John K Wiencke

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Association study of nicotinic acetylcholine receptor genes identifies a novel lung cancer susceptibility locus near CHRNA1 in African-Americans
    Kyle M Walsh
    Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
    Oncotarget 3:1428-38. 2012
  2. pmc Breast cancer DNA methylation profiles are associated with tumor size and alcohol and folate intake
    Brock C Christensen
    Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
    PLoS Genet 6:e1001043. 2010
  3. pmc DNA methylation arrays as surrogate measures of cell mixture distribution
    Eugene Andres Houseman
    College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA
    BMC Bioinformatics 13:86. 2012
  4. pmc Epigenetic biomarkers of T-cells in human glioma
    John K Wiencke
    Department of Neurological Surgery, University of California San Francisco, San Francisco, CA USA
    Epigenetics 7:1391-402. 2012
  5. pmc Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions
    E Andres Houseman
    Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, 02115, USA
    BMC Bioinformatics 9:365. 2008
  6. pmc Methylation of the PTEN promoter defines low-grade gliomas and secondary glioblastoma
    John K Wiencke
    Department of Neurological Surgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
    Neuro Oncol 9:271-9. 2007
  7. ncbi request reprint Differentially expressed genes are marked by histone 3 lysine 9 trimethylation in human cancer cells
    J K Wiencke
    Laboratory of Neuro and Molecular Epidemiology, Ambulatory Care AC 34, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
    Oncogene 27:2412-21. 2008
  8. pmc Fine-mapping of the 5p15.33, 6p22.1-p21.31, and 15q25.1 regions identifies functional and histology-specific lung cancer susceptibility loci in African-Americans
    Kyle M Walsh
    Program in Cancer Genetics, Helen Diller Family Comprehensive Cancer Cente, San Francisco, CA, USA
    Cancer Epidemiol Biomarkers Prev 22:251-60. 2013
  9. pmc CYP1A1/2 haplotypes and lung cancer and assessment of confounding by population stratification
    Melinda C Aldrich
    Department of Medicine and Division of Neuroepidemiology, University of California, San Francisco, California, USA
    Cancer Res 69:2340-8. 2009
  10. pmc Epigenetic profiling reveals etiologically distinct patterns of DNA methylation in head and neck squamous cell carcinoma
    Carmen J Marsit
    Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02912, USA
    Carcinogenesis 30:416-22. 2009

Detail Information

Publications93

  1. pmc Association study of nicotinic acetylcholine receptor genes identifies a novel lung cancer susceptibility locus near CHRNA1 in African-Americans
    Kyle M Walsh
    Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
    Oncotarget 3:1428-38. 2012
    ..These findings identify a novel lung cancer risk locus on 2q31.1 which correlates with CHRNA1 expression and replicate previous associations on 15q25.1 in African-Americans...
  2. pmc Breast cancer DNA methylation profiles are associated with tumor size and alcohol and folate intake
    Brock C Christensen
    Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
    PLoS Genet 6:e1001043. 2010
    ..0001) associated with methylation class membership. Breast cancer prognostic characteristics and risk-related exposures appear to be associated with gene-specific tumor methylation, as well as overall methylation patterns...
  3. pmc DNA methylation arrays as surrogate measures of cell mixture distribution
    Eugene Andres Houseman
    College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA
    BMC Bioinformatics 13:86. 2012
    ..Emerging research demonstrates that DNA methylation is responsible for cellular differentiation, and when measured in whole peripheral blood, serves to distinguish cancer cases from controls...
  4. pmc Epigenetic biomarkers of T-cells in human glioma
    John K Wiencke
    Department of Neurological Surgery, University of California San Francisco, San Francisco, CA USA
    Epigenetics 7:1391-402. 2012
    ....
  5. pmc Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions
    E Andres Houseman
    Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, 02115, USA
    BMC Bioinformatics 9:365. 2008
    ..Model-based cluster analysis is often used to identify DNA methylation subgroups in data, but it is unclear how to cluster DNA methylation data from arrays in a scalable and reliable manner...
  6. pmc Methylation of the PTEN promoter defines low-grade gliomas and secondary glioblastoma
    John K Wiencke
    Department of Neurological Surgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
    Neuro Oncol 9:271-9. 2007
    ....
  7. ncbi request reprint Differentially expressed genes are marked by histone 3 lysine 9 trimethylation in human cancer cells
    J K Wiencke
    Laboratory of Neuro and Molecular Epidemiology, Ambulatory Care AC 34, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
    Oncogene 27:2412-21. 2008
    ..Awareness of H3K9Me3 as a mark of gene activity, not repression, is especially important for the classification of human cancer using chromatin and histone profiles...
  8. pmc Fine-mapping of the 5p15.33, 6p22.1-p21.31, and 15q25.1 regions identifies functional and histology-specific lung cancer susceptibility loci in African-Americans
    Kyle M Walsh
    Program in Cancer Genetics, Helen Diller Family Comprehensive Cancer Cente, San Francisco, CA, USA
    Cancer Epidemiol Biomarkers Prev 22:251-60. 2013
    ..1-p21.31, and 15q25.1. We investigated whether these regions contain lung cancer susceptibly loci in African-Americans and refined previous association signals by using the reduced linkage disequilibrium observed in African-Americans...
  9. pmc CYP1A1/2 haplotypes and lung cancer and assessment of confounding by population stratification
    Melinda C Aldrich
    Department of Medicine and Division of Neuroepidemiology, University of California, San Francisco, California, USA
    Cancer Res 69:2340-8. 2009
    ..These results suggest that a variant occurring within the CYP1A2 region may be conferring an increased risk of lung cancer in Latinos...
  10. pmc Epigenetic profiling reveals etiologically distinct patterns of DNA methylation in head and neck squamous cell carcinoma
    Carmen J Marsit
    Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02912, USA
    Carcinogenesis 30:416-22. 2009
    ..We found that the etiologic heterogeneity of HNSCC is reflected in specific patterns of molecular epigenetic alterations within the tumors and that the DNA methylation profiles may hold clinical promise worthy of further study...
  11. pmc Nucleotide excision repair genes and risk of lung cancer among San Francisco Bay Area Latinos and African Americans
    Jeffrey S Chang
    Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
    Int J Cancer 123:2095-104. 2008
    ..61; 95% CI: 0.42-0.88). Our study suggests different elements of the NER pathway may be important in the different ethnic groups resulting either from different linkage relationship, genetic backgrounds and/or exposure histories...
  12. pmc Socioeconomic status and lung cancer: unraveling the contribution of genetic admixture
    Melinda C Aldrich
    at the time of the study, Melinda C Aldrich was with the Division of Epidemiology, School of Public Health, University of California, Berkeley Steve Selvin is with the Division of Biostatistics, School of Public Health, University of California, Berkeley Margaret R Wrensch, Helen M Hansen, and John K Wiencke are with the Department of Neurologic Surgery, University of California, San Francisco Jennette D Sison was with the Department of Neurologic Surgery, University of California, San Francisco Charles P Quesenberry Jr, is with the Division of Research, Kaiser Permanente, Oakland, CA Michael F Seldin is with the Departments of Biological Chemistry and Medicine, University of California, Davis Lisa F Barcellos and Patricia A Buffler are with the Division of Epidemiology, School of Public Health, University of California, Berkeley
    Am J Public Health 103:e73-80. 2013
    ..We examined the relationship between genetic ancestry, socioeconomic status (SES), and lung cancer among African Americans and Latinos...
  13. pmc Identification of methylated genes associated with aggressive bladder cancer
    Carmen J Marsit
    Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
    PLoS ONE 5:e12334. 2010
    ..Methylation of these genes may be useful as clinical markers of the disease and may point to genes and pathways worthy of additional examination as novel targets for therapeutic treatment...
  14. pmc Integrated profiling reveals a global correlation between epigenetic and genetic alterations in mesothelioma
    Brock C Christensen
    Departments of Pathology and Laboratory Medicine, Community Health, Center for Environmental Health and Technology, and Molecular Pharmacology and Physiology, Brown University, Providence, Rhode Island 02903, USA
    Cancer Res 70:5686-94. 2010
    ..Our findings define a strong association between global genetic and global epigenetic dysregulation in mesothelioma, rather than a discrete, local coordination of gene inactivation...
  15. ncbi request reprint Pathway analysis of single-nucleotide polymorphisms potentially associated with glioblastoma multiforme susceptibility using random forests
    Jeffrey S Chang
    Department of Epidemiology and Biostatistics, University of California, San Francisco, 44 Page Street, Suite 503, San Francisco, CA 94143 1215, USA
    Cancer Epidemiol Biomarkers Prev 17:1368-73. 2008
    ..Despite less than complete inclusion of genes and SNPs relevant to glioma and a small sample size, RF analysis identified one important biological pathway and several SNPs potentially associated with the development of glioblastoma...
  16. ncbi request reprint Allergy-related polymorphisms influence glioma status and serum IgE levels
    Joseph L Wiemels
    Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA 94143 0441, USA
    Cancer Epidemiol Biomarkers Prev 16:1229-35. 2007
    ..Further exploration of immune susceptibility factors, including genetics, in glioma etiology is advisable...
  17. pmc Fine mapping of chromosome 15q25.1 lung cancer susceptibility in African-Americans
    Helen M Hansen
    Division of Neuroepidemiology, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
    Hum Mol Genet 19:3652-61. 2010
    ..002). The identified regions contain SNPs predicted to affect gene regulation. There are multiple lung cancer risk loci in the 15q25.1 region in African-Americans...
  18. pmc Genetic variants in telomerase-related genes are associated with an older age at diagnosis in glioma patients: evidence for distinct pathways of gliomagenesis
    Kyle M Walsh
    Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
    Neuro Oncol 15:1041-7. 2013
    ..We examined associations of these 7 established glioma risk loci with age at diagnosis among patients with glioma...
  19. ncbi request reprint Serum IgE, tumor epidermal growth factor receptor expression, and inherited polymorphisms associated with glioma survival
    Margaret Wrensch
    Department of Neurological Surgery, University of California San Francisco, San Francisco, California 94102, USA
    Cancer Res 66:4531-41. 2006
    ..3 region influence survival. We also suggest that tumor EGFR expression be incorporated into clinical evaluation of anaplastic astrocytoma patients...
  20. pmc DNA methylation, isocitrate dehydrogenase mutation, and survival in glioma
    Brock C Christensen
    Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
    J Natl Cancer Inst 103:143-53. 2011
    ....
  21. pmc Genetic variants in the folate pathway and risk of childhood acute lymphoblastic leukemia
    Catherine Metayer
    School of Public Health, University of California, Berkeley, 1995 University Avenue, Suite 460, Berkeley, CA 94704 7392, USA
    Cancer Causes Control 22:1243-58. 2011
    ..We examined whether child's germline genetic variation in the folate pathway is associated with childhood acute lymphoblastic leukemia (ALL), and whether periconception maternal folate and alcohol intake modify the risk...
  22. pmc Inherited variant on chromosome 11q23 increases susceptibility to IDH-mutated but not IDH-normal gliomas regardless of grade or histology
    Terri Rice
    Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94107, USA
    Neuro Oncol 15:535-41. 2013
    ..Because the inherited variant in 11q23 has been associated with risk of lower grade glioma and not with glioblastomas, we hypothesized that this variant increases susceptibility to IDH-mutated gliomas, but not to IDH-wild-type gliomas...
  23. pmc Copy number variation has little impact on bead-array-based measures of DNA methylation
    E Andres Houseman
    Department of Community Health Center for Environmental Health and Technology, Brown University, Providence, RI 02912, USA
    Bioinformatics 25:1999-2005. 2009
    ..However, copy number variation may bias the measurement of DNA methylation. To investigate possible bias, we analyzed integrated data obtained from 19 head and neck squamous cell carcinoma (HNSCC) tumors and 23 mesothelioma tumors...
  24. ncbi request reprint CYP1A1 variants and smoking-related lung cancer in San Francisco Bay area Latinos and African Americans
    Margaret R Wrensch
    Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
    Int J Cancer 113:141-7. 2005
    ....
  25. pmc Epigenetic profiles distinguish pleural mesothelioma from normal pleura and predict lung asbestos burden and clinical outcome
    Brock C Christensen
    Department of Community Health, Center for Environmental Health and Technology, Brown University, 70 Ship Street, Providence, RI 02903, USA
    Cancer Res 69:227-34. 2009
    ..Importantly, these findings hold great promise for using epigenetic profiling in the diagnosis and prognosis of human cancers...
  26. ncbi request reprint Genetic polymorphisms in MTHFR 677 and 1298, GSTM1 and T1, and metabolism of arsenic
    Craig Steinmaus
    Arsenic Health Effects Research Program, School of Public Health, University of California, Berkeley, California, USA
    J Toxicol Environ Health A 70:159-70. 2007
    ..Overall, this study provides evidence that MTHFR and GSTM1 are involved in arsenic metabolism in humans, and polymorphisms in the genes that encode these enzymes may play a role in susceptibility to arsenic-induced cancer...
  27. pmc ERCC1 and ERCC2 polymorphisms and adult glioma
    Margaret Wrensch
    Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
    Neuro Oncol 7:495-507. 2005
    ..3). Given the numbers of comparisons made, these findings could be due to chance. However, the results might warrant clarification in additional series in conjunction with the nearby putative glioma suppressor genes (GLTSCR1 and GLTSCR2)...
  28. pmc Base excision repair genes and risk of lung cancer among San Francisco Bay Area Latinos and African-Americans
    Jeffrey S Chang
    Department of Epidemiology and Biostatistics, Division of Neuroepidemiology, University of California San Francisco, San Francisco, CA 94143 1215, USA
    Carcinogenesis 30:78-87. 2009
    ..This study suggests that there are genetic differences in the association between BER pathway and lung cancer between Latinos and African-Americans...
  29. pmc Comparison of statistical methods for estimating genetic admixture in a lung cancer study of African Americans and Latinos
    Melinda C Aldrich
    University of California, San Francisco, Box 2911 Rock Hall, Mission Bay 582, 1550 4th Street, San Francisco, CA 94143 2911, USA
    Am J Epidemiol 168:1035-46. 2008
    ..Genetic admixture proportions provide a quantitative measure of ancestry differences among Latinos that can be used in analyses of genetic risk factors...
  30. pmc Decreased NK cells in patients with head and neck cancer determined in archival DNA
    William P Accomando
    Department of Pathology and Laboratory Medicine, Department of Epidemiology, Brown University, Providence, Rhode Island 02912, USA
    Clin Cancer Res 18:6147-54. 2012
    ..To examine NK cell levels in archived bloods from a study of human head and neck squamous cell carcinoma (HNSCC), a new DNA-based quantification method was developed...
  31. ncbi request reprint Glutathione-S-transferase variants and adult glioma
    Margaret Wrensch
    University of California, San Francisco, CA 94143, USA
    Cancer Epidemiol Biomarkers Prev 13:461-7. 2004
    ..Conflicting findings have been reported for associations of primary brain tumors and constitutive polymorphisms in glutathione-S-transferases (GSTs)...
  32. ncbi request reprint Molecular biomarkers for the study of childhood leukemia
    Martyn T Smith
    Division of Environmental Health Sciences, School of Public Health, University of California, 140 Warren Hall, Berkeley, CA 94720 7360, USA
    Toxicol Appl Pharmacol 206:237-45. 2005
    ..Several proteins have been identified that may serve as useful biomarkers for rapidly identifying different forms of childhood leukemia...
  33. pmc DNA hypermethylation profiles associated with glioma subtypes and EZH2 and IGFBP2 mRNA expression
    Shichun Zheng
    Department of Neurological Surgery, University of California San Francisco, Helen Diller Family Cancer Center, 1450 3rd Street, San Francisco, CA 94158, USA
    Neuro Oncol 13:280-9. 2011
    ..DNA methylation markers are useful in characterizing distinct glioma subtypes and may hold promise for clinical applications...
  34. pmc Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies
    Kyle M Walsh
    Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
    Genet Epidemiol 37:222-8. 2013
    ..These results highlight that the deficiencies of the candidate-gene approach lay in selecting both appropriate genes and relevant SNPs within these genes...
  35. ncbi request reprint Molecular features of adult glioma associated with patient race/ethnicity, age, and a polymorphism in O6-methylguanine-DNA-methyltransferase
    John K Wiencke
    Division of Neuroepidemiology, Department of Neurological Surgery, School of Medicine, University of California San Francisco, Box 0441, San Francisco, CA 94143 0441, USA
    Cancer Epidemiol Biomarkers Prev 14:1774-83. 2005
    ..MGMT expression may depend on the TP53 status of cells...
  36. pmc HLA-DP genetic variation, proxies for early life immune modulation and childhood acute lymphoblastic leukemia risk
    Kevin Y Urayama
    School of Public Health, University of California, Berkeley, CA 94704, USA
    Blood 120:3039-47. 2012
    ..These findings support an immune mechanism in the etiology of childhood ALL involving the HLA-DPB1 gene in the context of an insufficiently modulated immune system...
  37. pmc Circulating levels of the innate and humoral immune regulators CD14 and CD23 are associated with adult glioma
    Mi Zhou
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California 94158, USA
    Cancer Res 70:7534-42. 2010
    ..These results augment the long-observed association between allergies and glioma and support a role for the innate and adaptive humoral functions of the immune system, in particular immunoregulatory proteins, in gliomagenesis...
  38. ncbi request reprint Reduced immunoglobulin E and allergy among adults with glioma compared with controls
    Joseph L Wiemels
    Laboratory for Molecular Epidemiology, Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California 94143 0560, USA
    Cancer Res 64:8468-73. 2004
    ..Furthermore, the results indicate a complex relationship between allergic disease and glioma risk that varies by allergen and allergic pathology...
  39. pmc Differentiation of lung adenocarcinoma, pleural mesothelioma, and nonmalignant pulmonary tissues using DNA methylation profiles
    Brock C Christensen
    Department of Community Health, Center for Environmental Health and Technology, Brown University, Providence, Rhode Island 02903, USA
    Cancer Res 69:6315-21. 2009
    ..Methylation profile-based differentiation of lung adenocarcinoma and mesothelioma is highly accurate, informs on the distinct etiologies of these diseases, and holds promise for clinical application...
  40. pmc Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context
    Brock C Christensen
    Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
    PLoS Genet 5:e1000602. 2009
    ..Collectively we reveal key issues to consider both in the construction of reference and disease-related epigenomes and in the interpretation of potentially pathologically important alterations...
  41. pmc The influence of aging, environmental exposures and local sequence features on the variation of DNA methylation in blood
    Scott M Langevin
    Department of Community Health, Brown University, Providence, RI, USA
    Epigenetics 6:908-19. 2011
    ....
  42. pmc Peripheral blood DNA methylation profiles are indicative of head and neck squamous cell carcinoma: an epigenome-wide association study
    Scott M Langevin
    Department of Epidemiology, Brown University, Providence, RI, USA
    Epigenetics 7:291-9. 2012
    ..This profile demonstrates the potential of DNA methylation measured in blood for development of non-invasive applications for detection of head and neck cancer...
  43. pmc SSBP2 variants are associated with survival in glioblastoma patients
    Yuanyuan Xiao
    Department of Epidemiology and Biostatistics, University of California, San Francisco 185 Berry St, Suite 5700, San Francisco, CA 94107, USA
    Clin Cancer Res 18:3154-62. 2012
    ..Glioblastoma is a devastating, incurable disease with few known prognostic factors. Here, we present the first genome-wide survival and validation study for glioblastoma...
  44. pmc SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system
    Alexander R Pico
    Gladstone Institute of Cardiovascular Disease, 1650 Owens Street, San Francisco, CA 94158, USA
    Nucleic Acids Res 37:D803-9. 2009
    ..We have found integration of SNP annotation in the context of pathway information and functional prediction scores to be a powerful approach to the analysis and interpretation of SNP-disease association data...
  45. pmc IgE, allergy, and risk of glioma: update from the San Francisco Bay Area Adult Glioma Study in the temozolomide era
    Joseph L Wiemels
    Department of Neurosurgery and Epidemiology, UCSF, San Francisco, CA 94143 0441, USA
    Int J Cancer 125:680-7. 2009
    ..These results have implications for the study of immunologic factors in glioma as well as for immunotherapy protocols for treating glioma...
  46. pmc Genetic polymorphisms in adaptive immunity genes and childhood acute lymphoblastic leukemia
    Jeffrey S Chang
    Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
    Cancer Epidemiol Biomarkers Prev 19:2152-63. 2010
    ..The lack of immune priming in early childhood may result in abnormal immune responses to infections later in life and increase ALL risk...
  47. pmc DNA methylation profiles delineate etiologic heterogeneity and clinically important subgroups of bladder cancer
    C S Wilhelm-Benartzi
    Department of Community Health, Center for Environmental Health and Technology, Brown University, Providence, RI 02912, USA
    Carcinogenesis 31:1972-6. 2010
    ..Exposures and demographic associated with increased risk of bladder cancer specifically associate with particular subgroups of tumors defined by DNA methylation profiling and these subgroups may define more aggressive disease...
  48. pmc Genetic and epigenetic somatic alterations in head and neck squamous cell carcinomas are globally coordinated but not locally targeted
    Graham M Poage
    Departments of Molecular Pharmacology and Physiology, Brown University, Providence, Rhode Island, United States of America
    PLoS ONE 5:e9651. 2010
    ....
  49. ncbi request reprint Investigation of genetic polymorphisms and smoking in a bladder cancer case-control study in Argentina
    Lee E Moore
    School of Public Health, Arsenic Health Effects Research Program, University of California, 140 Warren Hall, Berkeley, CA 94720 7360, USA
    Cancer Lett 211:199-207. 2004
    ..Having both null polymorphisms conferred the highest risks. The MTHFR 677 CT and TT polymorphisms appeared protective against bladder cancer...
  50. pmc Fetal growth and body size genes and risk of childhood acute lymphoblastic leukemia
    Anand P Chokkalingam
    School of Public Health, University of California Berkeley, Berkeley, CA, USA
    Cancer Causes Control 23:1577-85. 2012
    ..Additional studies are needed to confirm these findings and identify specific causal variants...
  51. pmc Haplotypes of DNA repair and cell cycle control genes, X-ray exposure, and risk of childhood acute lymphoblastic leukemia
    Anand P Chokkalingam
    Division of Epidemiology, School of Public Health, University of California Berkeley, 1995 University Avenue, Berkeley, CA 94704, USA
    Cancer Causes Control 22:1721-30. 2011
    ..These abnormalities may be influenced by altered DNA repair and cell cycle control processes...
  52. pmc Cigarette smoking associated with lung adenocarcinoma in situ in a large case-control study (SFBALCS)
    Paige M Bracci
    Departmentsof Epidemiology and Biostatistics, School of Medicine, University of California, San Francisco, California 94158, USA
    J Thorac Oncol 7:1352-60. 2012
    ..Compared with other lung cancer histologies, AIS patients are less likely to be smokers, yet associations with other lung cancer risk factors and differences by sex have not been determined...
  53. pmc Variants near TERT and TERC influencing telomere length are associated with high-grade glioma risk
    Kyle M Walsh
    1 Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA 2 Program in Cancer Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
    Nat Genet 46:731-5. 2014
    ..No other risk loci for glioma were associated with LTL. The identification of risk alleles for glioma near TERC and TERT that also associate with telomere length implicates telomerase in gliomagenesis. ..
  54. pmc Variation in xenobiotic transport and metabolism genes, household chemical exposures, and risk of childhood acute lymphoblastic leukemia
    Anand P Chokkalingam
    Division of Epidemiology, UC Berkeley School of Public Health, University of California Berkeley, 1995 University Ave, Berkeley, CA 94704, USA
    Cancer Causes Control 23:1367-75. 2012
    ..We sought to evaluate the role of genes involved in xenobiotic transport and metabolism in childhood ALL risk, both alone and in conjunction with household chemical exposures previously found to be associated with childhood ALL risk...
  55. ncbi request reprint PTPRG inhibition by DNA methylation and cooperation with RAS gene activation in childhood acute lymphoblastic leukemia
    Jianqiao Xiao
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA
    Int J Cancer 135:1101-9. 2014
    ..Evidence for additional roles for PTPR family member genes is also suggested. This provides a potential therapeutic target for RAS-related leukemias as well as insight into childhood ALL etiology and pathophysiology. ..
  56. pmc SNP association mapping across the extended major histocompatibility complex and risk of B-cell precursor acute lymphoblastic leukemia in children
    Kevin Y Urayama
    School of Public Health, University of California, Berkeley, Berkeley, California, USA
    PLoS ONE 8:e72557. 2013
    ..046). Our findings suggest that susceptibility to childhood BCP-ALL is influenced by genetic variation within the xMHC and indicate at least two important regions for future evaluation. ..
  57. pmc PTEN promoter methylation and activation of the PI3K/Akt/mTOR pathway in pediatric gliomas and influence on clinical outcome
    Sabine Mueller
    Department of Pediatrics, University of California, San Francisco, CA, USA
    Neuro Oncol 14:1146-52. 2012
    ..0475). Tumors with no PTEN expression had a higher MIB labeling index (P= .007). The majority of pediatric gliomas show activation of the PI3K/Akt/mTOR pathway, with methylation of the PTEN promoter occurring commonly in these tumors...
  58. pmc A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network
    Seung Tae Lee
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
    Nucleic Acids Res 40:11339-51. 2012
    ....
  59. pmc Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility
    Margaret Wrensch
    Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
    Nat Genet 41:905-8. 2009
    ..85 x 10(-10). On 20q13.3, rs6010620 intronic to RTEL1 had discovery P = 1.5 x 10(-7), replication P = 0.00035 and combined P = 3.40 x 10(-9). For both SNPs, the direction of association was the same in discovery and replication phases...
  60. pmc Risk of squamous cell carcinoma of the skin in relation to IgE: a nested case-control study
    Joseph L Wiemels
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
    Cancer Epidemiol Biomarkers Prev 20:2377-83. 2011
    ....
  61. ncbi request reprint Hypermethylation of the 5' CpG island of the FHIT gene is associated with hyperdiploid and translocation-negative subtypes of pediatric leukemia
    Shichun Zheng
    Laboratory for Molecular Epidemiology, Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA 94143 0560, USA
    Cancer Res 64:2000-6. 2004
    ..These results suggest that hypermethylation of the promoter region CpG island of the FHIT gene is a common event and may play an important role in the etiology and pathophysiology of specific cytogenetic subtypes of childhood ALL...
  62. pmc Backtracking RAS mutations in high hyperdiploid childhood acute lymphoblastic leukemia
    Joseph L Wiemels
    Laboratory for Molecular Epidemiology, Department of Epidemiology and Biostatistics, and Helen Diller Comprehensive Cancer Center, University of California San Francisco, CA 94158, USA
    Blood Cells Mol Dis 45:186-91. 2010
    ..We posit a natural history for hyperdiploid leukemia in which prenatal mitotic catastrophe is followed by a postnatal RAS mutation to produce the leukemic cell phenotype...
  63. pmc TEL-AML1 regulation of survivin and apoptosis via miRNA-494 and miRNA-320a
    Christofer Diakos
    Laboratory for Molecular Epidemiology, University of California, San Francisco, San Francisco, CA, USA
    Blood 116:4885-93. 2010
    ..In summary our data suggest that TEL-AML1 might exert its antiapoptotic action at least in part by suppressing miRNA-494 and miRNA-320a, lowering their expression causing enhanced survivin expression...
  64. pmc Chemokine polymorphisms and lymphoma: a pooled analysis
    Paige M Bracci
    Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94118 1944, USA
    Leuk Lymphoma 51:497-506. 2010
    ..The CCL5 -403A allele conferred reduced risks of FL and chronic lymphocytic leukemia/small lymphocytic lymphoma. Results should be interpreted conservatively. Continued investigation is warranted to confirm these findings...
  65. pmc Lack of increased genetic damage in 1,3-butadiene-exposed Chinese workers studied in relation to EPHX1 and GST genotypes
    Luoping Zhang
    School of Public Health, University of California, 140 Warren Hall, Berkeley, CA 94720 7360, USA
    Mutat Res 558:63-74. 2004
    ..Together, these studies suggest that low levels of occupational BD exposure do not pose a significant risk of genetic damage...
  66. ncbi request reprint MDR1 gene variants, indoor insecticide exposure, and the risk of childhood acute lymphoblastic leukemia
    Kevin Y Urayama
    Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94143 0560, USA
    Cancer Epidemiol Biomarkers Prev 16:1172-7. 2007
    ....
  67. pmc Teen smoking, field cancerization, and a "critical period" hypothesis for lung cancer susceptibility
    John K Wiencke
    Department of Epidemiology and Biostatistics, University of California San Francisco, School of Medicine, San Francisco, California 94143 0560, USA
    Environ Health Perspect 110:555-8. 2002
    ..Targeted intervention in adolescent smoking may yield even greater reductions in lung cancer occurrence than otherwise anticipated...
  68. ncbi request reprint DNA adduct burden and tobacco carcinogenesis
    John K Wiencke
    Laboratory for Molecular Epidemiology, Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, CA 94143 0560, USA
    Oncogene 21:7376-91. 2002
    ..As these trends continue a variety of innovative study designs and approaches will become important in human populations...
  69. ncbi request reprint Early age at smoking initiation and tobacco carcinogen DNA damage in the lung
    J K Wiencke
    Department of Epidemiology and Biostatistics, School of Medicine, University of California San Francisco, 94143 0560, USA
    J Natl Cancer Inst 91:614-9. 1999
    ....
  70. ncbi request reprint RAS mutation is associated with hyperdiploidy and parental characteristics in pediatric acute lymphoblastic leukemia
    J L Wiemels
    Laboratory for Molecular Epidemiology, Department of Epidemiology and Biostatistics, and UCSF Comprehensive Cancer Center, University of California, San Francisco, CA 94143, USA
    Leukemia 19:415-9. 2005
    ....
  71. ncbi request reprint DNA quantification of whole genome amplified samples for genotyping on a multiplexed bead array platform
    Helen M Hansen
    Department of Neurological Surgery, University of California, Suite AC 34, 1 Irving Street, San Francisco, CA 94143 0441, USA
    Cancer Epidemiol Biomarkers Prev 16:1686-90. 2007
    ..14-118.32, 0.29-2.19, and 0.01-0.27 ng/microL, respectively). Human-specific quantitative PCR is a highly useful guide for determining the suitability of wgaDNA before high-throughput single-nucleotide polymorphism analysis...
  72. pmc Lack of association of rare alleles in the HRAS variable number of tandem repeats (VNTR) region with adult glioma
    P Chen
    Department of Epidemiology and Biostatistics, School of Medicine, University of California, San Francisco 94143 0560, USA
    Neuro Oncol 2:120-4. 2000
    ..Our data do not suggest an excess of HRAS rare alleles among adult glioma cases...
  73. ncbi request reprint History of allergies among adults with glioma and controls
    Joseph L Wiemels
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94102, USA
    Int J Cancer 98:609-15. 2002
    ..Future work might reveal an important role for immunologic factors in gliomagenesis and potential preventative and/or therapeutic modalities...
  74. ncbi request reprint Impact of race/ethnicity on molecular pathways in human cancer
    John K Wiencke
    University of California San Francisco, Department of Epidemiology and Biostatistics, 500 Parnassus Avenue, San Francisco, California 94143, USA
    Nat Rev Cancer 4:79-84. 2004
  75. ncbi request reprint Ethnicity delineates different genetic pathways in malignant glioma
    P Chen
    Laboratory for Molecular Epidemiology, Department of Epidemiology and Biostatistics, School of Medicine, University of California, San Francisco, CA 94143, USA
    Cancer Res 61:3949-54. 2001
    ....
  76. ncbi request reprint A population-based, case-control study of polymorphisms in carcinogen-metabolizing genes, smoking, and pancreatic adenocarcinoma risk
    Eric J Duell
    Department of Cancer Cell Biology, Harvard School of Public Health, Boston, MA 02115, USA
    J Natl Cancer Inst 94:297-306. 2002
    ....
  77. ncbi request reprint A population-based study of the Arg399Gln polymorphism in X-ray repair cross- complementing group 1 (XRCC1) and risk of pancreatic adenocarcinoma
    Eric J Duell
    Department of Cancer Cell Biology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
    Cancer Res 62:4630-6. 2002
    ..Our findings, including stronger associations and interactions among women, require replication in additional study populations...
  78. ncbi request reprint Alterations of 9p in squamous cell carcinoma and adenocarcinoma of the lung: association with smoking, TP53, and survival
    Carmen J Marsit
    Department of Genetics and Complex Diseases, Harvard School of Public Health, Building I, Room 607, 665 Huntington Avenue, Boston, MA 02115, USA
    Cancer Genet Cytogenet 162:115-21. 2005
    ....
  79. ncbi request reprint DNA repair polymorphisms XRCC1 and MGMT and risk of adult gliomas
    Martha J Felini
    Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
    Neuroepidemiology 29:55-8. 2007
    ..26; CI 0.90-1.75) and the MGMT Ile143Val polymorphism (Ile or Val/Val versus Ile/Ile: adjusted OR = 1.20; CI 0.85-1.71)...
  80. ncbi request reprint DNA adducts in granulocytes of hospital workers exposed to ethylene oxide
    Lee C Yong
    Division of Surveillance, Hazard Evaluations and Field Studies, National Institute for Occupational Safety and Health, CDC, Cincinnati, Ohio 45226, USA
    Am J Ind Med 50:293-302. 2007
    ..Occupational EtO exposure in many countries is regulated at 1 ppm (8-hr TWA), but levels of EtO-DNA adducts in humans with low occupational EtO exposures have not been reported...
  81. ncbi request reprint Homozygous deletion of p16INK4a and tobacco carcinogen exposure in nonsmall cell lung cancer
    Kim S Kraunz
    Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA 02115, USA
    Int J Cancer 118:1364-9. 2006
    ....
  82. ncbi request reprint Positive and negative associations of human leukocyte antigen variants with the onset and prognosis of adult glioblastoma multiforme
    Jianming Tang
    Department of Medicine, University of Alabama at Birmingham, 1665 University Boulevard, RPHB Room 220A, Birmingham, AL 35294 0022, USA
    Cancer Epidemiol Biomarkers Prev 14:2040-4. 2005
    ..B*07 and the B*07-Cw*07 haplotype are much more common in Caucasians than other ethnic groups in the U.S., which may partially explain the higher incidence of glioblastoma multiforme in Caucasians...
  83. ncbi request reprint Lower specific micronutrient intake in colorectal cancer patients with tumors presenting promoter hypermethylation in p16(INK4a), p4(ARF) and hMLH1
    Sergi Mas
    Department of Pharmacology, School of Medicine, IDIBAPS, University of Barcelona, Casanova 143, 08036 Barcelona, Spain
    Anticancer Res 27:1151-6. 2007
    ....
  84. ncbi request reprint Ethnic difference in daycare attendance, early infections, and risk of childhood acute lymphoblastic leukemia
    Xiaomei Ma
    Department of Epidemiology and Public Health, Yale University School of Medicine, 60 College Street, New Haven, CT 06520 8034, USA
    Cancer Epidemiol Biomarkers Prev 14:1928-34. 2005
    ..These results offer indirect yet strong support for the infectious disease hypothesis in the etiology of ALL in non-Hispanic White children and highlight an important ethnic difference...
  85. ncbi request reprint Polyphenol associated-DNA adducts in lung and blood mononuclear cells from lung cancer patients
    Andrea Varkonyi
    Microbiology Research Group National Institute for Epidemiology, Budapest, Piheno u 1 H 1529, Hungary
    Cancer Lett 236:24-31. 2006
    ..46; P<0.01). To our knowledge these results are the only comparison of adducts in MNCs with lung tissue, and the only data set indicating that blood MNCs are a valid surrogate for lung adduct DNA burden...
  86. ncbi request reprint The C3435T polymorphism of MDR1 and susceptibility to adult glioma
    Katie L Miller
    Department of Environmental Health, Harvard School of Public Health, Boston, MA 02115, USA
    Neuroepidemiology 25:85-90. 2005
    ..We compare adult glioma cases and controls for the C3435T polymorphism that has been associated with reduced MDR1 expression...
  87. ncbi request reprint The race associated allele of Semaphorin 3B (SEMA3B) T415I and its role in lung cancer in African-Americans and Latino-Americans
    Carmen J Marsit
    Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA 02115, USA
    Carcinogenesis 26:1446-9. 2005
    ..This study points to the need for further examination of this gene and its variant in lung cancer and other diseases...
  88. ncbi request reprint Loss of heterozygosity of chromosome 3p21 is associated with mutant TP53 and better patient survival in non-small-cell lung cancer
    Carmen J Marsit
    Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA
    Cancer Res 64:8702-7. 2004
    ....
  89. ncbi request reprint Hypermethylation of RASSF1A and BLU tumor suppressor genes in non-small cell lung cancer: implications for tobacco smoking during adolescence
    Carmen J Marsit
    Department of Genetics and Complex Diseases, Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
    Int J Cancer 114:219-23. 2005
    ..1-2.3]. These results indicate that starting smoking under age 18 is an independent risk for RASSF1A hypermethylation, thus identifying a molecular alteration related to the epidemiologic effect of teenage smoking as a lung cancer risk...
  90. ncbi request reprint Population- and community-based recruitment of African Americans and Latinos: the San Francisco Bay Area Lung Cancer Study
    Daramöla N Cabral
    Northern California Cancer Center, Union City, CA 94587, USA
    Am J Epidemiol 158:272-9. 2003
    ..05). Further assessment of strategies for successful recruitment of minority participants into epidemiologic studies is warranted...
  91. ncbi request reprint PTEN expression in non-small-cell lung cancer: evaluating its relation to tumor characteristics, allelic loss, and epigenetic alteration
    Carmen J Marsit
    Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA 02115, USA
    Hum Pathol 36:768-76. 2005
    ..PTEN loss may also be a favorable prognostic marker, although further studies are needed to confirm this finding...
  92. ncbi request reprint Decrease in specific micronutrient intake in colorectal cancer patients with tumors presenting Ki-ras mutation
    Nuria Laso
    Department of Pharmacologys, School of Medicine, IDIBAPS, University of Barcelona, Casanova 143, 08036 Barcelona, Spain
    Anticancer Res 24:2011-20. 2004
    ....
  93. ncbi request reprint On the use of biomarkers for environmental health research
    Louise Ryan
    Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    Stat Methods Med Res 13:207-25. 2004
    ....

Research Grants17

  1. Biomarkers of survival in glioma epidemiology
    John K Wiencke; Fiscal Year: 2010
    ....
  2. Biomarkers of survival in glioma epidemiology
    John Wiencke; Fiscal Year: 2009
    ....
  3. BIOMARKERS OF LUNG CANCER SUSCEPTIBILITY IN MINORITIES
    John Wiencke; Fiscal Year: 2009
    ..This will be only the second large genetic epidemiologic study of lung cancer in African-Americans; African-American men in California have an 11% lifetime risk of lung cancer. ..
  4. BIOMARKERS OF LUNG CANCER SUSCEPTIBILITY IN MINORITIES
    John Wiencke; Fiscal Year: 2007
    ..This will be only the second large genetic epidemiologic study of lung cancer in African-Americans; African-American men in California have an 11% lifetime risk of lung cancer. ..
  5. BIOMARKERS OF LUNG CANCER SUSCEPTIBILITY IN MINORITIES
    John Wiencke; Fiscal Year: 2006
    ..This will be only the second large genetic epidemiologic study of lung cancer in African-Americans; African-American men in California have an 11% lifetime risk of lung cancer. ..
  6. BIOMARKERS OF LUNG CANCER SUSCEPTIBILITY IN MINORITIES
    John Wiencke; Fiscal Year: 2005
    ..This will be only the second large genetic epidemiologic study of lung cancer in African-Americans; African-American men in California have an 11% lifetime risk of lung cancer. ..
  7. BIOMARKERS OF LUNG CANCER SUSCEPTIBILITY IN MINORITIES
    John Wiencke; Fiscal Year: 2003
    ..The further note that the DNA bank and comprehensive questionnaire data on smoking and other important risk factors also will prove invaluable for continuing studies of the genetic epidemiology of lung cancer. ..
  8. BIOMARKERS OF LUNG CANCER SUSCEPTIBILITY IN MINORITIES
    John Wiencke; Fiscal Year: 2002
    ..The further note that the DNA bank and comprehensive questionnaire data on smoking and other important risk factors also will prove invaluable for continuing studies of the genetic epidemiology of lung cancer. ..
  9. BIOMARKERS OF LUNG CANCER SUSCEPTIBILITY IN MINORITIES
    John Wiencke; Fiscal Year: 2001
    ..The further note that the DNA bank and comprehensive questionnaire data on smoking and other important risk factors also will prove invaluable for continuing studies of the genetic epidemiology of lung cancer. ..
  10. BIOMARKERS OF LUNG CANCER SUSCEPTIBILITY IN MINORITIES
    John Wiencke; Fiscal Year: 2000
    ..The further note that the DNA bank and comprehensive questionnaire data on smoking and other important risk factors also will prove invaluable for continuing studies of the genetic epidemiology of lung cancer. ..
  11. BIOMARKERS OF LUNG CANCER SUSCEPTIBILITY IN MINORITIES
    John Wiencke; Fiscal Year: 1999
    ..The further note that the DNA bank and comprehensive questionnaire data on smoking and other important risk factors also will prove invaluable for continuing studies of the genetic epidemiology of lung cancer. ..
  12. Biomarkers of survival in glioma epidemiology
    John Wiencke; Fiscal Year: 2009
    ....