Browsing by Author "Chanock, Stephen J."

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  • A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci
    Rothman, Nathaniel; Real, Francisco X.; Serra, Consol; Lloreta Trull, Josep, 1958-; Chanock, Stephen J. (Nature Research, 2010)
    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 ...
  • A single nucleotide polymorphism tags variation in the arylamine N-acetyltransferase 2 phenotype in populations of European background
    García Closas, Montserrat; Hein, David W.; Silverman, Debra T.; Malats i Riera, Núria; Yeager, Meredith; Jacobs, Kevin; Doll, Mark A.; Figueroa, Jonine D.; Baris, Dalsu; Schwenn, Molly; Kogevinas, Manolis; Johnson, Alison; Chatterjee, Nilanjan; Moore, Lee E.; Moeller, Timothy; Real, Francisco X.; Chanock, Stephen J.; Rothman, Nathaniel (Lippincott Williams & Wilkins, 2011)
    The arylamine N-acetyltransferase 2 (NAT2) slow acetylation phenotype is an established risk factor for urinary bladder cancer. We reported earlier on this risk association using NAT2 phenotypic categories inferred from ...
  • Application of multi-SNP approaches Bayesian LASSO and AUC-RF to detect main effects of inflammatory-gene variants associated with bladder cancer risk
    López De Maturana, Evangelina; Ye, Yuanqing; Calle, M. Luz; Rothman, Nathaniel; Urrea, Víctor; Kogevinas, Manolis; Petrus, Sandra; Chanock, Stephen J.; Tardón, Adonina; García Closas, Montserrat; González Neira, Anna; Vellalta, Gemma; Carrato, Alfredo; Navarro i Cuartiellas, Arcadi, 1969-; Lorente-Galdós, Belén, 1981-; Silverman, Debra T.; Real, Francisco X.; Wu, Xifeng; Malats i Riera, Núria (Public Library of Science (PLoS), 2013)
    The relationship between inflammation and cancer is well established in several tumor types, including bladder cancer. We performed an association study between 886 inflammatory-gene variants and bladder cancer risk in ...
  • Characterization of large structural genetic mosaicism in human autosomes
    Machiela, Mitchell J.; Real, Francisco X.; Rodríguez Santiago, Benjamín; Pérez Jurado, Luis Alberto; Chanock, Stephen J. (Elsevier, 2015)
    Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a ...
  • Erratum to: The UBC-40 urothelial bladder cancer cell line index: a genomic resource for functional studies
    Earl, Julie; Rico, Daniel; Carrillo, Enrique; Rodríguez Santiago, Benjamín; Méndez Pertuz, Marinela; Auer, Herbert; Gómez, Gonzalo; Barton Grossman, Herbert; Pisano, David G.; Schulz, Wolfgang; Pérez Jurado, Luis Alberto; Carrato, Alfredo; Theodorescu, Dan; Chanock, Stephen J.; Valencia, Alfonso; Real, Francisco X. (BioMed Central, 2015)
    Following the publication of our recent article in BMC Genomics [1] a number of aspects were called to our attention. We have carefully reviewed the experiments reported in this manuscript, as well as additional data from ...
  • A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data
    González Ruiz, Juan Ramón; Rodríguez Santiago, Benjamín; Cáceres, Alejandro; Pique Regi, Roger; Rothman, Nathaniel; Chanock, Stephen J.; Armengol i Dulcet, Lluís; Pérez Jurado, Luis Alberto (BioMed Central, 2011)
    Background: Mosaicism for copy number and copy neutral chromosomal rearrangements has been recently identified as a relatively common source of genetic variation in the normal population. However its prevalence is poorly ...
  • Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome
    Machiela, Mitchell J.; Real, Francisco X.; Rodriguez-Santiago, Benjamin; Pérez Jurado, Luis Alberto; Chanock, Stephen J. (Nature Publishing Group, 2016)
    To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected ...
  • Genetic and non-genetic predictors of LINE-1 methylation in leukocyte DNA
    Tajuddin, Salman Muhammad; Amaral, André F.S.; Fernández, Agustín F.; Rodriguez Rodero, Sandra; Rodríguez, Ramón María; Moore, Lee E.; Tardón, Adonina; Carrato, Alfredo; García Closas, Montserrat; Silverman, Debra T.; Jackson, Brian P.; García Closas, Reina; Cook, Ashley L.; Cantor, Kenneth P; Chanock, Stephen J.; Kogevinas, Manolis; Rothman, Nathaniel; Real, Francisco X.; Malats i Riera, Núria (National Institute of Environmental Health Sciences (NIEHS), 2013)
    Background: Altered DNA methylation has been associated with various diseases. Objective: We evaluated the association between levels of methylation in leukocyte DNA at long interspersed nuclear element 1 (LINE-1) and ...
  • Genetic variation in the TP53 pathway and bladder cancer risk: a comprehensive analysis
    Pineda, Silvia; Milne, Roger L.; Calle, M. Luz; Rothman, Nathaniel; López De Maturana, Evangelina; Herranz, Jesús; Kogevinas, Manolis; Chanock, Stephen J.; Tardón, Adonina; Márquez, Mirari; Guey, Lin T.; García Closas, Montserrat; Lloreta Trull, Josep, 1958-; Baum, Erin; González Neira, Anna; Carrato, Alfredo; Navarro i Cuartiellas, Arcadi, 1969-; Silverman, Debra T.; Real, Francisco X.; Malats i Riera, Núria (Public Library of Science (PLoS), 2014)
    Introduction: Germline variants in TP63 have been consistently associated with several tumors, including bladder cancer, indicating the importance of TP53 pathway in cancer genetic susceptibility. However, variants in other ...
  • Genome-wide CNV analysis replicates the association between GSTM1 deletion and bladder cancer: a support for using continuous measurement from SNP-array data
    Marenne, Gaëlle; Real, Francisco X.; Rothman, Nathaniel; Rodríguez Santiago, Benjamín; Pérez Jurado, Luis Alberto; Kogevinas, Manolis; García Closas, Montserrat; Silverman, Debra T.; Chanock, Stephen J.; Génin, Emmanuelle; Malats i Riera, Núria (BioMed Central, 2012)
    BACKGROUND: Structural variations such as copy number variants (CNV) influence the expression of different phenotypic traits. Algorithms to identify CNVs through SNP-array platforms are available. The ability to evaluate ...
  • Genomic DNA hypomethylation as a biomarker for bladder cancer susceptibility in the Spanish Bladder Cancer Study: a case-control study
    Moore, Lee E.; Pfeiffer, Ruth M.; Poscablo, Cristina; Real, Francisco X.; Kogevinas, Manolis; Silverman, Debra T.; García Closas, Reina; Chanock, Stephen J.; Tardón, Adonina; Serra, Consol; Carrato, Alfredo; Dosemeci, Mustafa; García Closas, Montserrat; Esteller, Manel; Fraga, Mario F.; Rothman, Nathaniel; Malats i Riera, Núria (Elsevier, 2008)
    BACKGROUND: DNA hypomethylation has been suggested to cause genomic instability and increase cancer risk. We aimed to test the hypothesis that DNA hypomethylation is associated with increased risk of bladder cancer. METHODS: ...
  • Integration Analysis of Three Omics Data Using Penalized Regression Methods: An Application to Bladder Cancer.
    Pineda, Silvia; Real, Francisco X.; Kogevinas, Manolis; Carrato, Alfredo; Chanock, Stephen J.; Malats i Riera, Núria; Van Steen, Kristel (Public Library of Science, 2015)
    Omics data integration is becoming necessary to investigate the genomic mechanisms involved in complex diseases. During the integration process, many challenges arise such as data heterogeneity, the smaller number of ...
  • LINE-1 methylation in leukocyte DNA, interaction with phosphatidylethanolamine N-methyltransferase variants and bladder cancer risk
    Amaral, André F.S.; Tajuddin, Salman Muhammad; Fernández, Agustín F.; Chanock, Stephen J.; Silverman, Debra T.; Tardón, Adonina; Carrato, Alfredo; García Closas, Montserrat; Jackson, Brian P.; Toraño, Estela; Márquez, Miriam; González Urdinguio, Rocío; García Closas, Reina; Rothman, Nathaniel; Kogevinas, Manolis; Real, Francisco X.; Fernández Fraga, Mario; Malats i Riera, Núria (Cancer Research UK, 2014)
    Background: Aberrant global DNA methylation is shown to increase cancer risk. LINE-1 has been proven a measure of global DNA methylation. The objectives of this study were to assess the association between LINE-1 methylation ...
  • Mosaic loss of chromosome Y is associated with common variation near TCL1A
    Zhou, W.; Real, Francisco X.; Rodríguez Santiago, Benjamín; Pérez Jurado, Luis Alberto; Chanock, Stephen J. (Nature Publishing Group, 2016)
    Mosaic loss of chromosome Y (mLOY) leading to gonosomal XY/XO commonly occurs during aging, particularly in smokers. We investigated whether mLOY was associated with non-hematological cancer in three prospective cohorts ...
  • Mosaic uniparental disomies and aneuploidies as large structural variants of the human genome
    Rodríguez Santiago, Benjamín; Malats i Riera, Núria; Rothman, Nathaniel; Armengol i Dulcet, Lluís; García Closas, Montserrat; Kogevinas, Manolis; Villa, Olaya; Hutchinson, Amy; Earl, Julie; Marenne, Gaëlle; Jacobs, Kevin; Rico, Daniel; Tardón, Adonina; Carrato, Alfredo; Thomas, Gilles; Valencia, Alfonso; Silverman, Debra T.; Real, Francisco X.; Chanock, Stephen J.; Pérez Jurado, Luis Alberto (Elsevier, 2010)
    Mosaicism is defined as the coexistence of cells with different genetic composition within an individual, caused by postzygotic somatic mutation. Although somatic mosaicism for chromosomal abnormalities is a well-established ...
  • Polymorphisms in GSTT1, GSTZ1, AND CYP2E1, disinfection by-products, and risk of bladder cancer in Spain
    Cantor, Kenneth P; Villanueva Belmonte, Cristina; Silverman, Debra T.; Figueroa, Jonine D.; Real, Francisco X.; García Closas, Montserrat; Malats i Riera, Núria; Chanock, Stephen J.; Yeager, Meredith; Tardón, Adonina; García Closas, Reina; Serra, Consol; Carrato, Alfredo; Castaño Vinyals, Gemma; Samanic, Claudine; Rothman, Nathaniel; Kogevinas, Manolis (National Institute of Environmental Health Sciences (NIEHS), 2010)
    Background: Bladder cancer has been linked with long-term exposure to disinfection by-products (DBPs) in drinking water.Objectives: In this study we investigated the combined influence of DBP exposure and polymorphisms in ...
  • Prediction of non-muscle invasive bladder cancer outcomes assessed by innovative multimarker prognostic models.
    López De Maturana, Evangelina; Picornell, Antoni; Masson-Lecomte, Alexandra; Kogevinas, Manolis; Márquez, Mirari; Carrato, Alfredo; Tardón, Adonina; Lloreta Trull, Josep, 1958-; García Closas, Montserrat; Silverman, Debra T.; Rothman, Nathaniel; Chanock, Stephen J.; Real, Francisco X.; Goddard, M. E.; Malats i Riera, Núria; SBC/EPICURO Study Investigators (BioMed Central, 2016)
    BACKGROUND: We adapted Bayesian statistical learning strategies to the prognosis field to investigate if genome-wide common SNP improve the prediction ability of clinico-pathological prognosticators and applied it to ...
  • The UBC-40 urothelial bladder cancer cell line index: a genomic resource for functional studies
    Earl, Julie; Rico, Daniel; Carrillo, Enrique; Rodríguez Santiago, Benjamín; Méndez Pertuz, Marinela; Auer, Herbert; Gómez, Gonzalo; Barton Grossman, Herbert; Pisano, David G.; Schulz, Wolfgang; Pérez Jurado, Luis Alberto; Carrato, Alfredo; Theodorescu, Dan; Chanock, Stephen J.; Valencia, Alfonso; Real, Francisco X. (BioMed Central, 2015)
    Background. Urothelial bladder cancer is a highly heterogeneous disease. Cancer cell lines are useful tools for its study. This is a comprehensive genomic characterization of 40 urothelial bladder carcinoma (UBC) cell lines ...