Kimberly Siegmund

Summary

Affiliation: University of Southern California
Country: USA

Publications

  1. ncbi request reprint Hierarchical clustering of lung cancer cell lines using DNA methylation markers
    Arvind K Virmani
    Hamon Center for Therapeutic Oncology Research and Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9593, USA
    Cancer Epidemiol Biomarkers Prev 11:291-7. 2002
  2. ncbi request reprint Ascertainment bias in family-based case-control studies
    Kimberly D Siegmund
    Department of Preventive Medicine, University of Southern California, 1540 Alcazar Street, Suite 220, Los Angeles, CA 90089 9011, USA
    Am J Epidemiol 155:875-80. 2002
  3. ncbi request reprint Analysis of complex methylation data
    Kimberly D Siegmund
    Department of Preventive Medicine, University of Southern California Keck School of Medicine, 1441 Eastlake Avenue, Los Angeles, CA 90089 9176, USA
    Methods 27:170-8. 2002
  4. ncbi request reprint A comparison of cluster analysis methods using DNA methylation data
    Kimberly D Siegmund
    Department of Preventive Medicine, Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles 90089, USA
    Bioinformatics 20:1896-904. 2004
  5. ncbi request reprint Modeling exposures for DNA methylation profiles
    Kimberly D Siegmund
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 1540 Alcazar Street, CHP 220, Los Angeles, CA 90089, USA
    Cancer Epidemiol Biomarkers Prev 15:567-72. 2006
  6. pmc Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer
    Paul P Anglim
    Department of Surgery, Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089 9176, USA
    Mol Cancer 7:62. 2008
  7. pmc Identification of a panel of sensitive and specific DNA methylation markers for lung adenocarcinoma
    Jeffrey A Tsou
    Norris Cancer Center and Department of Surgery and of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 9176, USA
    Mol Cancer 6:70. 2007
  8. pmc Human and great ape red blood cells differ in plasmalogen levels and composition
    Ann B Moser
    Hugo W Moser Research Institute at Kennedy Krieger, and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Lipids Health Dis 10:101. 2011
  9. pmc Copy number variation in the Framingham Heart Study
    Corina Shtir
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 1540 Alcazar Street, CHP 220, Los Angeles, California 90089, USA
    BMC Proc 3:S133. 2009
  10. pmc Identification of differences in human and great ape phytanic acid metabolism that could influence gene expression profiles and physiological functions
    Paul A Watkins
    Department ofNeurology, Johns Hopkins University School of Medicine, Hugo W Moser Research Institute at Kennedy Krieger, Baltimore, MD 21205, USA
    BMC Physiol 10:19. 2010

Research Grants

  1. Statistical Models in Epigenomics
    Kimberly D Siegmund; Fiscal Year: 2010
  2. Statistical Models in Epigenomics
    Kimberly Siegmund; Fiscal Year: 2005
  3. Statistical Models in Epigenomics
    Kimberly Siegmund; Fiscal Year: 2007
  4. Statistical Models in Epigenomics
    Kimberly Siegmund; Fiscal Year: 2009

Detail Information

Publications53

  1. ncbi request reprint Hierarchical clustering of lung cancer cell lines using DNA methylation markers
    Arvind K Virmani
    Hamon Center for Therapeutic Oncology Research and Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9593, USA
    Cancer Epidemiol Biomarkers Prev 11:291-7. 2002
    ..Our results show that DNA methylation patterns differ between NSCLC and SCLC cell lines and suggest that these patterns could be developed into a powerful molecular marker to achieve accurate diagnosis of lung cancer...
  2. ncbi request reprint Ascertainment bias in family-based case-control studies
    Kimberly D Siegmund
    Department of Preventive Medicine, University of Southern California, 1540 Alcazar Street, Suite 220, Los Angeles, CA 90089 9011, USA
    Am J Epidemiol 155:875-80. 2002
    ..This suggests that we must use caution in interpreting parameters that estimate environmental main effects from a family-based case-control study if controls are selected from outside the case-ascertainment region...
  3. ncbi request reprint Analysis of complex methylation data
    Kimberly D Siegmund
    Department of Preventive Medicine, University of Southern California Keck School of Medicine, 1441 Eastlake Avenue, Los Angeles, CA 90089 9176, USA
    Methods 27:170-8. 2002
    ..We then describe the basic statistics and bioinformatic principles relevant to the analysis of simple and complex methylation data...
  4. ncbi request reprint A comparison of cluster analysis methods using DNA methylation data
    Kimberly D Siegmund
    Department of Preventive Medicine, Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles 90089, USA
    Bioinformatics 20:1896-904. 2004
    ..Established tools to analyze this type of data do not exist. Here, we evaluate a variety of methods for cluster analysis to determine which is most reliable...
  5. ncbi request reprint Modeling exposures for DNA methylation profiles
    Kimberly D Siegmund
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 1540 Alcazar Street, CHP 220, Los Angeles, CA 90089, USA
    Cancer Epidemiol Biomarkers Prev 15:567-72. 2006
    ..Thus, when the clusters are not identified with certainty, the extended mixture model is preferred for valid estimation of the OR and CI...
  6. pmc Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer
    Paul P Anglim
    Department of Surgery, Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089 9176, USA
    Mol Cancer 7:62. 2008
    ....
  7. pmc Identification of a panel of sensitive and specific DNA methylation markers for lung adenocarcinoma
    Jeffrey A Tsou
    Norris Cancer Center and Department of Surgery and of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 9176, USA
    Mol Cancer 6:70. 2007
    ....
  8. pmc Human and great ape red blood cells differ in plasmalogen levels and composition
    Ann B Moser
    Hugo W Moser Research Institute at Kennedy Krieger, and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Lipids Health Dis 10:101. 2011
    ..Plasmalogen deficiency is also found in the brain tissue of individuals with Alzheimer disease...
  9. pmc Copy number variation in the Framingham Heart Study
    Corina Shtir
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 1540 Alcazar Street, CHP 220, Los Angeles, California 90089, USA
    BMC Proc 3:S133. 2009
    ..Furthermore, our results indicate a relatively poor level of agreement between copy number calls resulting from the two programs. We then examined potential causes for this difference in results and the implications for future studies...
  10. pmc Identification of differences in human and great ape phytanic acid metabolism that could influence gene expression profiles and physiological functions
    Paul A Watkins
    Department ofNeurology, Johns Hopkins University School of Medicine, Hugo W Moser Research Institute at Kennedy Krieger, Baltimore, MD 21205, USA
    BMC Physiol 10:19. 2010
    ..Furthermore, phytanic acid is an activator of the PPAR-alpha transcription factor that influences the expression of genes relevant to lipid metabolism...
  11. pmc Lack of increases in methylation at three CpG-rich genomic loci in non-mitotic adult tissues during aging
    Michelle W Chu
    Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
    BMC Med Genet 8:50. 2007
    ..Somatic genomes may record their mitotic ages because greater numbers of replication errors should accumulate after greater numbers of divisions. Mitotic ages will vary between cell types if they divide at different times and rates...
  12. pmc Age-related human small intestine methylation: evidence for stem cell niches
    Jung Yeon Kim
    Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
    BMC Med 3:10. 2005
    ..Potentially age-related methylation also occurs in human small intestines, which would allow characterization of their stem cells and comparisons with the colon...
  13. pmc mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft
    Darren Magda
    Department of Biochemistry and Molecular Biology, University of Southern California, 2250 Alcazar Street, IGM 240, Los Angeles, CA 90089, USA
    BMC Genomics 9:521. 2008
    ..In order to address this issue, we characterized the gene expression profiles of A549 lung cancer cells and their mtDNA-depleted rho0 counterparts grown in culture and as tumor xenografts in immune-deficient mice...
  14. pmc Identifying susceptibility genes by using joint tests of association and linkage and accounting for epistasis
    Joshua Millstein
    National Oceanic and Atmospheric Administration National Marine Fisheries Service, Alaska Fisheries Science Center, 7600 Sand Point Way NE, Seattle, WA 98115, USA
    BMC Genet 6:S147. 2005
    ..The strongest effect was for SNP B03T3056, which had a median p-value of 1.98 x 10(-34). No two- or three-locus effects were found in more than one replicate...
  15. pmc Modeling measurement error in tumor characterization studies
    Cyril Rakovski
    Department of Preventive Medicine, USC Keck School of Medicine, Los Angeles, California 90089 9176, USA
    BMC Bioinformatics 12:284. 2011
    ..We illustrate the phenomenon using the MethyLight technology, applying our proposed analysis to compare MLH1 DNA methylation levels in males and females studied in the Colon Cancer Family Registry...
  16. pmc Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees
    Donna M Toleno
    Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
    BMC Bioinformatics 10:77. 2009
    ..In this process, only data from oligonucleotide probes predicted to have robust hybridization sensitivity and specificity for both transcriptomes are retained for analysis...
  17. pmc Cluster analysis for DNA methylation profiles having a detection threshold
    Paul Marjoram
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
    BMC Bioinformatics 7:361. 2006
    ..This suggests that conventional clustering methodology may not perform well on this data...
  18. doi request reprint Modeling DNA methylation in a population of cancer cells
    Kimberly D Siegmund
    USC Keck School of Medicine, University of Southern California, USA
    Stat Appl Genet Mol Biol 7:Article 18. 2008
    ..The inferred cancer trees are consistent with Gompertzian growth, a well-known cancer growth pattern...
  19. pmc Testing linkage disequilibrium in sibships
    K D Siegmund
    Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
    Am J Hum Genet 67:244-8. 2000
    ..Finally, we concluded that although the standard analysis may lead to correct inference for practical purposes, the new test is valid, even under extreme residual familial correlation and with no cost in power at the causal locus...
  20. ncbi request reprint Stratified case sampling and the use of family controls
    K D Siegmund
    Department of Preventive Medicine, University of Southern California, Los Angeles 90089 9011, USA
    Genet Epidemiol 20:316-27. 2001
    ..Overall, the most efficient study design for studying gene-environment interaction was the case-sib-control design with over-sampling of positive-family-history-cases...
  21. pmc Statistical approaches for the analysis of DNA methylation microarray data
    Kimberly D Siegmund
    Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA 90089, USA
    Hum Genet 129:585-95. 2011
    ..I finish with a section describing downstream analyses of the data, focusing on methods that model percentage DNA methylation as the outcome, and methods for integrating DNA methylation with gene expression or genotype data...
  22. ncbi request reprint Association tests in nuclear families
    K D Siegmund
    Department of Preventive Medicine, University of Southern California, Los Angeles, Calif 9089 9011, USA
    Hum Hered 52:66-76. 2001
    ..They also led to equivalent power to detect linkage disequilibrium at the 5% significance level...
  23. pmc Repeated assessment by high-throughput assay demonstrates that sperm DNA methylation levels are highly reproducible
    Victoria K Cortessis
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
    Fertil Steril 96:1325-30. 2011
    ..To assess reliability of a high-throughput assay of sperm DNA methylation...
  24. pmc Molecular characterization of MSI-H colorectal cancer by MLHI promoter methylation, immunohistochemistry, and mismatch repair germline mutation screening
    Jenny N Poynter
    Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033 9176, USA
    Cancer Epidemiol Biomarkers Prev 17:3208-15. 2008
    ..These results reinforce the importance of distinguishing between the underlying causes of MSI in studies of etiology and prognosis...
  25. ncbi request reprint CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer
    Daniel J Weisenberger
    Department of Surgery, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90089 9176, USA
    Nat Genet 38:787-93. 2006
    ..Sporadic cases of mismatch repair deficiency occur almost exclusively as a consequence of CIMP-associated methylation of MLH1 . We propose a robust new marker panel to classify CIMP+ tumors...
  26. ncbi request reprint Diet, cancer and aging in DNA mismatch repair deficient mice
    Jen Lan Tsao
    Department of Pathology, Molecular Biology and Surgery, Norris Cancer Center, University of Southern California School of Medicine, Los Angeles, CA 90033, USA
    Carcinogenesis 23:1807-10. 2002
    ..Our studies indicate that MMR deficiency may be epistatic to certain otherwise strong environmental influences on carcinogenesis or aging...
  27. pmc Widespread epigenetic abnormalities suggest a broad DNA methylation erasure defect in abnormal human sperm
    Sahar Houshdaran
    Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
    PLoS ONE 2:e1289. 2007
    ..Incomplete reprogramming of the male germ line could, in theory, result in both altered sperm DNA methylation and compromised spermatogenesis...
  28. ncbi request reprint XRCC1, XRCC3, and XPD polymorphisms as modifiers of the effect of smoking and alcohol on colorectal adenoma risk
    Mariana C Stern
    University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, 1441 Eastlake Avenue, Room 5421A, Los Angeles, CA 90089, USA
    Cancer Epidemiol Biomarkers Prev 15:2384-90. 2006
    ..04). Our data suggest that the effects of smoking and alcohol may vary depending on the genetic background of proteins that participate in the base excision repair and nucleotide excision repair pathways...
  29. pmc Hormone therapy, DNA methylation and colon cancer
    Anna H Wu
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, Los Angeles, CA, USA
    Carcinogenesis 31:1060-7. 2010
    ..055) and increased DNA methylation of ESR1 in the 'tumorous' colonic tissues (P = 0.056). These findings on DNA methylation and hormone therapy use need confirmation in larger studies...
  30. doi request reprint Older individuals appear to acquire mitotically older colorectal cancers
    Yen Jung Woo
    Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
    J Pathol 217:483-8. 2009
    ..Cell division per se may be an important mechanism underlying the increased incidence of colorectal cancer with ageing, because the neoplastic phase appears more commonly to start from mitotically older crypt stem cells...
  31. ncbi request reprint Variants on 9p24 and 8q24 are associated with risk of colorectal cancer: results from the Colon Cancer Family Registry
    Jenny N Poynter
    Department of Preventive Medicine, University of Southern California, 1441 Eastlake Avenue, NOR4411A, Los Angeles, CA 90089 9175, USA
    Cancer Res 67:11128-32. 2007
    ..These data suggest that common variants may play important roles in the risk of CRC...
  32. ncbi request reprint DNA repair single-nucleotide polymorphisms in colorectal cancer and their role as modifiers of the effect of cigarette smoking and alcohol in the Singapore Chinese Health Study
    Mariana C Stern
    Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, 1441 Eastlake Avenue, Room 5421A, Los Angeles, CA 90089, USA
    Cancer Epidemiol Biomarkers Prev 16:2363-72. 2007
    ..8; 95% CI, 1.0-8.1). Our results support a role for reactive oxygen species as relevant genotoxins that may account for the effects of both smoking and alcohol on colorectal cancer risk...
  33. ncbi request reprint XRCC1 and XRCC3 polymorphisms and their role as effect modifiers of unsaturated fatty acids and antioxidant intake on colorectal adenomas risk
    Mariana C Stern
    Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
    Cancer Epidemiol Biomarkers Prev 14:609-15. 2005
    ....
  34. pmc Unique DNA methylation patterns distinguish noninvasive and invasive urothelial cancers and establish an epigenetic field defect in premalignant tissue
    Erika M Wolff
    Department of Urology, USC Epigenome Center, and Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, University of Southern California, Keck School of Medicine, Los Angeles, CA 90089, USA
    Cancer Res 70:8169-78. 2010
    ..In addition, an epithelium-wide epigenetic defect in bladders with cancer might contribute to a loss of epithelial integrity and create a permissible environment for tumors to arise...
  35. pmc Using DNA methylation patterns to infer tumor ancestry
    You Jin Hong
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
    PLoS ONE 5:e12002. 2010
    ....
  36. doi request reprint Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns
    Hyang Min Byun
    Jane Anne Nohl Division of Hematology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
    Hum Mol Genet 18:4808-17. 2009
    ..05). Finally, we found that the Illumina GoldenGate assay features a large number of probes (265/1505 probes, 17.6%) that contain single-nucleotide polymorphisms, which may interfere with DNA methylation analyses in genome-wide studies...
  37. pmc Associations between smoking, alcohol consumption, and colorectal cancer, overall and by tumor microsatellite instability status
    Jenny N Poynter
    Department of Preventive Medicine, University of Southern California, Los Angeles, California, USA
    Cancer Epidemiol Biomarkers Prev 18:2745-50. 2009
    ..Reports have suggested that these associations may differ by tumor molecular subtype, with stronger associations for microsatellite unstable (MSI-H) tumors...
  38. pmc Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers
    Kimberly D Siegmund
    Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
    Proc Natl Acad Sci U S A 106:4828-33. 2009
    ..Our study illustrates the potential to reconstruct the unperturbed biology of human cancers from epigenetic passenger variations in their present-day genomes...
  39. doi request reprint Inferring relative numbers of human leucocyte genome replications
    Michelle Chu
    Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
    Br J Haematol 141:862-71. 2008
    ..These studies tentatively support the hypothesis that methylation at certain CpG rich sequences in leucocytes could record their mitotic ages...
  40. pmc Red meat and poultry intake, polymorphisms in the nucleotide excision repair and mismatch repair pathways and colorectal cancer risk
    Amit D Joshi
    Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, CA 90089, USA
    Carcinogenesis 30:472-9. 2009
    ..These findings highlight the possible contribution of diets high in red meat to the formation of lesions that elicit the NER pathway, such as carcinogen-induced bulky adducts...
  41. doi request reprint Shorter androgen receptor CAG repeat lengths associated with cryptorchidism risk among Hispanic white boys
    Carol Davis-Dao
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Children s Hospital Los Angeles, 1441 Eastlake Avenue, MC 9175, Los Angeles, California 90033, USA
    J Clin Endocrinol Metab 97:E393-9. 2012
    ..Androgens are essential for testicular descent, and functional genetic polymorphisms in the androgen receptor gene (AR) are postulated to influence cryptorchidism risk...
  42. ncbi request reprint Detection of methylated apoptosis-associated genes in urine sediments of bladder cancer patients
    Martin G Friedrich
    Departments of Urology, Clinical Pathology, and Preventive Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089 9176, USA
    Clin Cancer Res 10:7457-65. 2004
    ....
  43. pmc DNA methylation in the human cerebral cortex is dynamically regulated throughout the life span and involves differentiated neurons
    Kimberly D Siegmund
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
    PLoS ONE 2:e895. 2007
    ..Therefore, DNA methylation is dynamically regulated in the human cerebral cortex throughout the lifespan, involves differentiated neurons, and affects a substantial portion of genes predominantly by an age-related increase...
  44. ncbi request reprint Prognostic relevance of methylation markers in patients with non-muscle invasive bladder carcinoma
    Martin G Friedrich
    Department of Urology, University of Southern California, 1441 Eastlake Avenue, Los Angeles, CA 90089 9176, USA
    Eur J Cancer 41:2769-78. 2005
    ..We identified one gene (TIMP-3) where methylation was associated with a more favourable outcome. Our data strongly support the usefulness of gene methylation as a prognostic marker in patients with non-muscle invasive bladder cancer...
  45. ncbi request reprint Distinct DNA methylation profiles in malignant mesothelioma, lung adenocarcinoma, and non-tumor lung
    Jeffrey A Tsou
    Norris Cancer Center and Department of Surgery and Biochemistry, Room NOR 6420, 1441 Eastlake Ave, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 9176, USA
    Lung Cancer 47:193-204. 2005
    ..Our observations support the strong potential of methylation markers as tools for accurate diagnosis of neoplasms in and around the lung...
  46. pmc DNA methylation profile of 28 potential marker loci in malignant mesothelioma
    Jeffrey A Tsou
    Norris Cancer Center and Department of Surgery, Keck School of Medicine, University of Southern California, Room NOR6420, 1441 Eastlake Avenue, Los Angeles, CA 90089 9176, USA
    Lung Cancer 58:220-30. 2007
    ....
  47. ncbi request reprint Many colorectal cancers are "flat" clonal expansions
    Kimberly D Siegmund
    Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
    Cell Cycle 8:2187-93. 2009
    ....
  48. ncbi request reprint A case-control study of cyclin D1 CCND1 870A-->G polymorphism and bladder cancer
    Victoria K Cortessis
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, MC 9175, Los Angeles, CA 90033, USA
    Carcinogenesis 24:1645-50. 2003
    ..90, 95% confidence interval 0.60-1.33). The null association was not appreciably modified by bladder cancer risk factors, including lifetime smoking history, or by histopathologic classification...
  49. pmc Identification and functional relevance of de novo DNA methylation in cancerous B-cell populations
    Xiao Ming Wang
    Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, California 90089, USA
    J Cell Biochem 109:818-27. 2010
    ..Furthermore, we propose that similar to de novo genetic mutations, the majority of de novo DNA methylation events observed in tumors are passengers not causally involved in tumorigenesis...
  50. ncbi request reprint Association of breast cancer DNA methylation profiles with hormone receptor status and response to tamoxifen
    Martin Widschwendter
    Department of Urology, University of Southern California, Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, California, 90089 9176, USA
    Cancer Res 64:3807-13. 2004
    ....
  51. ncbi request reprint Statistical methods for evaluating DNA methylation as a marker for early detection or prognosis
    Todd A Alonzo
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
    Dis Markers 23:113-20. 2007
    ..It is important to know what factors may affect the accuracy of a marker and in which subpopulations the marker may be more accurate. Such an understanding is extremely important when comparing marker accuracy in two groups of subjects...
  52. pmc Hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladders with cancer
    Erika M Wolff
    Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
    PLoS Genet 6:e1000917. 2010
    ..These data show that, in addition to contributing to chromosomal instability, hypomethylation of LINE-1s can alter the functional transcriptome and plays a role not only in human disease but also in disease predisposition...
  53. ncbi request reprint Testing association and linkage using affected-sib-parent study designs
    Joshua Millstein
    National Oceanic and Atmospheric Administration National Marine Fisheries Service, Alaska Fisheries Science Center, Seattle, Washington 98115, USA
    Genet Epidemiol 29:225-33. 2005
    ..8% by FBAT, and 82.5% by our joint test of linkage and association. Our model can also be used to obtain tests of linkage conditional on association and association conditional on linkage, which can be helpful in fine mapping...

Research Grants7

  1. Statistical Models in Epigenomics
    Kimberly D Siegmund; Fiscal Year: 2010
    ..We propose to develop mathematical models that can retrospectively reconstruct tumor histories, allowing us to address important biological questions about the growth and spread of cancer. ..
  2. Statistical Models in Epigenomics
    Kimberly Siegmund; Fiscal Year: 2005
    ..3. Apply methods to studies of DNA methylation in colorectacl adenomas and lung cancer. ..
  3. Statistical Models in Epigenomics
    Kimberly Siegmund; Fiscal Year: 2007
    ..4. Apply the methods to DNA methylation patterns observed in primary tumors of the colon and distant metastasis in humans and in mice. ..
  4. Statistical Models in Epigenomics
    Kimberly Siegmund; Fiscal Year: 2009
    ..We propose to develop mathematical models that can retrospectively reconstruct tumor histories, allowing us to address important biological questions about the growth and spread of cancer. ..