Juan Pablo Lewinger

Summary

Affiliation: University of Southern California
Country: USA

Publications

  1. ncbi request reprint Hierarchical Bayes prioritization of marker associations from a genome-wide association scan for further investigation
    Juan Pablo Lewinger
    Department of Preventive Medicine, University of Southern California, Los Angeles, California 90089 9011, USA
    Genet Epidemiol 31:871-82. 2007
  2. pmc Gene-environment interaction in genome-wide association studies
    Cassandra E Murcray
    Department of Preventive Medicine, University of Southern California, Los Angeles, California 90089 9010, USA
    Am J Epidemiol 169:219-26. 2009
  3. pmc Hormone metabolism pathway genes and mammographic density change after quitting estrogen and progestin combined hormone therapy in the California Teachers Study
    Eunjung Lee
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, 1441 Eastlake Avenue, Los Angeles, CA, 90089, USA
    Breast Cancer Res 16:477. 2014
  4. doi request reprint Efficient two-step testing of gene-gene interactions in genome-wide association studies
    Juan Pablo Lewinger
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90032, USA
    Genet Epidemiol 37:440-51. 2013
  5. pmc Comparison of family-based association tests in chromosome regions selected by linkage-based confidence intervals
    Juan Pablo Lewinger
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada
    BMC Genet 6:S62. 2005
  6. pmc Efficient genome-wide association testing of gene-environment interaction in case-parent trios
    W James Gauderman
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, 90033, USA
    Am J Epidemiol 172:116-22. 2010
  7. pmc Red meat and poultry, cooking practices, genetic susceptibility and risk of prostate cancer: results from a multiethnic case-control study
    Amit D Joshi
    Department of Preventive Medicine, University of Southern California Keck School of Medicine, Norris Comprehensive Cancer Center Los Angeles, CA 90033, USA
    Carcinogenesis 33:2108-18. 2012
  8. pmc Tobacco smoking, polymorphisms in carcinogen metabolism enzyme genes, and risk of localized and advanced prostate cancer: results from the California Collaborative Prostate Cancer Study
    Ahva Shahabi
    Department of Preventive Medicine, Keck School of Medicine of USC, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, 90033
    Cancer Med 3:1644-55. 2014
  9. pmc Comprehensive analyses of DNA repair pathways, smoking and bladder cancer risk in Los Angeles and Shanghai
    Roman Corral
    Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
    Int J Cancer 135:335-47. 2014
  10. pmc Confounding and heterogeneity in genetic association studies with admixed populations
    Jinghua Liu
    Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
    Am J Epidemiol 177:351-60. 2013

Detail Information

Publications29

  1. ncbi request reprint Hierarchical Bayes prioritization of marker associations from a genome-wide association scan for further investigation
    Juan Pablo Lewinger
    Department of Preventive Medicine, University of Southern California, Los Angeles, California 90089 9011, USA
    Genet Epidemiol 31:871-82. 2007
    ..We show that the ranking by posterior expectations performs better at selecting the true positive association than a simple ranking of p-values if at least some of the prior covariates have predictive value...
  2. pmc Gene-environment interaction in genome-wide association studies
    Cassandra E Murcray
    Department of Preventive Medicine, University of Southern California, Los Angeles, California 90089 9010, USA
    Am J Epidemiol 169:219-26. 2009
    ..The procedure complements screening for marginal genetic effects and thus has the potential to uncover new genetic signals that have not been identified previously...
  3. pmc Hormone metabolism pathway genes and mammographic density change after quitting estrogen and progestin combined hormone therapy in the California Teachers Study
    Eunjung Lee
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, 1441 Eastlake Avenue, Los Angeles, CA, 90089, USA
    Breast Cancer Res 16:477. 2014
    ..Here, we evaluate the association between polymorphisms in hormone metabolism pathway genes and MD changes when women quit EPT...
  4. doi request reprint Efficient two-step testing of gene-gene interactions in genome-wide association studies
    Juan Pablo Lewinger
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90032, USA
    Genet Epidemiol 37:440-51. 2013
    ..We demonstrate the computational feasibility of the two-step G × G procedure by performing a G × G scan in the asthma GWAS of the University of Southern California Children's Health Study...
  5. pmc Comparison of family-based association tests in chromosome regions selected by linkage-based confidence intervals
    Juan Pablo Lewinger
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada
    BMC Genet 6:S62. 2005
    ....
  6. pmc Efficient genome-wide association testing of gene-environment interaction in case-parent trios
    W James Gauderman
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, 90033, USA
    Am J Epidemiol 172:116-22. 2010
    ..This 2-step scan for G x E interaction is independent of any prior scan that may have been conducted for genetic main effects, and thus has the potential to uncover new genes in a GWAS that have not been previously identified...
  7. pmc Red meat and poultry, cooking practices, genetic susceptibility and risk of prostate cancer: results from a multiethnic case-control study
    Amit D Joshi
    Department of Preventive Medicine, University of Southern California Keck School of Medicine, Norris Comprehensive Cancer Center Los Angeles, CA 90033, USA
    Carcinogenesis 33:2108-18. 2012
    ..008). Our results support a role for carcinogens that accumulate in meats cooked at high temperatures as potential PCA risk factors, and may support a role for heterocyclic amines (HCAs) in PCA etiology...
  8. pmc Tobacco smoking, polymorphisms in carcinogen metabolism enzyme genes, and risk of localized and advanced prostate cancer: results from the California Collaborative Prostate Cancer Study
    Ahva Shahabi
    Department of Preventive Medicine, Keck School of Medicine of USC, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, 90033
    Cancer Med 3:1644-55. 2014
    ..This association was modified by a genetic variant in CYP1A2, thus supporting a role for tobacco carcinogens in PCa risk...
  9. pmc Comprehensive analyses of DNA repair pathways, smoking and bladder cancer risk in Los Angeles and Shanghai
    Roman Corral
    Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
    Int J Cancer 135:335-47. 2014
    ..A SNP that tags both the XRCC6 and SREBF2 genes strongly modifies the association between bladder cancer risk and smoking. ..
  10. pmc Confounding and heterogeneity in genetic association studies with admixed populations
    Jinghua Liu
    Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
    Am J Epidemiol 177:351-60. 2013
    ..The analysis highlights rs10519951 (P = 8.5 × 10(-7)), a SNP lacking any evidence of association from a conventional analysis (P = 0.5)...
  11. pmc Sample size requirements to detect gene-environment interactions in genome-wide association studies
    Cassandra E Murcray
    Department of Preventive Medicine, University of Southern California, Los Angeles, California 90089 9010, USA
    Genet Epidemiol 35:201-10. 2011
    ..15, and a binary exposure with prevalence 0.3, the Murcray, Kooperberg and hybrid methods are 1.90, 1.27, and 1.87 times as efficient, respectively, as the traditional case-control analysis to detect an interaction effect size of 2.0...
  12. pmc Genetic variation in the base excision repair pathway, environmental risk factors, and colorectal adenoma risk
    Roman Corral
    Department of Preventive Medicine, Keck School of Medicine of USC, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
    PLoS ONE 8:e71211. 2013
    ..Our findings strengthen the role of oxidative damage induced by key lifestyle and dietary risk factors in colorectal adenoma formation. ..
  13. pmc Finding novel genes by testing G × E interactions in a genome-wide association study
    W James Gauderman
    Department of Preventive Medicine, University of Southern California, Los Angeles, California 90089, USA
    Genet Epidemiol 37:603-13. 2013
    ..We distribute a new software program (G×Escan, available at http://biostats.usc.edu/software) that implements this new method as well as several other GWIS approaches. ..
  14. pmc Genes involved with folate uptake and distribution and their association with colorectal cancer risk
    Jane C Figueiredo
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 1450 Biggy Street Room 1509J, Los Angeles, CA 90033, USA
    Cancer Causes Control 21:597-608. 2010
    ..In conclusion, we found no significant evidence that genetic variants in FOLR1, GGH, FPGS and SLC19A1 are associated with the risk of colorectal cancer...
  15. pmc Genotype-environment interactions in microsatellite stable/microsatellite instability-low colorectal cancer: results from a genome-wide association study
    Jane C Figueiredo
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
    Cancer Epidemiol Biomarkers Prev 20:758-66. 2011
    ..Therefore, it is unclear whether current hits are modified by environmental exposures or whether there are additional hits whose effects are dependent on environmental exposures...
  16. pmc Using extreme phenotype sampling to identify the rare causal variants of quantitative traits in association studies
    Dalin Li
    Medical Genetics Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
    Genet Epidemiol 35:790-9. 2011
    ..Finally, we expanded the current analysis and design framework to accommodate the CMC approach where multiple rare-variants in the same gene region are analyzed jointly...
  17. pmc Detecting Gene-Environment Interactions for a Quantitative Trait in a Genome-Wide Association Study
    Pingye Zhang
    Department of Preventive Medicine, University of Southern California, Los Angeles, United States of America
    Genet Epidemiol 40:394-403. 2016
    ..Application of this method to a G × Hispanic-ethnicity scan for childhood lung function reveals a SNP near the MARCO locus that was not identified by previous marginal-effect scans. ..
  18. pmc Meat intake, cooking methods, dietary carcinogens, and colorectal cancer risk: findings from the Colorectal Cancer Family Registry
    Amit D Joshi
    Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, 90089
    Cancer Med 4:936-52. 2015
    ..002). Our results support the role of specific meat types and cooking practices as possible sources of human carcinogens relevant for CRC risk...
  19. pmc Hormone metabolism genes and mammographic density in Singapore Chinese women
    Eunjung Lee
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
    Cancer Epidemiol Biomarkers Prev 22:984-6. 2013
    ..We investigated the association between genetic variation in the hormone metabolism and signaling pathway and mammographic density, a strong predictor of breast cancer risk...
  20. doi request reprint Genetic admixture and risk of hypertensive disorders of pregnancy among Latinas in Los Angeles County
    Ahva Shahabi
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
    Epidemiology 24:285-94. 2013
    ..This study examines the role of genetic ancestry and environmental risk factors in the risk of hypertensive disorder of pregnancy among Latinas in Los Angeles County...
  21. pmc Invited commentary: GE-Whiz! Ratcheting gene-environment studies up to the whole genome and the whole exposome
    Duncan C Thomas
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
    Am J Epidemiol 175:203-7; discussion 208-9. 2012
    ....
  22. ncbi request reprint Confidence intervals for multinomial logistic regression in sparse data
    Shelley B Bull
    Samuel Lunenfeld Research Institute, Prosserman Centre for Health Research, Mount Sinai Hospital, Toronto, Ont, Canada M5G 1X5
    Stat Med 26:903-18. 2007
    ..Furthermore, when finite sample bias and data separation are likely to occur, we prefer PLE profile CIs over MLE methods...
  23. pmc Testicular germ cell tumor susceptibility associated with the UCK2 locus on chromosome 1q23
    Fredrick R Schumacher
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
    Hum Mol Genet 22:2748-53. 2013
    ..3 × 10(-3)). Here, we provide substantial evidence for the association between UCK2 genetic variation and TGCT risk...
  24. ncbi request reprint Validity, efficiency, and robustness of a family-based test of association
    Juan Pablo Lewinger
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
    Genet Epidemiol 30:62-76. 2006
    ..To assess robustness, we also evaluated the performance of the tests under scenarios with population stratification and found that although there is a loss of efficiency, our proposed test remains a strong competitor to FBAT...
  25. doi request reprint Novel Gene Expression Signature Predictive of Clinical Recurrence After Radical Prostatectomy in Early Stage Prostate Cancer Patients
    Ahva Shahabi
    Department of Preventive Medicine, Keck School of Medicine of USC, Norris Comprehensive Cancer Center, Los Angeles, California
    Prostate 76:1239-56. 2016
    ..We aimed to identify a gene expression signature that jointly with clinical variables could improve upon the prediction of clinical recurrence after RP for patients with stage T2 PCa...
  26. pmc Adaptive Set-Based Methods for Association Testing
    Yu Chen Su
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
    Genet Epidemiol 40:113-22. 2016
    ..We found the standard ARTP test to have the highest power across our simulations followed closely by the global model of random effects (GMRE) and a least absolute shrinkage and selection operator (LASSO)-based test. ..
  27. pmc Radical Prostatectomy or External Beam Radiation Therapy vs No Local Therapy for Survival Benefit in Metastatic Prostate Cancer: A SEER-Medicare Analysis
    Raj Satkunasivam
    University of Southern California Institute of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine of University of Southern California, Los Angeles, California Norris Comprehensive Cancer Center, Keck School of Medicine of University of Southern California, Los Angeles, California Electronic address
    J Urol 194:378-85. 2015
    ....
  28. pmc Polymorphisms in carcinogen metabolism enzymes, fish intake, and risk of prostate cancer
    Chelsea Catsburg
    Department of Preventive Medicine, University of Southern California Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
    Carcinogenesis 33:1352-9. 2012
    ..However, the gene-diet interactions should be interpreted with caution given the limited sample size. Thus, our findings require further validation with additional studies...
  29. pmc The association of polymorphisms in hormone metabolism pathway genes, menopausal hormone therapy, and breast cancer risk: a nested case-control study in the California Teachers Study cohort
    Eunjung Lee
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, Los Angeles, CA 90089, USA
    Breast Cancer Res 13:R37. 2011
    ..It therefore seems plausible that variation in genes involved in metabolism of these hormones may affect breast cancer risk, and that these associations may vary depending on menopausal status and use of hormone therapy...