John S Witte

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc HOXB13 mutation and prostate cancer: studies of siblings and aggressive disease
    John S Witte
    Departments of Epidemiology and Biostatistics and Urology, University of California San Francisco, San Francisco, CA 94158, USA
    Cancer Epidemiol Biomarkers Prev 22:675-80. 2013
  2. pmc Rare genetic variants and treatment response: sample size and analysis issues
    John S Witte
    Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California, San Francisco, CA 94143, U S A
    Stat Med 31:3041-50. 2012
  3. pmc Parallel biocomputing
    Kenneth S Kompass
    Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
    Source Code Biol Med 6:4. 2011
  4. doi request reprint Personalized prostate cancer screening: improving PSA tests with genomic information
    John S Witte
    Department of Epidemiology and Biostatistics, Institute for Human Genetics, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
    Sci Transl Med 2:62ps55. 2010
  5. doi request reprint Genome-wide association studies and beyond
    John S Witte
    Institute for Human Genetics, Departments of Epidemiology and Biostatistics and Urology, University of California, San Francisco, San Francisco, California 94158 9001, USA
    Annu Rev Public Health 31:9-20 4 p following 20. 2010
  6. pmc Polygenic modeling of genome-wide association studies: an application to prostate and breast cancer
    John S Witte
    Institute for Human Genetics, Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
    OMICS 15:393-8. 2011
  7. ncbi request reprint Introduction to Genetic Analysis Workshop 15 summaries
    John S Witte
    Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California at San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
    Genet Epidemiol 31:S1-6. 2007
  8. pmc Prostate cancer genomics: towards a new understanding
    John S Witte
    Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California, San Francisco, 513 Parnassus Avenue, Room S965, San Francisco, California 94143 0794, USA
    Nat Rev Genet 10:77-82. 2009
  9. pmc Association of the innate immunity and inflammation pathway with advanced prostate cancer risk
    Rémi Kazma
    Department of Epidemiology, and Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 7:e51680. 2012
  10. pmc 8q24 and prostate cancer: association with advanced disease and meta-analysis
    Iona Cheng
    Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143 0794, USA
    Eur J Hum Genet 16:496-505. 2008

Collaborators

Detail Information

Publications81

  1. pmc HOXB13 mutation and prostate cancer: studies of siblings and aggressive disease
    John S Witte
    Departments of Epidemiology and Biostatistics and Urology, University of California San Francisco, San Francisco, CA 94158, USA
    Cancer Epidemiol Biomarkers Prev 22:675-80. 2013
    ..Recent work detected for the first time a high-risk prostate cancer mutation, in homeobox B13 (HOXB13) among European-Americans...
  2. pmc Rare genetic variants and treatment response: sample size and analysis issues
    John S Witte
    Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California, San Francisco, CA 94143, U S A
    Stat Med 31:3041-50. 2012
    ..Such analyses provide a valuable opportunity to more fully decipher the genomic basis of response to treatment...
  3. pmc Parallel biocomputing
    Kenneth S Kompass
    Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
    Source Code Biol Med 6:4. 2011
    ..abstract:..
  4. doi request reprint Personalized prostate cancer screening: improving PSA tests with genomic information
    John S Witte
    Department of Epidemiology and Biostatistics, Institute for Human Genetics, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
    Sci Transl Med 2:62ps55. 2010
    ..These findings are an important step toward incorporating genetic markers into PSA screening, with the ultimate goal of devising personalized PSA tests for use in the clinic...
  5. doi request reprint Genome-wide association studies and beyond
    John S Witte
    Institute for Human Genetics, Departments of Epidemiology and Biostatistics and Urology, University of California, San Francisco, San Francisco, California 94158 9001, USA
    Annu Rev Public Health 31:9-20 4 p following 20. 2010
    ..Such studies should help clarify the potential value of genetic testing to the public's health...
  6. pmc Polygenic modeling of genome-wide association studies: an application to prostate and breast cancer
    John S Witte
    Institute for Human Genetics, Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
    OMICS 15:393-8. 2011
    ..This supports the further development and application of polygenic models to genomic data...
  7. ncbi request reprint Introduction to Genetic Analysis Workshop 15 summaries
    John S Witte
    Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California at San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
    Genet Epidemiol 31:S1-6. 2007
    ..Further details on GAW15 are provided here, and the primary findings from the workshop are highlighted in the following group summary papers...
  8. pmc Prostate cancer genomics: towards a new understanding
    John S Witte
    Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California, San Francisco, 513 Parnassus Avenue, Room S965, San Francisco, California 94143 0794, USA
    Nat Rev Genet 10:77-82. 2009
    ..Lessons learned from these studies provide strategies for further deciphering the genetic causes of prostate cancer and other diseases...
  9. pmc Association of the innate immunity and inflammation pathway with advanced prostate cancer risk
    Rémi Kazma
    Department of Epidemiology, and Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 7:e51680. 2012
    ..Our results suggest that the innate immunity and inflammation pathway may play a modest role in the etiology of advanced prostate cancer through multiple small effects...
  10. pmc 8q24 and prostate cancer: association with advanced disease and meta-analysis
    Iona Cheng
    Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143 0794, USA
    Eur J Hum Genet 16:496-505. 2008
    ..Our findings provide the first confirmation that the three 8q24 regions independently influence the risk of prostate cancer and, in particular, advanced disease...
  11. ncbi request reprint Association of testis derived transcript gene variants and prostate cancer risk
    Xin Liu
    Department of Epidemiology and Biostatistics, and Institute for Human Genetics, University of California, San Francisco, San Francisco, California 94143 0794, USA
    J Urol 177:894-8. 2007
    ..To investigate this concept we evaluated the effects of 7 tagging single nucleotide polymorphisms that comprehensively captured the common genetic variants in TES on aggressive prostate cancer in a case-control study...
  12. pmc Carboxypeptidase 4 gene variants and early-onset intermediate-to-high risk prostate cancer
    Phillip L Ross
    Department of Urology, University of California San Francisco, San Francisco, CA, USA
    BMC Cancer 9:69. 2009
    ..We examined the association between genetic variation in CPA4 and intermediate-to-high risk prostate cancer...
  13. ncbi request reprint Plasminogen activator inhibitor type-1 (PAI-1) polymorphism 4G/5G is associated with prostate cancer among men with a positive family history
    Eric Jorgenson
    Department of Epidemiology and Biostatistics, Center for Human Genetics, University of California, San Francisco, San Francisco, California 94143 0794, USA
    Prostate 67:172-7. 2007
    ..To evaluate the effect of PAI-1 expression on cancer development, we examined the association of the 4G/5G polymorphism in a sibling-based case-control study of prostate cancer...
  14. ncbi request reprint Polymorphisms in polycyclic aromatic hydrocarbon metabolism and conjugation genes, interactions with smoking and prostate cancer risk
    Nora L Nock
    Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, USA
    Cancer Epidemiol Biomarkers Prev 15:756-61. 2006
    ..95; 95% CI, 0.53-1.71). Our results highlight the importance of considering genetic modifiers of carcinogens when evaluating smoking in prostate cancer...
  15. ncbi request reprint Nonsteroidal antiinflammatory drugs and decreased risk of advanced prostate cancer: modification by lymphotoxin alpha
    Xin Liu
    Department of Epidemiology and Biostatistics and Center for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
    Am J Epidemiol 164:984-9. 2006
    ..30). The authors observed similar associations when examining dose/duration of NSAID use. This suggests that any potential chemoprevention of prostate cancer by NSAIDs may be most appropriate for men with the LTA +80CC genotype...
  16. ncbi request reprint Polymorphisms in estrogen bioactivation, detoxification and oxidative DNA base excision repair genes and prostate cancer risk
    Nora L Nock
    Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
    Carcinogenesis 27:1842-8. 2006
    ....
  17. pmc Novel missense mutations of the Deleted-in-AZoospermia-Like (DAZL) gene in infertile women and men
    Joyce Y Tung
    Human Embryonic Stem Cell Center, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California at San Francisco, San Francisco, CA 94143, USA
    Reprod Biol Endocrinol 4:40. 2006
    ..Recently, we showed that there are several common polymorphisms within the DAZL gene that are associated with age at ovarian failure/menopause and sperm count...
  18. doi request reprint The impact of improved microarray coverage and larger sample sizes on future genome-wide association studies
    Karla J Lindquist
    Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158 9001, USA
    Genet Epidemiol 37:383-92. 2013
    ..Furthermore, increasing sample size has a much larger impact than increasing coverage on the potential of future GWAS to detect additional SNP-disease associations and heritability...
  19. ncbi request reprint Genome-wide scan of brothers: replication and fine mapping of prostate cancer susceptibility and aggressiveness loci
    John S Witte
    Department of Epidemiology and Biostatistics, University of California, San Francisco, California 94143 0560, USA
    Prostate 57:298-308. 2003
    ..Here we investigate prostate cancer susceptibility and aggressiveness with genome-wide linkage analyses of affected brothers...
  20. ncbi request reprint Toll-like receptor 4 genetic variation and advanced prostate cancer risk
    Iona Cheng
    Department of Epidemiology and Biostatistics and Center of Human Genetics, University of California at San Francisco, 94143 0794, USA
    Cancer Epidemiol Biomarkers Prev 16:352-5. 2007
    ..006). We estimated through permutation analysis that a similarly strong result would occur by chance 2.5% of the time. Our findings support previous studies and suggest that inherited differences in TLR4 influence prostate cancer risk...
  21. ncbi request reprint Case-control analyses: Geneopardy!
    Eric Jorgenson
    Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, California 94143, USA
    Genet Epidemiol 29:S86-90. 2005
    ..Finally, one group examined the optimal number of markers for the genomic control approach to population stratification...
  22. pmc The association between a Darc gene polymorphism and clinical outcomes in African American patients with acute lung injury
    Kirsten Neudoerffer Kangelaris
    Department of Medicine, Division of General Internal Medicine, University of California, San Francisco, San Francisco, CA 94143 0131, USA
    Chest 141:1160-9. 2012
    ..We sought to determine the effect of the functional rs2814778 polymorphism, C/C genotype (Duffy null state), on clinical outcomes in African Americans with acute lung injury...
  23. doi request reprint Impact of polymorphisms in drug pathway genes on disease-free survival in adults with acute myeloid leukemia
    Sook Wah Yee
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
    J Hum Genet 58:353-61. 2013
    ..7, P=0.028 for 125 non-European patients). Thus, for the first time, genetic variants in drug pathway genes are shown to be associated with DFS in AML patients treated with chemotherapy-based autologous ASCT. ..
  24. ncbi request reprint No association between a tetranucleotide repeat polymorphism of CYP19 and prostate cancer
    Li Li
    Department of Epidemiology and Biostatistics, University of California at San Francisco, 500 Parnassus Avenue, MU 420 West, San Francisco, CA 94143 0560
    Cancer Epidemiol Biomarkers Prev 13:2280-1. 2004
  25. ncbi request reprint No association between genetic polymorphisms in insulin and insulin receptor substrate-1 and prostate cancer
    Li Li
    Department of Epidemiology and Biostatistics, University of California, San Francisco, 500 Parnassus Avenue, MU 420 West, San Francisco, CA 94143 0560, USA
    Cancer Epidemiol Biomarkers Prev 14:2462-3. 2005
  26. pmc VALID: visualization of association study results and linkage disequilibrium
    Eric Jorgenson
    Department of Biopharmaceutical Sciences, University of California, San Francisco, San Francisco, California 94143 0794, USA
    Genet Epidemiol 33:599-603. 2009
    ....
  27. ncbi request reprint Trans-fatty acid intake and increased risk of advanced prostate cancer: modification by RNASEL R462Q variant
    Xin Liu
    Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California, San Francisco, CA 94143 0794, USA
    Carcinogenesis 28:1232-6. 2007
    ..This suggests that among Caucasians, positive association between higher trans-fatty acid consumption and prostate cancer may be modified by the functional RNASEL variant R462Q...
  28. ncbi request reprint Relationship between body size and prostate cancer in a sibling based case-control study
    Xin Liu
    Department of Epidemiology and Biostatistics, University of California San Francisco, 500 Parnassus Avenue, San Francisco, CA 94143 0560, USA
    J Urol 174:2169-73. 2005
    ..To further understand this we examined the effects of weight, height, body mass index and lean body mass (LBM) on PCa risk and aggressiveness in a sibling based case-control study...
  29. pmc Co-regulatory expression quantitative trait loci mapping: method and application to endometrial cancer
    Kenneth S Kompass
    Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California, San Francisco, USA
    BMC Med Genomics 4:6. 2011
    ..Expression quantitative trait loci (eQTL) studies have helped identify the genetic determinants of gene expression. Understanding the potential interacting mechanisms underlying such findings, however, is challenging...
  30. pmc Hierarchical modeling in association studies of multiple phenotypes
    Xin Liu
    Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94143 0560, USA
    BMC Genet 6:S104. 2005
    ..We observed that using HM to evaluate the association between SNPs and multiple related phenotypes slightly increased power for detecting the true associations and also led to fewer false-positive results...
  31. ncbi request reprint A gene-centric approach to genome-wide association studies
    Eric Jorgenson
    Department of Epidemiology and Biostatistics, and Center for Human Genetics, University of California, San Francisco, California 94143 0794, USA
    Nat Rev Genet 7:885-91. 2006
    ..We therefore argue that resources should be developed to make gene-centric genome-wide association studies feasible...
  32. ncbi request reprint MIC1 and IL1RN genetic variation and advanced prostate cancer risk
    Iona Cheng
    Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94143 0794, USA
    Cancer Epidemiol Biomarkers Prev 16:1309-11. 2007
  33. pmc Coverage and power in genomewide association studies
    Eric Jorgenson
    Department of Epidemiology and Biostatistics, Center for Human Genetics, University of California San Francisco, San Francisco, CA 94143 0794, USA
    Am J Hum Genet 78:884-8. 2006
    ..In contrast, use of the "cumulative r2 adjusted power" measure presented here gives more-accurate estimates of power for genomewide association studies...
  34. pmc A meta-analysis identifies new loci associated with body mass index in individuals of African ancestry
    Keri L Monda
    The Center for Observational Research, Amgen, Inc Thousand Oaks, California, USA
    Nat Genet 45:690-6. 2013
    ..7 × 10(-7)), five of which reached genome-wide significance. These findings provide strong support for shared BMI loci across populations, as well as for the utility of studying ancestrally diverse populations...
  35. pmc Impact of meat consumption, preparation, and mutagens on aggressive prostate cancer
    Sanoj Punnen
    Department of Urology, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 6:e27711. 2011
    ..The association between meat consumption and prostate cancer remains unclear, perhaps reflecting heterogeneity in the types of tumors studied and the method of meat preparation--which can impact the production of carcinogens...
  36. ncbi request reprint Genome-wide association analyses of expression phenotypes
    Gary K Chen
    Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California at San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
    Genet Epidemiol 31:S7-S11. 2007
    ..Finally, for datasets with small sample sizes but a large number of features like the Genetic Analysis Workshop 15 dataset, machine learning approaches may be more practical than traditional parametric approaches...
  37. pmc A genetic signature of spina bifida risk from pathway-informed comprehensive gene-variant analysis
    Nicholas J Marini
    Department of Molecular and Cellular Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
    PLoS ONE 6:e28408. 2011
    ..Furthermore, the identification of ethnic-specific risk signatures for spina bifida resonated with epidemiological data suggesting that the underlying pathogenesis may differ between Hispanic and non-Hispanic groups...
  38. pmc Enriching the analysis of genomewide association studies with hierarchical modeling
    Gary K Chen
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143 0794, USA
    Am J Hum Genet 81:397-404. 2007
    ..By quantitatively harnessing all available information in GWAs, hierarchical modeling may more clearly distinguish true causal variants from noise...
  39. pmc Comprehensive approach to analyzing rare genetic variants
    Thomas J Hoffmann
    Department of Epidemiology and Biostatistics and Institute of Human Genetics, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 5:e13584. 2010
    ..This agnostic approach allows one to efficiently analyze the association between rare variants and disease while avoiding assumptions required by other approaches for grouping such variants...
  40. ncbi request reprint Genome-wide association studies of cancer
    Eric Jorgenson
    University of California, Department of Epidemiology and Biostatistics, San Francisco, CA 94143 0794, USA
    Future Oncol 3:419-27. 2007
    ..g., colorectal). Here we discuss the major issues involved in conducting genome-wide association studies and how these studies can be used to examine cancer phenotypes...
  41. pmc Dietary omega-3 fatty acids, cyclooxygenase-2 genetic variation, and aggressive prostate cancer risk
    Vincent Fradet
    Departments of Urology, Institute for Human Genetics, University of California at San Francisco, San Francisco, California 94143 0794, USA
    Clin Cancer Res 15:2559-66. 2009
    ..This potential effect may be modified by genetic variation in cyclooxygenase-2 (COX-2), a key enzyme in fatty acid metabolism and inflammation...
  42. doi request reprint Antioxidant and vitamin E transport genes and risk of high-grade prostate cancer and prostate cancer recurrence
    Scott R Bauer
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
    Prostate 73:1786-95. 2013
    ..Thus, we examined circulating vitamin E and vitamin E-related genes in relation to risk of high-grade prostate cancer and prostate cancer recurrence among men initially diagnosed with clinically organ-confined disease...
  43. doi request reprint Turning of COGS moves forward findings for hormonally mediated cancers
    Lori C Sakoda
    Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
    Nat Genet 45:345-8. 2013
    ..We summarize and provide insights into this collection of papers from COGS and discuss the implications of the results and future directions for such efforts...
  44. pmc A genome-wide association study identifies novel loci for paclitaxel-induced sensory peripheral neuropathy in CALGB 40101
    R Michael Baldwin
    Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th Street RH584E, San Francisco, CA 94158 2911, USA
    Clin Cancer Res 18:5099-109. 2012
    ..Sensory peripheral neuropathy is a common and sometimes debilitating toxicity associated with paclitaxel therapy. This study aims to identify genetic risk factors for the development of this toxicity...
  45. doi request reprint Joint association testing of common and rare genetic variants using hierarchical modeling
    Niall J Cardin
    Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California, San Francisco, California 94158 9001, USA
    Genet Epidemiol 36:642-51. 2012
    ....
  46. pmc Hierarchical modeling of linkage disequilibrium: genetic structure and spatial relations
    David V Conti
    Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, 44106, USA
    Am J Hum Genet 72:351-63. 2003
    ..This work demonstrates that hierarchical modeling of linkage disequilibrium is a valuable and flexible approach for fine-scale mapping...
  47. pmc Impact of consumption of vegetable, fruit, grain, and high glycemic index foods on aggressive prostate cancer risk
    Jill Hardin
    Department of Epidemiology, University of California at San Francisco, San Francisco, California 94158 9001, USA
    Nutr Cancer 63:860-72. 2011
    ..02). These results were driven by a number of specific foods within the food groups. Our findings support the hypothesis that diets high in vegetables and low in high glycemic index foods decrease risk of aggressive prostate cancer...
  48. pmc Genome-wide association study of prostate cancer in men of African ancestry identifies a susceptibility locus at 17q21
    Christopher A Haiman
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, California, USA
    Nat Genet 43:570-3. 2011
    ..Further studies are needed to investigate the biological contribution of this allele to prostate cancer risk. These findings emphasize the importance of conducting genome-wide association studies in diverse populations...
  49. pmc Comparison of missing data approaches in linkage analysis
    Chao Xing
    Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, USA
    BMC Genet 4:S44. 2003
    ..Therefore, we compare here six methods of imputing missing repeated phenotypes on results from genome-wide linkage analyses of four quantitative traits from the Framingham Heart Study cohort...
  50. pmc Omega-3 fatty acids, genetic variants in COX-2 and prostate cancer
    Adam C Reese
    Department of Urology, University of California San Francisco, CA 94158, USA
    J Nutrigenet Nutrigenomics 2:149-58. 2009
    ..Overall, results to date support the hypothesis that long-chain omega-3 PUFAs may impact prostate inflammation and carcinogenesis via the COX-2 enzymatic pathway...
  51. doi request reprint Does accounting for gene-environment interactions help uncover association between rare variants and complex diseases?
    Rémi Kazma
    Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California, San Francisco, CA, USA
    Hum Hered 74:205-14. 2012
    ....
  52. pmc Socioeconomic status and prostate cancer incidence and mortality rates among the diverse population of California
    Iona Cheng
    Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143 0794, USA
    Cancer Causes Control 20:1431-40. 2009
    ..Furthermore, previous studies have focused primarily on the differences between African-Americans and non-Hispanic Whites, and little is known for Hispanics and Asian/Pacific Islanders...
  53. ncbi request reprint Acute lung injury and the coagulation pathway: Potential role of gene polymorphisms in the protein C and fibrinolytic pathways
    Anil Sapru
    Pediatric Critical Care Medicine, University of California, 505 Parnassus Avenue, Moffitt 680 B, San Francisco, CA 94143 0106, USA
    Intensive Care Med 32:1293-303. 2006
    ....
  54. ncbi request reprint Analysis of mutational spectra: locating hotspots and clusters of mutations using recursive segmentation
    Bonnie A Fijal
    Department of Epidemiology and Biostatistics, Case Western Reserve University, 2109 Adelbert Road, Cleveland, OH 44106 4945, USA
    Stat Med 21:1867-85. 2002
    ..Here, recursive segmentation identified the boundaries of apparent clusters better than did other methods, and this approach could identify clusters of mutations which corresponded to biologically important regions of the p53 protein...
  55. pmc An empirical evaluation of the common disease-common variant hypothesis
    Gary K Chen
    Department of Epidemiology and Biostatistics, Institute for Human Genetics, Universityof California, San Francisco, California 94143 0794, USA
    BMC Proc 1:S5. 2007
    ..We did not find any statistically significant differences between these two sets. However, our power calculations show that these results may be inconclusive...
  56. pmc Segmentation and estimation for SNP microarrays: a Bayesian multiple change-point approach
    Yu Chuan Tai
    Institute for Human Genetics, Department of Epidemiology and Biostatistics, University of California, San Francisco, California 94143 0794, USA
    Biometrics 66:675-83. 2010
    ..Finally, for studies of CNVs in tumors, we incorporate an adjustment factor for signal attenuation due to tumor heterogeneity or normal contamination that can improve copy number estimates...
  57. ncbi request reprint Relation between tumour necrosis factor polymorphism TNFalpha-308 and risk of asthma
    John S Witte
    Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106 4945, USA
    Eur J Hum Genet 10:82-5. 2002
    ..16 (95% CI=1.04-9.66; P=0.04). LTalpha-NcoI*1 was weakly associated with asthma, and analysis of both genes suggests that only the TNFalpha-308*2 allele increases risk of asthma...
  58. ncbi request reprint Androgen receptor CAG repeats and prostate cancer
    Kevin A Nelson
    Department of Epidemiology and Biostatistics, Case Western Reserve University, 2109 Adelbert Road, Cleveland, OH 44106 4945, USA
    Am J Epidemiol 155:883-90. 2002
    ..CAG repeat length can be determined with high sensitivity and specificity. Presently, there is no recommended population screening for AR CAG repeat length...
  59. doi request reprint The role of genetic variation in Toll-like receptor 4 in prostate cancer susceptibility: a review
    Iona Cheng
    University of California, Department of Epidemiology and Biostatistics, Institute of Human Genetics, San Francisco, CA 94143 0794, USA 1 415 502 6882 1 415 476 1356
    Expert Opin Med Diagn 2:143-9. 2008
    ....
  60. pmc Use of principal components to aggregate rare variants in case-control and family-based association studies in the presence of multiple covariates
    Rémi Kazma
    Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California San Francisco, 1450 Third Street, Box 3110, San Francisco, CA 94148 3110, USA
    BMC Proc 5:S29. 2011
    ..The two methods provide a fast way to analyze simultaneously rare and common variants at the gene level while adjusting for covariates. However, further evaluation of the statistical efficiency of this approach is warranted...
  61. ncbi request reprint Variants in Deleted in AZoospermia-Like (DAZL) are correlated with reproductive parameters in men and women
    Joyce Y Tung
    Department of Obstetrics, Program in Human Embryonic Stem Cell Biology, Center for Reproductive Sciences, University of California at San Francisco, San Francisco, CA 94143, USA
    Hum Genet 118:730-40. 2006
    ..Single SNP and haplotype analysis suggested that SNPs in the DAZL gene may act jointly to affect common reproductive characteristics in the human population...
  62. ncbi request reprint Increased power for case-control studies of single nucleotide polymorphisms through incorporation of family history and genetic constraints
    Deborah Thompson
    Unit of Genetic Epidemiology, International Agency for Research on Cancer, Lyon, France
    Genet Epidemiol 27:215-24. 2004
    ..Stratifying by FH also improves the precision of the RR estimates. In situations where basic FH data are already available, this study shows that efficiency can be improved by the inclusion of even this small amount of extra information...
  63. ncbi request reprint Vitamin D receptor genotypes/haplotypes and prostate cancer risk
    Mine S Cicek
    Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Ohio, USA
    Cancer Epidemiol Biomarkers Prev 15:2549-52. 2006
    ..This would help explain the somewhat equivocal results for VDR genotype-level associations with prostate cancer...
  64. ncbi request reprint RNASEL Arg462Gln variant is implicated in up to 13% of prostate cancer cases
    Graham Casey
    Department of Cancer Biology, ND50, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
    Nat Genet 32:581-3. 2002
    ..Men that are heterozygous with respect to the mutated allele have 50% greater risk of prostate cancer than non-carriers, and homozygotes have more than double the risk...
  65. pmc Prostate cancer aggressiveness locus on chromosome 7q32-q33 identified by linkage and allelic imbalance studies
    Phillippa J Neville
    Department of Cancer Biology, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
    Neoplasia 4:424-31. 2002
    ..05). These data imply that we have localized a prostate cancer tumor aggressiveness loci to chromosome 7q32-q33 that is involved in familial and nonfamilial forms of prostate cancer...
  66. ncbi request reprint Multiple prostate cancer risk variants on 8q24
    John S Witte
    Nat Genet 39:579-80. 2007
  67. ncbi request reprint Prostate cancer aggressiveness locus on chromosome segment 19q12-q13.1 identified by linkage and allelic imbalance studies
    Phillippa J Neville
    Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195, USA
    Genes Chromosomes Cancer 36:332-9. 2003
    ..06). These data provide strong evidence that we have mapped a prostate tumor aggressiveness locus to chromosome segments 19q12-q13.11 that may play a role in both familial and non-familial forms of prostate cancer...
  68. ncbi request reprint CYP3A4 and CYP3A5 genotypes, haplotypes, and risk of prostate cancer
    Sarah J Plummer
    Department of Cancer Biology, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, Ohio, USA
    Cancer Epidemiol Biomarkers Prev 12:928-32. 2003
    ..07; 95% CI, 0.01-0.51; P=0.009). These findings suggest that the CYP3A4 and CYP3A5 variants, or other alleles on the haplotypes they help distinguish, are associated with prostate cancer risk and aggressiveness...
  69. ncbi request reprint Relationship between methylenetetrahydrofolate reductase C677T and A1298C genotypes and haplotypes and prostate cancer risk and aggressiveness
    Mine S Cicek
    Department of Cancer Biology, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, USA
    Cancer Epidemiol Biomarkers Prev 13:1331-6. 2004
    ..47, 95% CI 0.29-0.76; P = 0.002). Our findings suggest that 677T and 1298A, or another variant on their haplotype, may be associated with a reduced risk of progression to more advanced prostate cancer...
  70. ncbi request reprint Using hierarchical modeling in genetic association studies with multiple markers: application to a case-control study of bladder cancer
    Rayjean J Hung
    Internal Agency for Research on Cancer Epidemiology, 150 cours Albert Thomas, 69008 Lyon, France
    Cancer Epidemiol Biomarkers Prev 13:1013-21. 2004
    ..Using data from a case-control study of bladder cancer, we showed how to use hierarchical modeling in genetic epidemiologic studies with multiple markers to control overestimation of effects and potential false-positive associations...
  71. ncbi request reprint Genetic dissection of complex traits with chromosome substitution strains of mice
    Jonathan B Singer
    Broad Institute, Cambridge, MA 02142, USA
    Science 304:445-8. 2004
    ..These results demonstrate that CSSs greatly facilitate the detection and identification of genes that control the wide diversity of naturally occurring phenotypic variation in the A/J and C57BL/6J inbred strains...
  72. ncbi request reprint No association between genetic polymorphisms in IGF-I and IGFBP-3 and prostate cancer
    Li Li
    Department of Family Medicine and Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
    Cancer Epidemiol Biomarkers Prev 13:497-8. 2004
  73. ncbi request reprint Association of prostate cancer risk and aggressiveness to androgen pathway genes: SRD5A2, CYP17, and the AR
    Mine S Cicek
    Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
    Prostate 59:69-76. 2004
    ....
  74. ncbi request reprint Role of androgen metabolism genes CYP1B1, PSA/KLK3, and CYP11alpha in prostate cancer risk and aggressiveness
    Mine S Cicek
    Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Lerner School of Medicine, Ohio, USA
    Cancer Epidemiol Biomarkers Prev 14:2173-7. 2005
    ..71; 95% CI, 1.06-6.94; P = 0.04). Our findings suggest that CYP1B1 and PSA variants may affect the risk of prostate cancer and tumor aggressiveness...
  75. ncbi request reprint DNA repair gene XRCC1 and XPD polymorphisms and risk of prostate cancer
    Benjamin A Rybicki
    Department of Biostatistics and Research Epidemiology, Henry Ford Health System, Detroit, Michigan, USA
    Cancer Epidemiol Biomarkers Prev 13:23-9. 2004
    ....
  76. ncbi request reprint Podocalyxin variants and risk of prostate cancer and tumor aggressiveness
    Graham Casey
    Department of Cancer Biology, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, OH 44195, USA
    Hum Mol Genet 15:735-41. 2006
    ..48, 95%CI=1.02-2.14, P=0.04). These results implicate PODXL as a candidate prostate cancer tumor aggressiveness gene mapping to chromosome 7q32-q33...
  77. ncbi request reprint Comprehensive evaluation of the association between prostate cancer and genotypes/haplotypes in CYP17A1, CYP3A4, and SRD5A2
    Anu Loukola
    Amersham Biosciences, Sunnyvale, CA 94085, USA
    Eur J Hum Genet 12:321-32. 2004
    ..02). Undertaking a two-phase study comprising SNP discovery, haplotype tagging, and association analyses allowed us to more fully decipher the relation between CYP17A1, CYP3A4, and SRD5A2 and prostate cancer...
  78. ncbi request reprint Point: population stratification: a problem for case-control studies of candidate-gene associations?
    Duncan C Thomas
    Department of Preventive Medicine, University of Southern California, Los Angeles, California 90033 9987, USA
    Cancer Epidemiol Biomarkers Prev 11:505-12. 2002
  79. ncbi request reprint Haplotype tagging single nucleotide polymorphisms and association studies
    Deborah Thompson
    Unit of Genetic Cancer Epidemiology, International Agency for Cancer Research, Lyon, France
    Hum Hered 56:48-55. 2003
    ..We investigated by simulation how the size of the subsample affects the power of association studies, and what type of subjects it should include...
  80. ncbi request reprint Relation of serum insulin-like growth factor-I (IGF-I) and IGF binding protein-3 to risk of prostate cancer (United States)
    Li Li
    Department of Family Medicine, Case Western Reserve University, Cleveland, OH 44106 4945, USA
    Cancer Causes Control 14:721-6. 2003
    ..Previous studies have inconsistently associated IGF-I and IGFBP-3 with prostate cancer. To try and further clarify these potential associations, we undertook a sibling-matched case-control study...
  81. ncbi request reprint Dissecting effects of complex mixtures: who's afraid of informative priors?
    Duncan C Thomas
    Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089 9011, USA
    Epidemiology 18:186-90. 2007
    ..In doing so - and by directly incorporating into our analyses information from other studies or allied fields - we can improve our ability to distinguish true causes of disease from noise and bias...