Genome-wide association study identifies multiple risk loci for renal cell carcinoma

. 2017 Jun 09 ; 8 () : 15724. [epub] 20170609

Jazyk angličtina Země Velká Británie, Anglie Médium electronic

Typ dokumentu časopisecké články, metaanalýza, Research Support, N.I.H., Extramural, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid28598434

Grantová podpora
10124 Cancer Research UK - United Kingdom
U01 CA155309 NCI NIH HHS - United States
6858 Cancer Research UK - United Kingdom
MR/N003284/1 Medical Research Council - United Kingdom
G0401527 Medical Research Council - United Kingdom
14136 Cancer Research UK - United Kingdom
RP-PG-0707-10101 Department of Health - United Kingdom
001 World Health Organization - International
G1000143 Medical Research Council - United Kingdom
16561 Cancer Research UK - United Kingdom

Previous genome-wide association studies (GWAS) have identified six risk loci for renal cell carcinoma (RCC). We conducted a meta-analysis of two new scans of 5,198 cases and 7,331 controls together with four existing scans, totalling 10,784 cases and 20,406 controls of European ancestry. Twenty-four loci were tested in an additional 3,182 cases and 6,301 controls. We confirm the six known RCC risk loci and identify seven new loci at 1p32.3 (rs4381241, P=3.1 × 10-10), 3p22.1 (rs67311347, P=2.5 × 10-8), 3q26.2 (rs10936602, P=8.8 × 10-9), 8p21.3 (rs2241261, P=5.8 × 10-9), 10q24.33-q25.1 (rs11813268, P=3.9 × 10-8), 11q22.3 (rs74911261, P=2.1 × 10-10) and 14q24.2 (rs4903064, P=2.2 × 10-24). Expression quantitative trait analyses suggest plausible candidate genes at these regions that may contribute to RCC susceptibility.

1st Faculty of Medicine Institute of Hygiene and Epidemiology Charles University 128 00 Prague 2 Czech Republic

2nd Faculty of Medicine Institute of Public Health and Preventive Medicine Charles University 150 06 Prague 5 Czech Republic

American Cancer Society Atlanta Georgia 30303 USA

Brigham and Women's Hospital and VA Boston Boston Massachusetts 02115 USA

Cancer Epidemiology Centre Cancer Council Victoria Melbourne Victoria 3004 Australia

Cancer Prevention Program Fred Hutchinson Cancer Research Center Seattle Washington 98109 USA

Carol Davila University of Medicine and Pharmacy Th Burghele Hospital 050659 Bucharest Romania

Center 'Bioengineering' of the Russian Academy of Sciences Moscow 117312 Russia

Centre de Recherche en Épidémiologie et Santé des Populations Université Paris Saclay UPS UVSQ Gustave Roussy 94805 Villejuif France

Centre for Epidemiology and Biostatistics Melbourne School of Population and Global Health The University of Melbourne Carlton Victoria 3053 Australia

Centre National de Genotypage Institut de Genomique Commissariat à l'Energie Atomique et aux Energies Alternatives 91057 Evry France

CeRePP Tenon Hospital 75020 Paris France

Clinical Center of Serbia Clinic of Urology University of Belgrade Faculty of Medicine 11000 Belgrade Serbia

College of Human Medicine Michigan State University Grand Rapids Michigan 49503 USA

Dana Farber Cancer Institute Boston Massachusetts 02215 USA

Department of Cancer Epidemiology and Genetics Masaryk Memorial Cancer Institute 656 53 Brno Czech Republic

Department of Community Medicine Faculty of Health Sciences University of Tromsø The Arctic University of Norway 9037 Tromsø Norway

Department of Computational Biology St Jude Children's Research Hospital Memphis Tennessee 38105 USA

Department of Epidemiology and Biostatistics School of Public Health Indiana University Bloomington Bloomington Indiana 47405 USA

Department of Epidemiology Division of Cancer Prevention and Population Sciences The University of Texas MD Anderson Cancer Center Houston Texas 77230 USA

Department of Epidemiology German Institute of Human Nutrition Potsdam Rehbrücke 14558 Nuthetal Germany

Department of Epidemiology Institute of Occupational Medicine 91 348 Lodz Poland

Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai New York New York 10029 USA

Department of Health National Institute for Health and Welfare 00271 Helsinki Finland

Department of Health Sciences Research Mayo Clinic Jacksonville Florida 32224 USA

Department of Health Sciences Research Mayo Clinic Rochester Minnesota 55905 USA

Department of Medical Epidemiology and Biostatistics Karolinska Institutet 171 77 Stockholm Sweden

Department of Medicine The University of Melbourne Melbourne Victoria 3010 Australia

Department of Oncology Cambridge University Hospitals NHS Foundation Trust Cambridge CB2 0QQ UK

Department of Oncology University of Cambridge Cambridge CB1 8RN UK

Department of Preventive Medicine Faculty of Medicine Palacky University 775 15 Olomouc Czech Republic

Department of Public Health and General Practice Faculty of Medicine Norwegian University of Science and Technology Trondheim 7491 Norway

Department of Public Health and Primary Care University of Cambridge Cambridge CB2 0QQ UK

Department of Research Cancer Registry of Norway Institute of Population Based Cancer Research 0304 Oslo Norway

Department of Surgical and Perioperative Sciences Urology and Andrology Umeå University 901 85 Umeå Sweden

Department of Urology Mayo Medical School and Mayo Clinic Rochester Minnesota 55902 USA

Department of Urology The University of Texas M D Anderson Cancer Center Houston Texas 77030 USA

Division of Cancer Epidemiology and Genetics National Cancer Institute National Institutes of Health Department Health and Human Services Bethesda Maryland 20892 USA

Division of Genetics and Epidemiology The Institute of Cancer Research London SW7 3RP UK

Division of Molecular Pathology The Institute of Cancer Research London SW7 3RP UK

Division of Urology Spectrum Health Grand Rapids Michigan 49503 USA

Fondation Jean Dausset Centre d'Etude du Polymorphisme Humain 75010 Paris France

Genetic Epidemiology Group Folkhälsan Research Center 00250 Helsinki Finland

Genetic Medicine and Family Cancer Clinic Royal Melbourne Hospital Parkville Victoria 3050 Australia

Harvard T H Chan School of Public Health Boston Massachusetts 02115 USA

Human Genetics Foundation 10126 Torino Italy

HUNT Research Centre Department of Public Health and General Practice Norwegian University of Science and Technology Levanger 7600 Norway

Institute of Environmental Medicine Karolinska Institutet 171 77 Stockholm Sweden

Institute of Pathology School of Medicine University of Belgrade 11000 Belgrade Serbia

International Agency for Research on Cancer 69008 Lyon France

International Hereditary Cancer Center Department of Genetics and Pathology Pomeranian Medical University 70 204 Szczecin Poland

Kurchatov Scientific Center Moscow 123182 Russia

Leeds Institute of Cancer and Pathology University of Leeds Cancer Research Building St James's University Hospital Leeds LS9 7TF UK

London School of Hygiene and Tropical Medicine University of London London WC1H 9SH UK

McGill University and Genome Quebec Innovation Centre Montreal Quebec Canada H3A 0G1

Medical Oncology Royal Marsden NHS Foundation Trust London SW3 6JJ UK

National Institute of Public Health 050463 Bucharest Romania

National Public Health Center National Directorate of Environmental Health 1097 Budapest Hungary

QIMR Berghofer Medical Research Institute Herston Queensland 4006 Australia

Regional Authority of Public Health in Banska Bystrica 975 56 Banska Bystrica Slovakia

Russian N N Blokhin Cancer Research Centre Moscow 115478 Russian Federation

School of Public Health The University of Queensland Brisbane Queensland 4072 Australia

The M Sklodowska Curie Cancer Center and Institute of Oncology 02 034 Warsaw Poland

Université Paris Diderot INSERM Unité Variabilité Génétique et Maladies Humaines 75010 Paris France

UPMC Univ Paris 06 GRC n°5 75013 Paris France

Van Andel Research Institute Center for Cancer Genomics and Quantitative Biology Grand Rapids Michigan 49503 USA

Vanderbilt Ingram Cancer Center Department of Urology Vanderbilt University Medical Center Nashville Tennessee 37232 USA

Vanderbilt Ingram Cancer Center Division of Epidemiology Department of Medicine Institute for Medicine and Public Health Vanderbilt Genetics Institute Vanderbilt University Medical Center Nashville Tennessee 37209 USA

Vanderbilt Ingram Cancer Center Division of Epidemiology Department of Medicine Institute for Medicine and Public Health Vanderbilt University Medical Center Nashville Tennessee 37203 USA

Warren Alpert Medical School of Brown University Providence Rhode Island 02903 USA

Zobrazit více v PubMed

Znaor A., Lortet-Tieulent J., Laversanne M., Jemal A. & Bray F. International variations and trends in renal cell carcinoma incidence and mortality. Eur. Urol. 67, 519–530 (2015). PubMed

Gormally E. et al.. TP53 and KRAS2 mutations in plasma DNA of healthy subjects and subsequent cancer occurrence: a prospective study. Cancer Res. 66, 6871–6876 (2006). PubMed

Cheville J. C., Lohse C. M., Zincke H., Weaver A. L. & Blute M. L. Comparisons of outcome and prognostic features among histologic subtypes of renal cell carcinoma. Am. J. Surg. Pathol. 27, 612–624 (2003). PubMed

Mucci L. A. et al.. Familial risk and heritability of cancer among twins in Nordic countries. JAMA 315, 68–76 (2016). PubMed PMC

Haas N. B. & Nathanson K. L. Hereditary kidney cancer syndromes. Adv. Chronic Kidney Dis. 21, 81–90 (2014). PubMed PMC

Linehan W. M., Srinivasan R. & Schmidt L. S. The genetic basis of kidney cancer: a metabolic disease. Nat. Rev. Urol. 7, 277–285 (2010). PubMed PMC

Hung R. J. et al.. Family history and the risk of kidney cancer: a multicenter case-control study in Central Europe. Cancer Epidemiol. Biomark. Prev. 16, 1287–1290 (2007). PubMed

Karami S. et al.. Family history of cancer and renal cell cancer risk in Caucasians and African Americans. Br. J. Cancer 102, 1676–1680 (2010). PubMed PMC

Purdue M. P. et al.. Genome-wide association study of renal cell carcinoma identifies two susceptibility loci on 2p21 and 11q13.3. Nat. Genet. 43, 60–65 (2011). PubMed PMC

Wu X. et al.. A genome-wide association study identifies a novel susceptibility locus for renal cell carcinoma on 12p11.23. Hum. Mol. Genet. 21, 456–462 (2012). PubMed PMC

Henrion M. et al.. Common variation at 2q22.3 (ZEB2) influences the risk of renal cancer. Hum. Mol. Genet. 22, 825–831 (2013). PubMed PMC

Gudmundsson J. et al.. A common variant at 8q24.21 is associated with renal cell cancer. Nat. Commun. 4, 2776 (2013). PubMed

Schodel J. et al.. Common genetic variants at the 11q13.3 renal cancer susceptibility locus influence binding of HIF to an enhancer of cyclin D1 expression. Nat. Genet. 44, 420–425 (2012). PubMed PMC

Bigot P. et al.. Functional characterization of the 12p12.1 renal cancer-susceptibility locus implicates BHLHE41. Nat. Commun. 7, 12098 (2016). PubMed PMC

Henrion M. Y. et al.. Common variation at 1q24.1 (ALDH9A1) is a potential risk factor for renal cancer. PLoS ONE 10, e0122589 (2015). PubMed PMC

Han S. S. et al.. The chromosome 2p21 region harbors a complex genetic architecture for association with risk for renal cell carcinoma. Hum. Mol. Genet. 21, 1190–1200 (2012). PubMed PMC

Machiela M. J. & Chanock S. J. LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants. Bioinformatics 31, 3555–3557 (2015). PubMed PMC

Ward L. D. & Kellis M. HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease. Nucleic Acids Res. 44, D877–D881 (2016). PubMed PMC

Boyle A. P. et al.. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res. 22, 1790–1797 (2012). PubMed PMC

Cancer Genome Atlas Research Network. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 499, 43–49 (2013). PubMed PMC

Wozniak M. B. et al.. Integrative genome-wide gene expression profiling of clear cell renal cell carcinoma in Czech Republic and in the United States. PLoS ONE 8, e57886 (2013). PubMed PMC

Roadmap Epigenomics Consortium. et al.. Integrative analysis of 111 reference human epigenomes. Nature 518, 317–330 (2015). PubMed PMC

Scelo G. et al.. Variation in genomic landscape of clear cell renal cell carcinoma across Europe. Nat. Commun. 5, 5135 (2014). PubMed

Brugarolas J. Molecular genetics of clear-cell renal cell carcinoma. J. Clin. Oncol. 32, 1968–1976 (2014). PubMed PMC

Zhang L. et al.. Fas-associated factor 1 is a scaffold protein that promotes beta-transducin repeat-containing protein (beta-TrCP)-mediated beta-catenin ubiquitination and degradation. J. Biol. Chem. 287, 30701–30710 (2012). PubMed PMC

Linehan W. M., Rubin J. S. & Bottaro D. P. VHL loss of function and its impact on oncogenic signaling networks in clear cell renal cell carcinoma. Int. J. Biochem. Cell Biol. 41, 753–756 (2009). PubMed PMC

DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium. et al.. Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. Nat. Genet. 46, 234–244 (2014). PubMed PMC

Harder M. N. et al.. The type 2 diabetes risk allele of TMEM154-rs6813195 associates with decreased beta cell function in a study of 6,486 Danes. PLoS ONE 10, e0120890 (2015). PubMed PMC

Finnberg N., Klein-Szanto A. J. & El-Deiry W. S. TRAIL-R deficiency in mice promotes susceptibility to chronic inflammation and tumorigenesis. J. Clin. Invest. 118, 111–123 (2008). PubMed PMC

Kumar P., Henikoff S. & Ng P. C. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc. 4, 1073–1081 (2009). PubMed

Adzhubei I. A. et al.. A method and server for predicting damaging missense mutations. Nat. Methods 7, 248–249 (2010). PubMed PMC

Suarez F. et al.. Incidence, presentation, and prognosis of malignancies in ataxia-telangiectasia: a report from the French national registry of primary immune deficiencies. J. Clin. Oncol. 33, 202–208 (2015). PubMed

Savage S. A. & Bertuch A. A. The genetics and clinical manifestations of telomere biology disorders. Genet. Med. 12, 753–764 (2010). PubMed PMC

Codd V. et al.. Identification of seven loci affecting mean telomere length and their association with disease. Nat. Genet. 45, 422–427 (2013). PubMed PMC

Chubb D. et al.. Common variation at 3q26.2, 6p21.33, 17p11.2 and 22q13.1 influences multiple myeloma risk. Nat. Genet. 45, 1221–1225 (2013). PubMed PMC

Speedy H. E. et al.. A genome-wide association study identifies multiple susceptibility loci for chronic lymphocytic leukemia. Nat. Genet. 46, 56–60 (2014). PubMed

Figueroa J. D. et al.. Genome-wide association study identifies multiple loci associated with bladder cancer risk. Hum. Mol. Genet. 23, 1387–1398 (2014). PubMed PMC

Houlston R. S. et al.. Meta-analysis of three genome-wide association studies identifies susceptibility loci for colorectal cancer at 1q41, 3q26.2, 12q13.13 and 20q13.33. Nat. Genet. 42, 973–977 (2010). PubMed PMC

Walsh K. M. et al.. Variants near TERT and TERC influencing telomere length are associated with high-grade glioma risk. Nat. Genet. 46, 731–735 (2014). PubMed PMC

Levy D. et al.. Genome-wide association identifies OBFC1 as a locus involved in human leukocyte telomere biology. Proc. Natl Acad. Sci. USA 107, 9293–9298 (2010). PubMed PMC

Law M. H. et al.. Genome-wide meta-analysis identifies five new susceptibility loci for cutaneous malignant melanoma. Nat. Genet. 47, 987–995 (2015). PubMed PMC

Howie B., Fuchsberger C., Stephens M., Marchini J. & Abecasis G. R. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat. Genet. 44, 955–959 (2012). PubMed PMC

Howie B. N., Donnelly P. & Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 5, e1000529 (2009). PubMed PMC

Lee S. H., Wray N. R., Goddard M. E. & Visscher P. M. Estimating missing heritability for disease from genome-wide association studies. Am. J. Hum. Genet. 88, 294–305 (2011). PubMed PMC

Yang J. et al.. Common SNPs explain a large proportion of the heritability for human height. Nat. Genet. 42, 565–569 (2010). PubMed PMC

Sampson J. N. et al.. Analysis of heritability and shared heritability based on genome-wide association studies for thirteen cancer types. J. Natl Cancer Inst. 107, djv279 (2015). PubMed PMC

Du P., Kibbe W. A. & Lin S. M. lumi: a pipeline for processing Illumina microarray. Bioinformatics 24, 1547–1548 (2008). PubMed

Li H. & Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 7 (2009). PubMed PMC

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...