnar T, Hildebrandt MAT, Kiltie AE, Cussenot O, Golka K, Kumar R, Taylor JA, Mayordomo JI, Jacobs KB, Kogevinas M, Hutchinson A, Wang Z, Fu YP, Prokunina-Olsson L, Burdette L, Yeager M, Wheeler W, Tardón A, Serra C, Carrato A, García-Closas R, Lloreta J, Johnson A, Schwenn M, Karagas MR, Schned A, Andriole G, Grubb R, Black A, Jacobs EJ, Diver WR, Gapstur SM, Weinstein SJ, Virtamo J, Cortessis VK, Gago-Dominguez M, Pike MC, Stern MC, Yuan JM, Hunter D, McGrath M, Dinney CP, Czerniak B, Chen M, Yang H, Vermeulen SH, Aben KK, Witjes JA, Makkinje RR, Sulem P, Besenbacher S, Stefansson K, Riboli E, Brennan P, Panico S, Navarro C, Allen NE, Bueno-de-Mesquita HB, Trichopoulos D, Caporaso N, Landi MT, Canzian F, Ljungberg B, Tjonneland A, Clavel-Chapelon F, Bishop DT, Teo MTW, Knowles MA, Guarrera S, Polidoro S, Ricceri F, Sacerdote C, Allione A, Cancel-Tassin G, Selinski S, Hengstler JG, Dietrich H, Fletcher T, Rudnai P, Gurzau E, Koppova K, Bolick SCE, Godfrey A, Xu Z, Sanz-Velez JI, García-Prats MD, Sanchez M, Valdivia G, Porru S, Benhamou S, Hoover RN, Fraumeni JF, Silverman DT, Chanock SJ. A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci. Nat Genet 2010; 42:978-84. [PMID: 20972438 PMCID: PMC3049891 DOI: 10.1038/ng.687] [Citation(s) in RCA: 363] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 08/19/2010] [Indexed: 12/12/2022]
Abstract
We conducted a multi-stage, genome-wide association study of bladder cancer with a primary scan of 591,637 SNPs in 3,532 affected individuals (cases) and 5,120 controls of European descent from five studies followed by a replication strategy, which included 8,382 cases and 48,275 controls from 16 studies. In a combined analysis, we identified three new regions associated with bladder cancer on chromosomes 22q13.1, 19q12 and 2q37.1: rs1014971, (P = 8 × 10⁻¹²) maps to a non-genic region of chromosome 22q13.1, rs8102137 (P = 2 × 10⁻¹¹) on 19q12 maps to CCNE1 and rs11892031 (P = 1 × 10⁻⁷) maps to the UGT1A cluster on 2q37.1. We confirmed four previously identified genome-wide associations on chromosomes 3q28, 4p16.3, 8q24.21 and 8q24.3, validated previous candidate associations for the GSTM1 deletion (P = 4 × 10⁻¹¹) and a tag SNP for NAT2 acetylation status (P = 4 × 10⁻¹¹), and found interactions with smoking in both regions. Our findings on common variants associated with bladder cancer risk should provide new insights into the mechanisms of carcinogenesis.
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Affiliation(s)
- Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Nuria Malats
- Spanish National Cancer Research Centre, Madrid, Spain
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Francisco X Real
- Spanish National Cancer Research Centre, Madrid, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - David Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Giuseppe Matullo
- Department of Genetics, Biology and Biochemistry, University of Torino, Torino, Italy
- Human Genetics Foundation (HuGeF), Torino, Italy
| | - Dalsu Baris
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Michael Thun
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - Lambertus A Kiemeney
- Department of Epidemiology, Biostatistics and Health Technology Assessment, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- Comprehensive Cancer Center East, Nijmegen, The Netherlands
- Department of Urology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Paolo Vineis
- Human Genetics Foundation (HuGeF), Torino, Italy
- Imperial College London, London, UK
| | - Immaculata De Vivo
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | | | - Michelle A T Hildebrandt
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Anne E Kiltie
- Gray Institute for Radiation Oncology and Biology, University of Oxford, Oxford, UK
| | - Olivier Cussenot
- Department of Urology, Assistance Publique-Hôpitaux de Paris, Tenon Hospital, Paris, France
- Centre de Recherche sur les Pathologies Prostatiques, Paris, France
| | - Klaus Golka
- Leibniz Research Centre for Working Environment and Human Factors, Dortmund, Germany
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Jack A Taylor
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | | | - Kevin B Jacobs
- Core Genotype Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Manolis Kogevinas
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Municipal Institute of Medical Research, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- National School of Public Health, Athens, Greece
| | - Amy Hutchinson
- Core Genotype Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Zhaoming Wang
- Core Genotype Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Yi-Ping Fu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Ludmila Prokunina-Olsson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Laurie Burdette
- Core Genotype Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Meredith Yeager
- Core Genotype Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - William Wheeler
- Information Management Services, Inc., Rockville, Maryland, USA
| | - Adonina Tardón
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | | | | | - Reina García-Closas
- Unidad de Investigación, Hospital Universitario de Canarias, La Laguna, Spain
| | - Josep Lloreta
- Hospital del Mar-IMIM, Univesitat Pompeu Fabra, Barcelona, Spain
| | | | | | | | - Alan Schned
- Dartmouth Medical School, Hanover, New Hampshire, USA
| | - Gerald Andriole
- Department of Urology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Robert Grubb
- Department of Urology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Amanda Black
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Eric J Jacobs
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Jarmo Virtamo
- National Institute for Health and Welfare, Helsinki, Finland
| | - Victoria K Cortessis
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Manuela Gago-Dominguez
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Malcolm C Pike
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Mariana C Stern
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jian-Min Yuan
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - David Hunter
- Department of Epidemiology, Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Monica McGrath
- Department of Epidemiology, Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Colin P Dinney
- Department of Urology, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Bogdan Czerniak
- Department of Pathology, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Meng Chen
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Hushan Yang
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Sita H Vermeulen
- Department of Epidemiology, Biostatistics and Health Technology Assessment, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Katja K Aben
- Department of Epidemiology, Biostatistics and Health Technology Assessment, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- Comprehensive Cancer Center East, Nijmegen, The Netherlands
| | - J Alfred Witjes
- Department of Urology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Remco R Makkinje
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | | | | | - Kari Stefansson
- deCODE Genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Salvatore Panico
- Department of Clinical and Experimental Medicine, Federico II University, Naples, Italy
| | - Carmen Navarro
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Department of Epidemiology, Murcia Regional Health Council, Murcia, Spain
| | - Naomi E Allen
- Cancer Epidemiology Unit, Nuffield Department of Clinical Medicine University of Oxford, Oxford, UK
| | | | - Dimitrios Trichopoulos
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
- Bureau of Epidemiologic Research, Academy of Athens, Greece
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center, Heidelberg, Germany
| | - Borje Ljungberg
- Department of Surgical and Perioperative Sciences, University of Umea, Umea, Sweden
| | - Anne Tjonneland
- Danish Cancer Society, Institute of Cancer Epidemiology, Copenhagen, Denmark
| | - Francoise Clavel-Chapelon
- Centre for Research in Epidemiology and Population Health, Institute Gustave-Roussy, Paris South University, Villejuif, France
| | - David T Bishop
- Leeds Institute of Molecular Medicine, St James’s University Hospital, University of Leeds, Leeds, UK
| | - Mark T W Teo
- Leeds Institute of Molecular Medicine, St James’s University Hospital, University of Leeds, Leeds, UK
| | - Margaret A Knowles
- Leeds Institute of Molecular Medicine, St James’s University Hospital, University of Leeds, Leeds, UK
| | | | | | - Fulvio Ricceri
- Department of Genetics, Biology and Biochemistry, University of Torino, Torino, Italy
- Human Genetics Foundation (HuGeF), Torino, Italy
| | - Carlotta Sacerdote
- Human Genetics Foundation (HuGeF), Torino, Italy
- Unit of Cancer Epidemiology, University of Torino, Torino, Italy
| | | | | | - Silvia Selinski
- Leibniz Research Centre for Working Environment and Human Factors, Dortmund, Germany
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors, Dortmund, Germany
| | - Holger Dietrich
- Department of Urology, Paul Gerhardt Foundation, Wittenberg, Germany
| | - Tony Fletcher
- Institute of Hygiene and Tropical Medicine, London, UK
| | - Peter Rudnai
- National Institute of Environmental Health, Budapest, Hungary
| | - Eugen Gurzau
- Babes Bolyai University, Environmental Health Center, Cluj-Napoca, Romania
| | | | - Sophia C E Bolick
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Ashley Godfrey
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Zongli Xu
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | | | | | | | | | - Stefano Porru
- Department of Experimental and Applied Medicine, Section of Occupational Medicine and Industrial Hygiene, University of Brescia, Italy
| | - Simone Benhamou
- Institut national de la santé et de la recherche médicale, U946, Fondation Jean Dausset-CEPH, Paris, France
- Centre national de la recherche scientifique, UMR8200, Institut Gustave-Roussy, Villejuif, France
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Joseph F Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Debra T Silverman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
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Stadler ZK, Vijai J, Thom P, Kirchhoff T, Hansen NA, Kauff ND, Robson M, Offit K. Genome-wide Association Studies of Cancer Predisposition. Hematol Oncol Clin North Am 2010; 24:973-96. [DOI: 10.1016/j.hoc.2010.06.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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184
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Chen M, Hildebrandt MAT, Clague J, Kamat AM, Picornell A, Chang J, Zhang X, Izzo J, Yang H, Lin J, Gu J, Chanock S, Kogevinas M, Rothman N, Silverman DT, Garcia-Closas M, Grossman HB, Dinney CP, Malats N, Wu X. Genetic variations in the sonic hedgehog pathway affect clinical outcomes in non-muscle-invasive bladder cancer. Cancer Prev Res (Phila) 2010; 3:1235-45. [PMID: 20858759 DOI: 10.1158/1940-6207.capr-10-0035] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Sonic hedgehog (Shh) pathway genetic variations may affect bladder cancer risk and clinical outcomes. Therefore, we genotyped 177 single-nucleotide polymorphisms (SNP) in 11 Shh pathway genes in a study including 803 bladder cancer cases and 803 controls. We assessed SNP associations with cancer risk and clinical outcomes in 419 cases of non-muscle-invasive bladder cancer (NMIBC) and 318 cases of muscle-invasive and metastatic bladder cancer (MiMBC). Only three SNPs (GLI3 rs3823720, rs3735361, and rs10951671) reached nominal significance in association with risk (P ≤ 0.05), which became nonsignificant after adjusting for multiple comparisons. Nine SNPs reached a nominally significant individual association with recurrence of NMIBC in patients who received transurethral resection (TUR) only (P ≤ 0.05), of which two (SHH rs1233560 and GLI2 rs11685068) were replicated independently in 356 TUR-only NMIBC patients, with P values of 1.0 × 10(-3) (SHH rs1233560) and 1.3 × 10(-3) (GLI2 rs11685068). Nine SNPs also reached a nominally significant individual association with clinical outcome of NMIBC patients who received Bacillus Calmette-Guérin (BCG; P ≤ 0.05), of which two, the independent GLI3 variants rs6463089 and rs3801192, remained significant after adjusting for multiple comparisons (P = 2 × 10(-4) and 9 × 10(-4), respectively). The wild-type genotype of either of these SNPs was associated with a lower recurrence rate and longer recurrence-free survival (versus the variants). Although three SNPs (GLI2 rs735557, GLI2 rs4848632, and SHH rs208684) showed nominal significance in association with overall survival in MiMBC patients (P ≤ 0.05), none remained significant after multiple-comparison adjustments. Germ-line genetic variations in the Shh pathway predicted clinical outcomes of TUR and BCG for NMIBC patients.
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Affiliation(s)
- Meng Chen
- Department of Epidemiology, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
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Stadler ZK, Thom P, Robson ME, Weitzel JN, Kauff ND, Hurley KE, Devlin V, Gold B, Klein RJ, Offit K. Genome-wide association studies of cancer. J Clin Oncol 2010; 28:4255-67. [PMID: 20585100 PMCID: PMC2953976 DOI: 10.1200/jco.2009.25.7816] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 04/19/2010] [Indexed: 12/20/2022] Open
Abstract
Knowledge of the inherited risk for cancer is an important component of preventive oncology. In addition to well-established syndromes of cancer predisposition, much remains to be discovered about the genetic variation underlying susceptibility to common malignancies. Increased knowledge about the human genome and advances in genotyping technology have made possible genome-wide association studies (GWAS) of human diseases. These studies have identified many important regions of genetic variation associated with an increased risk for human traits and diseases including cancer. Understanding the principles, major findings, and limitations of GWAS is becoming increasingly important for oncologists as dissemination of genomic risk tests directly to consumers is already occurring through commercial companies. GWAS have contributed to our understanding of the genetic basis of cancer and will shed light on biologic pathways and possible new strategies for targeted prevention. To date, however, the clinical utility of GWAS-derived risk markers remains limited.
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Affiliation(s)
- Zsofia K. Stadler
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
| | - Peter Thom
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
| | - Mark E. Robson
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
| | - Jeffrey N. Weitzel
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
| | - Noah D. Kauff
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
| | - Karen E. Hurley
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
| | - Vincent Devlin
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
| | - Bert Gold
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
| | - Robert J. Klein
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
| | - Kenneth Offit
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
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186
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Keller B, Martini S, Sedor J, Kretzler M. Linking variants from genome-wide association analysis to function via transcriptional network analysis. Semin Nephrol 2010; 30:177-84. [PMID: 20347646 DOI: 10.1016/j.semnephrol.2010.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
A current challenge in interpretation of genome-wide association studies is to establish the mechanistic links between the measured genotype and observed phenotype. The integration of gene expression with disease genome-wide association studies is emerging as an important strategy for deciphering these regulatory mechanisms. For renal disease, the availability of both tissue- and disease-specific expression data makes the strategy a compelling option. In this review, three approaches of integrating single nucleotide polymorphism (SNP) genotypes with transcriptional regulation are discussed as follows: (1) interpreting the functional role of transcripts affected by a SNP, (2) identifying the mechanistic role of noncoding SNPs in regulation, and (3) identifying regulatory candidate SNPs with expression associations. Combining these strategies in an integrative manner should allow the discovery of more extensive regulatory information. Linking genetics to systems biology more directly promises the opportunity to explain how genetic variants contribute to disease in a truly holistic manner.
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Affiliation(s)
- Benjamin Keller
- Computer Science, Eastern Michigan University, Ann Arbor, MI, USA
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187
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Sullivan PS, Chan JB, Levin MR, Rao J. Urine cytology and adjunct markers for detection and surveillance of bladder cancer. Am J Transl Res 2010; 2:412-440. [PMID: 20733951 PMCID: PMC2923865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 07/22/2010] [Indexed: 05/29/2023]
Abstract
Urine cytology coupled with cystoscopic examination has been and remains the standard in the initial evaluation of lower urinary tract lesions to rule out bladder cancer. However, cystoscopy is invasive and may miss some flat lesions, whereas cytology has low sensitivity in low-grade papillary disease. Additional lab-based or office-based markers are needed to aid in the evaluation of these lesions. Recently, many such markers have been developed for the purpose of improving the cytologic diagnosis of bladder malignancies. In this review, we will first discuss conventional cytomorphologic analysis of urine cytology followed by a discussion of markers that have been developed in the past for detection and surveillance of urothelial carcinoma. We will focus on how these markers can be used in conjunction with urine cytology in daily practice.
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188
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Liu Y, Shete S, Wang LE, El-Zein R, Etzel CJ, Liang FW, Armstrong G, Tsavachidis S, Gilbert MR, Aldape KD, Xing J, Wu X, Wei Q, Bondy ML. Gamma-radiation sensitivity and polymorphisms in RAD51L1 modulate glioma risk. Carcinogenesis 2010; 31:1762-9. [PMID: 20610542 DOI: 10.1093/carcin/bgq141] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND DNA strand breaks pose the greatest threat to genomic stability. Genetically determined mutagen sensitivity predisposes individuals to a variety of cancers, including glioma. However, polymorphisms in DNA strand break repair genes that may determine mutagen sensitivity are not well studied in cancer risk, especially in gliomas. METHODS We correlated genotype data for tag single-nucleotide polymorphisms (tSNPs) of DNA strand break repair genes with a gamma-radiation-induced mutagen sensitivity phenotype [expressed as mean breaks per cell (B/C)] in samples from 426 glioma patients. We also conducted analysis to assess joint and haplotype effects of single-nucleotide polymorphisms (SNPs) on mutagen sensitivity. We further validate our results in an independent external control group totaling 662 subjects. RESULTS Of the 392 tSNPs examined, we found that mutagen sensitivity was modified by one tSNP in the EME2 gene and six tSNPs in the RAD51L1 gene (P < 0.01). Among the six RAD51L1 SNPs tested in the validation set, one (RAD51L1 rs2180611) was significantly associated with mutagen sensitivity (P = 0.025). Moreover, we found a significant dose-response relationship between the mutagen sensitivity and the number of adverse tSNP genotypes. Furthermore, haplotype analysis revealed that RAD51L1 haplotypes F-A (zero adverse allele) and F-E (six adverse alleles) exhibited the lowest (0.42) and highest (0.93) mean B/C values, respectively. A similar dose-response relationship also existed between the mutagen sensitivity and the number of adverse haplotypes. CONCLUSION These results suggest that polymorphisms in and haplotypes of the RAD51L1 gene, which is involved in the double-strand break repair pathway, modulate gamma-radiation-induced mutagen sensitivity.
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Affiliation(s)
- Yanhong Liu
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
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189
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Yoshida T, Ono H, Kuchiba A, Saeki N, Sakamoto H. Genome-wide germline analyses on cancer susceptibility and GeMDBJ database: Gastric cancer as an example. Cancer Sci 2010; 101:1582-9. [PMID: 20507324 PMCID: PMC11159415 DOI: 10.1111/j.1349-7006.2010.01590.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The power of an SNP-based genome-wide association study (GWAS) was first demonstrated in Japan using the JSNP database and is currently a major strategy adopted around the world for a number of common diseases including cancers. The hypothesis-free strategy can lead us to a novel hypothesis for carcinogenesis and may contribute to identifying a high risk group for research and, in the future, practice of personalized prevention. We performed a GWAS on diffuse-type gastric cancer and identified a significant association with SNPs in the PSCA (prostate stem cell antigen) gene. The association was validated by a Korean gastric case-control analysis. The PSCA protein is expressed predominantly in the stem cell/precursor-rich region of the gastric epithelium, which is considered as the origin of diffuse-type gastric cancer, and showed tumor suppressor-like characteristics. Individuals with a low PSCA promoter activity are susceptible to diffuse-type gastric cancer. By contrast, the polymorphism does not significantly predispose to intestinal-type gastric cancer, congruous to the hypothesis of the two distinct carcinogenesis pathways for the two major types of gastric cancer. In addition to publication on a specific gene, the sharing of GWAS data through a database on the web is expected to accelerate validation and discovery by other investigators. GeMDBJ (Genome Medicine Database of Japan), started in 2005 in Japan, is one of such attempts. Moreover, the advent of "next generation" sequencers may herald a new era in which the poorly explored domains of the genetic architecture of disease susceptibility may be unveiled.
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Affiliation(s)
- Teruhiko Yoshida
- Genetics Division, National Cancer Center Research Institute, Tokyo, Japan.
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190
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Zhang L, Zhang W, Chen K. Search for cancer risk factors with microarray-based genome-wide association studies. Technol Cancer Res Treat 2010; 9:107-21. [PMID: 20218734 DOI: 10.1177/153303461000900201] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Large-scale genome-wide association studies (GWASs) have emerged as a powerful approach to identify genetic polymorphisms that are associated with risk of developing cancer and other complex diseases. Currently, microarrays are the genotype screening technology of choice in GWASs because they permit interrogation of more than one-million single-nucleotide polymorphisms (SNPs) at the same time. Many novel loci and genetic variants have been identified as markers of cancer risk in a series of recent reports. With improvement of microarray technologies, population-based GWASs coupled with more quantitative validation methods are poised to reveal, in a systematic manner, numerous small changes in complex genetic networks that in combination can have a major impact on a patient's risk of developing cancer. Here, we review recent advancement in GWAS in the search and identification of cancer risk factors.
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Affiliation(s)
- Lina Zhang
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
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191
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Ioannidis JPA, Castaldi P, Evangelou E. A compendium of genome-wide associations for cancer: critical synopsis and reappraisal. J Natl Cancer Inst 2010; 102:846-58. [PMID: 20505153 DOI: 10.1093/jnci/djq173] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Since 2007, genome-wide association (GWA) studies have identified numerous well-supported, novel genetic risk loci for common cancers; however, there are concerns that this technology is reaching its limits. We provide an overview of GWA-identified genetic associations with solid tumors. We simulated the distribution of population risk alleles for colorectal, prostate, testicular, and thyroid cancers based on genetic variants identified in GWA studies. We also evaluated whether statistical power to detect typical genetic effects could be improved with studies performing GWA analyses of all available samples rather than multistage designs. Fifty-six eligible articles yielded 92 eligible associations between cancer phenotypes and genetic variants with a median per-allele odds ratio (OR) of 1.22 (interquartile range = 1.15-1.36). Half of the associations pertained to prostate, colorectal, or breast cancer. Individuals at the upper quartile of simulated risk had only 2.1- to 4.2-fold higher relative risk than those in the lower quartile. Comprehensive evaluation of currently available samples with GWA platforms would yield few additional variants with per-allele OR = 1.4, but many more variants with OR = 1.2 could be detected; statistical power to detect weak associations (OR = 1.07) would still be negligible. The GWA approach is effective in identifying common genetic variants with moderate effect; however, identifying loci with very small effects and rare variants will require major new efforts. At present, the utility of GWA-identified risk loci in risk stratification for cancer is limited.
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Affiliation(s)
- John P A Ioannidis
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina 45110, Greece.
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192
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Saeki N, Gu J, Yoshida T, Wu X. Prostate stem cell antigen: a Jekyll and Hyde molecule? Clin Cancer Res 2010; 16:3533-8. [PMID: 20501618 DOI: 10.1158/1078-0432.ccr-09-3169] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Prostate stem cell antigen (PSCA) is a glycosylphosphatidylinositol (GPI)-anchored cell surface protein. Although PSCA is thought to be involved in intracellular signaling, much remains unknown about its physiological function and regulatory mechanism in normal and cancer cells. It is up-regulated in several major cancers including prostate, bladder, and pancreatic cancers. The expression of PSCA is positively correlated with advanced clinical stage and metastasis in prostate cancers and is also associated with malignant progression of premalignant prostate lesions. Therefore, PSCA has been proposed as a biomarker of diagnosis and prognosis, as well as a target of therapy for these cancers. In addition, PSCA has also shown clinical potential in immunotherapy as a prostate-specific antigen, which, when presented by dendritic cells, may elicit strong tumor-specific immunity. In contrast, PSCA is down-regulated in esophageal and gastric cancer and may have a tumor-suppressing function in the gastric epithelium. Recent exciting findings that genetic variations of PSCA conferred increased risks of gastric cancer and bladder cancer have opened up a new avenue of research about the pathological function of PSCA. PSCA seems to be a Jekyll and Hyde molecule that plays differential roles, tumor promoting or suppressing, depending on the cellular context.
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Affiliation(s)
- Norihisa Saeki
- Genetics Division, National Cancer Center Research Institute, Tokyo, Japan
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193
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Abstract
This Timeline article looks back at 40 years of research into the inherited genetic basis of cancer and the insights these studies have yielded. Early epidemiological research provided evidence for the 'two-hit' model of cancer predisposition. During the 1980s and 1990s linkage and positional cloning analyses led to the identification of high-penetrance cancer susceptibility genes. The past decade has seen a shift from models of predisposition based on single-gene causative mutations to multigenic models. These models suggest that a high proportion of cancers may arise in a genetically susceptible minority as a consequence of the combined effects of common low-penetrance alleles and rare disease-causing variants that confer moderate cancer risks.
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Affiliation(s)
- Olivia Fletcher
- Olivia Fletcher is at the Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, UK
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194
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Kiemeney LA, Sulem P, Besenbacher S, Vermeulen SH, Sigurdsson A, Thorleifsson G, Gudbjartsson DF, Stacey SN, Gudmundsson J, Zanon C, Kostic J, Masson G, Bjarnason H, Palsson ST, Skarphedinsson OB, Gudjonsson SA, Witjes JA, Grotenhuis AJ, Verhaegh GW, Bishop DT, Sak SC, Choudhury A, Elliott F, Barrett JH, Hurst CD, de Verdier PJ, Ryk C, Rudnai P, Gurzau E, Koppova K, Vineis P, Polidoro S, Guarrera S, Sacerdote C, Campagna M, Placidi D, Arici C, Zeegers MP, Kellen E, Gutierrez BS, Sanz-Velez JI, Sanchez-Zalabardo M, Valdivia G, Garcia-Prats MD, Hengstler JG, Blaszkewicz M, Dietrich H, Ophoff RA, van den Berg LH, Alexiusdottir K, Kristjansson K, Geirsson G, Nikulasson S, Petursdottir V, Kong A, Thorgeirsson T, Mungan NA, Lindblom A, van Es MA, Porru S, Buntinx F, Golka K, Mayordomo JI, Kumar R, Matullo G, Steineck G, Kiltie AE, Aben KKH, Jonsson E, Thorsteinsdottir U, Knowles MA, Rafnar T, Stefansson K. A sequence variant at 4p16.3 confers susceptibility to urinary bladder cancer. Nat Genet 2010; 42:415-9. [PMID: 20348956 PMCID: PMC2923020 DOI: 10.1038/ng.558] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Accepted: 03/03/2010] [Indexed: 12/17/2022]
Abstract
Previously, we reported germline DNA variants associated with risk of urinary bladder cancer (UBC) in Dutch and Icelandic subjects. Here we expanded the Icelandic sample set and tested the top 20 markers from the combined analysis in several European case-control sample sets, with a total of 4,739 cases and 45,549 controls. The T allele of rs798766 on 4p16.3 was found to associate with UBC (odds ratio = 1.24, P = 9.9 x 10(-12)). rs798766 is located in an intron of TACC3, 70 kb from FGFR3, which often harbors activating somatic mutations in low-grade, noninvasive UBC. Notably, rs798766[T] shows stronger association with low-grade and low-stage UBC than with more aggressive forms of the disease and is associated with higher risk of recurrence in low-grade stage Ta tumors. The frequency of rs798766[T] is higher in Ta tumors that carry an activating mutation in FGFR3 than in Ta tumors with wild-type FGFR3. Our results show a link between germline variants, somatic mutations of FGFR3 and risk of UBC.
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Affiliation(s)
- Lambertus A Kiemeney
- Department of Epidemiology, Biostatistics and Health Technology Assessment, Nijmegen, The Netherlands.
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195
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Marra E, Uva P, Viti V, Simonelli V, Dogliotti E, De Rinaldis E, Lahm A, La Monica N, Nicosia A, Ciliberto G, Palombo F. Growth delay of human bladder cancer cells by Prostate Stem Cell Antigen downregulation is associated with activation of immune signaling pathways. BMC Cancer 2010; 10:129. [PMID: 20374648 PMCID: PMC2858747 DOI: 10.1186/1471-2407-10-129] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 04/07/2010] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Prostate stem cell antigen (PSCA) is a glycosylphosphatidylinositol (GPI) anchored protein expressed not only in prostate but also in pancreas and bladder cancer as shown by immunohistochemistry and mRNA analysis. It has been targeted by monoclonal antibodies in preclinical animal models and more recently in a clinical trial in prostate cancer patients. The biological role played in tumor growth is presently unknown. In this report we have characterized the contribution of PSCA expression to tumor growth. METHODS A bladder cell line was engineered to express a doxycycline (dox) regulated shRNA against PSCA. To shed light on the PSCA biological role in tumor growth, microarray analysis was carried out as a function of PSCA expression. Expression of gene set of interest was further analyzed by qPCR RESULTS: Down regulation of the PSCA expression was associated with reduced cell proliferation in vitro and in vivo. Mice bearing subcutaneous tumors showed a reduced tumor growth upon treatment with dox, which effectively induced shRNA against PSCA as revealed by GFP expression. Pathway analysis of deregulated genes suggests a statistical significant association between PSCA downregulation and activation of genes downstream of the IFNalpha/beta receptor. CONCLUSIONS These experiments established for the first time a correlation between the level of PSCA expression and tumor growth and suggest a role of PSCA in counteracting the natural immune response.
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Affiliation(s)
- Emanuele Marra
- Istituto di Ricerche Biologia Molecolare P, Angeletti, Via Pontina Km 30,600 00040 Pomezia (Rome) Italy
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196
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Lin J, Wang J, Greisinger AJ, Grossman HB, Forman MR, Dinney CP, Hawk ET, Wu X. Energy balance, the PI3K-AKT-mTOR pathway genes, and the risk of bladder cancer. Cancer Prev Res (Phila) 2010; 3:505-17. [PMID: 20354165 DOI: 10.1158/1940-6207.capr-09-0263] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We evaluated the association between energy balance and risk of bladder cancer and assessed the joint effects of genetic variants in the mammalian target of rapamycin (mTOR) pathway genes with energy balance. The study included 803 Caucasian bladder cancer patients and 803 healthy Caucasian controls matched to cases by age (+/-5 years) and gender. High energy intake [odds ratio, 1.60; 95% confidence interval (95% CI), 1.23-2.09] and low physical activity (odds ratio, 2.82; 95% CI, 2.10-3.79) were each associated with significantly increased risk of bladder cancer with dose-response pattern (P(trend) < 0.001). However, obesity (body mass index, > or =30) was not associated with the risk. Among 222 single nucleotide polymorphisms, 28 single nucleotide polymorphisms located in six genes of mTOR pathway were significantly associated with the risk. Further, the risk associated with high energy intake and low physical activity was only observed among subjects carrying a high number of unfavorable genotypes in the pathway. Moreover, when physical activity, energy intake, and genetic variants were analyzed jointly, the study population was clearly stratified into a range of low- to high-risk subgroups as defined energy balance status. Compared with subjects within the most favorable energy balance category (low energy intake, intensive physical activity, low number of unfavorable genotypes), subjects in the worst energy balance category (high energy intake, low physical activity, and carrying > or =7 unfavorable genotypes) had 21.93-fold increased risk (95% CI, 6.7-71.77). Our results provide the first strong evidence that physical activity, energy intake, and genetic variants in the mTOR pathway jointly influence bladder cancer susceptibility and that these results have implications for bladder cancer prevention.
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Affiliation(s)
- Jie Lin
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, 1155 Hermann Pressler Boulevard, Houston, TX 77030, USA
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197
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Genome-wide association studies of bladder cancer risk: a field synopsis of progress and potential applications. Cancer Metastasis Rev 2010; 28:269-80. [PMID: 20016998 DOI: 10.1007/s10555-009-9190-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The advent of the genome era after the completion of the Human Genome Project has resulted in intensive efforts to identify all genetic variants that modify human health and disease, including cancer. The development of genome-wide association study (GWAS) approach has facilitated this goal by unbiased examination of the entire human genome for disease association. Here, we review some of the GWAS data, particularly for bladder cancer, and assess their significance in risk prediction and prognosis. A mechanistic understanding of the risk association through functional studies and phenotypic assays is also discussed. The ultimate goal is the development of a comprehensive risk prediction model which integrates genetic, environment, and person risk factors to benefit disease diagnosis, prevention, and treatment.
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198
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Abstract
It is now 5 years since the first genome-wide association studies (GWAS), published in 2005, identified a common risk allele with large effect size for age-related macular degeneration in a small sample set. Following this exciting finding, researchers have become optimistic about the prospect of the genome-wide association approach. However, most of the risk alleles identified in the subsequent GWAS for various complex diseases are common with small effect sizes (odds ratio <1.5). So far, more than 450 GWAS have been published and the associations of greater than 2000 single nucleotide polymorphisms (SNPs) or genetic loci were reported. The aim of this review paper is to give an overview of the evolving field of GWAS, discuss the progress that has been made by GWAS and some of the interesting findings, and summarize what we have learned over the past 5 years about the genetic basis of human complex diseases. This review will focus on GWAS of SNPs association for complex diseases but not studies of copy number variations.
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199
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Kiltie AE. Common predisposition alleles for moderately common cancers: bladder cancer. Curr Opin Genet Dev 2010; 20:218-24. [PMID: 20153630 DOI: 10.1016/j.gde.2010.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 01/20/2010] [Indexed: 11/30/2022]
Abstract
Bladder cancer is the 5th commonest cancer and two major risk factors are smoking and occupational chemical exposure. There is also evidence of a genetic component to its aetiology. Candidate gene studies have mostly focused on genes involved in adduct metabolism and DNA repair, including a recent consortium-based meta-analysis. Recently, two genome-wide association studies in bladder cancer have been published and a third is awaited with interest. These first two studies have identified three SNPs of genome-wide significance, two located within the 8q24 'gene desert'. These SNPs are positioned near or within loci of genes potentially implicated in cancer predisposition, namely MYC, TP63 and PSCA, although the functional significance of this is as yet unclear.
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Affiliation(s)
- Anne E Kiltie
- Gray Institute for Radiation Oncology and Biology, Old Road Campus Research Building, Headington, Oxford, United Kingdom.
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200
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Wang S, Tang J, Wang M, Yuan L, Zhang Z. Genetic variation in PSCA and bladder cancer susceptibility in a Chinese population. Carcinogenesis 2010; 31:621-4. [DOI: 10.1093/carcin/bgp323] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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