Faculty

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Kimberly Siegmund, PhD
Professor of Preventive Medicine
Preventive Medicine
SSB 202W 2001 N. Soto Street Health Sciences Campus Los Angeles
+1 323 442 1310

Overview

Dr. Siegmund is a biostatistician with expertise in cancer modeling and the statistical analysis of epigenetic data in human disease. She has published numerous papers studying DNA methylation, and teaches a course on the statistical analysis of high-dimensional data. Her current research focuses on developing mathematical models to understand the growth and spread of cancer. These models address fundamental questions about aging through modeling cell division processes from a molecular phylogenetic approach.

Dr. Siegmund is interested the analysis of DNA methylation and gene expression data. She is developing mathematical models that will allow the identification of disease sub-types based on DNA methylation profiles. Other interests and skills relate to the design and analysis of family studies for gene characterization.

Publications

Cross-Species Transcriptome Profiling Identifies New Alveolar Epithelial Type I Cell-Specific Genes. Am J Respir Cell Mol Biol. 2017 Mar; 56(3):310-321. View in: PubMed

Improving needle biopsy accuracy in small renal mass using tumor-specific DNA methylation markers. Oncotarget. 2017 Jan 17; 8(3):5439-5448. View in: PubMed

Identifying aggressive prostate cancer foci using a DNA methylation classifier. Genome Biol. 2017 Jan 12; 18(1):3. View in: PubMed

Early mutation bursts in colorectal tumors. PLoS One. 2017; 12(3):e0172516. View in: PubMed

Impact of Chromosomal Rearrangement upon DNA Methylation Patterns in Leukemia. Open Med (Wars). 2017; 12:76-85. View in: PubMed

Prenatal Air Pollution Exposures, DNA Methyl Transferase Genotypes, and Associations with Newborn LINE1 and Alu Methylation and Childhood Blood Pressure and Carotid Intima-Media Thickness in the Children's Health Study. Environ Health Perspect. 2016 Dec; 124(12):1905-1912. View in: PubMed

An evaluation of processing methods for HumanMethylation450 BeadChip data. BMC Genomics. 2016 Jun 22; 17:469. View in: PubMed

At least two well-spaced samples are needed to genotype a solid tumor. BMC Cancer. 2016 Mar 25; 16:250. View in: PubMed

Genetic complexity at expression quantitative trait loci. BMC Proc. 2016; 10(Suppl 7):85-89. View in: PubMed

Identification of DNA Methylation-Independent Epigenetic Events Underlying Clear Cell Renal Cell Carcinoma. Cancer Res. 2016 04 01; 76(7):1954-64. View in: PubMed

Many private mutations originate from the first few divisions of a human colorectal adenoma. J Pathol. 2015 Nov; 237(3):355-62. View in: PubMed

A Big Bang model of human colorectal tumor growth. Nat Genet. 2015 Mar; 47(3):209-16. View in: PubMed

Identifying differential transcription factor binding in ChIP-seq. Front Genet. 2015; 6:169. View in: PubMed

Transcriptomic Profiling of Primary Alveolar Epithelial Cell Differentiation in Human and Rat. Genom Data. 2014 Dec 01; 2:105-109. View in: PubMed

Ancestral inference in tumors: how much can we know? J Theor Biol. Ancestral inference in tumors: how much can we know? J Theor Biol. 2014 Oct 21; 359:136-45. View in: PubMed

Non-specific filtering of beta-distributed data. BMC Bioinformatics. 2014 Jun 19; 15:199. View in: PubMed

NOS1 methylation and carotid artery intima-media thickness in children. Circ Cardiovasc Genet. 2014 Apr; 7(2):116-22. View in: PubMed

A panel of three markers hyper- and hypomethylated in urine sediments accurately predicts bladder cancer recurrence. Clin Cancer Res. 2014 Apr 01; 20(7):1978-89. View in: PubMed

Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue. Nat Commun. 2014 Feb 27; 5:3365. View in: PubMed

Distinct, genome-wide, gene-specific selectivity patterns of four glucocorticoid receptor coregulators. Nucl Recept Signal. 2014; 12:e002. View in: PubMed

Prenatal tobacco smoke exposure is associated with childhood DNA CpG methylation. PLoS One. 2014; 9(6):e99716. View in: PubMed

Null association between histology of first and second primary malignancies in men with bilateral testicular germ cell tumors. Am J Epidemiol. 2013 Oct 15; 178(8):1240-5. View in: PubMed

Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods. 2013 Oct; 10(10):949-55. View in: PubMed

Testicular germ cell tumor susceptibility associated with the UCK2 locus on chromosome 1q23. Hum Mol Genet. 2013 Jul 01; 22(13):2748-53. View in: PubMed

Integrated transcriptomic and epigenomic analysis of primary human lung epithelial cell differentiation. PLoS Genet. 2013 Jun; 9(6):e1003513. View in: PubMed

Low-level processing of Illumina Infinium DNA Methylation BeadArrays. Nucleic Acids Res. 2013 Apr; 41(7):e90. View in: PubMed

G9a functions as a molecular scaffold for assembly of transcriptional coactivators on a subset of glucocorticoid receptor target genes. Proc Natl Acad Sci U S A. 2012 Nov 27; 109(48):19673-8. View in: PubMed

Environmental epigenetics: prospects for studying epigenetic mediation of exposure-response relationships. Hum Genet. 2012 Oct; 131(10):1565-89. View in: PubMed

Particulate matter, DNA methylation in nitric oxide synthase, and childhood respiratory disease. Environ Health Perspect. 2012 Sep; 120(9):1320-6. View in: PubMed

Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biol. 2012 Jul 11; 13(7):R61. View in: PubMed

Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression. Genome Res. 2012 Jul; 22(7):1197-211. View in: PubMed

Carcinogen metabolism genes, red meat and poultry intake, and colorectal cancer risk. Int J Cancer. 2012 Apr 15; 130(8):1898-907. View in: PubMed

Shorter androgen receptor CAG repeat lengths associated with cryptorchidism risk among Hispanic white boys. J Clin Endocrinol Metab. 2012 Mar; 97(3):E393-9. View in: PubMed

Selective roles for cAMP response element-binding protein binding protein and p300 protein as coregulators for androgen-regulated gene expression in advanced prostate cancer cells. J Biol Chem. 2012 Feb 03; 287(6):4000-13. View in: PubMed

Repeated assessment by high-throughput assay demonstrates that sperm DNA methylation levels are highly reproducible. Fertil Steril. 2011 Dec; 96(6):1325-30. View in: PubMed

Soy food supplementation, dietary fat reduction and peripheral blood gene expression in postmenopausal women--a randomized, controlled trial. Mol Nutr Food Res. 2011 Sep; 55 Suppl 2:S264-77. View in: PubMed

Heterogenous effect of androgen receptor CAG tract length on testicular germ cell tumor risk: shorter repeats associated with seminoma but not other histologic types. Carcinogenesis. 2011 Aug; 32(8):1238-43. View in: PubMed

DNA methylation in the arginase-nitric oxide synthase pathway is associated with exhaled nitric oxide in children with asthma. Am J Respir Crit Care Med. 2011 Jul 15; 184(2):191-7. View in: PubMed

Modeling measurement error in tumor characterization studies. BMC Bioinformatics. 2011 Jul 13; 12:284. View in: PubMed

Human and great ape red blood cells differ in plasmalogen levels and composition. Lipids Health Dis. 2011 Jun 17; 10:101. View in: PubMed

Statistical approaches for the analysis of DNA methylation microarray data. Hum Genet. 2011 Jun; 129(6):585-95. View in: PubMed

High DNA methylation pattern intratumoral diversity implies weak selection in many human colorectal cancers. PLoS One. 2011; 6(6):e21657. View in: PubMed

Genome-scale screen for DNA methylation-based detection markers for ovarian cancer. PLoS One. 2011; 6(12):e28141. View in: PubMed

DNA methylation changes in atypical adenomatous hyperplasia, adenocarcinoma in situ, and lung adenocarcinoma. PLoS One. 2011; 6(6):e21443. View in: PubMed

The PREMM(1,2,6) model predicts risk of MLH1, MSH2, and MSH6 germline mutations based on cancer history. Gastroenterology. 2011 Jan; 140(1):73-81. View in: PubMed

Epigenetic subgroups of esophageal and gastric adenocarcinoma with differential GATA5 DNA methylation associated with clinical and lifestyle factors. PLoS One. 2011; 6(10):e25985. View in: PubMed

Polymorphisms in base excision repair genes as colorectal cancer risk factors and modifiers of the effect of diets high in red meat. Cancer Epidemiol Biomarkers Prev. 2010 Dec; 19(12):3167-73. View in: PubMed

Unique DNA methylation patterns distinguish noninvasive and invasive urothelial cancers and establish an epigenetic field defect in premalignant tissue. Cancer Res. 2010 Oct 15; 70(20):8169-78. View in: PubMed

Identification of differences in human and great ape phytanic acid metabolism that could influence gene expression profiles and physiological functions. BMC Physiol. 2010 Oct 08; 10:19. View in: PubMed

Using DNA methylation patterns to infer tumor ancestry. PLoS One. 2010 Aug 09; 5(8):e12002. View in: PubMed

Hormone therapy, DNA methylation and colon cancer. Carcinogenesis. 2010 Jun; 31(6):1060-7. View in: PubMed

Hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladders with cancer. PLoS Genet. 2010 Apr 22; 6(4):e1000917. View in: PubMed

Identification and functional relevance of de novo DNA methylation in cancerous B-cell populations. J Cell Biochem. 2010 Mar 01; 109(4):818-27. View in: PubMed

Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns. Hum Mol Genet. 2009 Dec 15; 18(24):4808-17. View in: PubMed

Copy number variation in the Framingham Heart Study. BMC Proc. 2009 Dec 15; 3 Suppl 7:S133. View in: PubMed

Associations between smoking, alcohol consumption, and colorectal cancer, overall and by tumor microsatellite instability status. Cancer Epidemiol Biomarkers Prev. 2009 Oct; 18(10):2745-50. View in: PubMed

Many colorectal cancers are "flat" clonal expansions. Cell Cycle. 2009 Jul 15; 8(14):2187-93. View in: PubMed

Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers. Proc Natl Acad Sci U S A. 2009 Mar 24; 106(12):4828-33. View in: PubMed

Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees. BMC Bioinformatics. 2009 Mar 05; 10:77. View in: PubMed

Red meat and poultry intake, polymorphisms in the nucleotide excision repair and mismatch repair pathways and colorectal cancer risk. Carcinogenesis. 2009 Mar; 30(3):472-9. View in: PubMed

The association of tumor microsatellite instability phenotype with family history of colorectal cancer. Cancer Epidemiol Biomarkers Prev. 2009 Mar; 18(3):967-75. View in: PubMed

Older individuals appear to acquire mitotically older colorectal cancers. J Pathol. 2009 Mar; 217(4):483-8. View in: PubMed

mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft. BMC Genomics. 2008 Nov 03; 9:521. View in: PubMed

Molecular characterization of MSI-H colorectal cancer by MLHI promoter methylation, immunohistochemistry, and mismatch repair germline mutation screening. Cancer Epidemiol Biomarkers Prev. 2008 Nov; 17(11):3208-15. View in: PubMed

Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer. Mol Cancer. 2008 Jul 10; 7:62. View in: PubMed

Inferring relative numbers of human leucocyte genome replications. Br J Haematol. 2008 Jun; 141(6):862-71. View in: PubMed

Modeling DNA methylation in a population of cancer cells. Stat Appl Genet Mol Biol. 2008; 7(1):Article 18. View in: PubMed

Widespread epigenetic abnormalities suggest a broad DNA methylation erasure defect in abnormal human sperm. PLoS One. 2007 Dec 12; 2(12):e1289. View in: PubMed

Morbid obesity adversely impacts pelvic floor function in females seeking attention for weight loss surgery. Dis Colon Rectum. 2007 Dec; 50(12):2096-103. View in: PubMed

Variants on 9p24 and 8q24 are associated with risk of colorectal cancer: results from the Colon Cancer Family Registry. Cancer Res. 2007 Dec 01; 67(23):11128-32. View in: PubMed

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. Cancer Epidemiol Biomarkers Prev. 2007 Nov; 16(11):2363-72. View in: PubMed

DNA methylation profile of 28 potential marker loci in malignant mesothelioma. Lung Cancer. 2007 Nov; 58(2):220-30. View in: PubMed

Identification of a panel of sensitive and specific DNA methylation markers for lung adenocarcinoma. Mol Cancer. 2007 Oct 29; 6:70. View in: PubMed

DNA methylation in the human cerebral cortex is dynamically regulated throughout the life span and involves differentiated neurons. PLoS One. 2007 Sep 19; 2(9):e895. View in: PubMed

Lack of increases in methylation at three CpG-rich genomic loci in non-mitotic adult tissues during aging. BMC Med Genet. 2007 Jul 31; 8:50. View in: PubMed

Statistical methods for evaluating DNA methylation as a marker for early detection or prognosis. Dis Markers. 2007; 23(1-2):113-20. View in: PubMed

XRCC1, XRCC3, and XPD polymorphisms as modifiers of the effect of smoking and alcohol on colorectal adenoma risk. Cancer Epidemiol Biomarkers Prev. 2006 Dec; 15(12):2384-90. View in: PubMed

Cluster analysis for DNA methylation profiles having a detection threshold. BMC Bioinformatics. 2006 Jul 26; 7:361. View in: PubMed

CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat Genet. 2006 Jul; 38(7):787-93. View in: PubMed

Modeling exposures for DNA methylation profiles. Cancer Epidemiol Biomarkers Prev. 2006 Mar; 15(3):567-72. View in: PubMed

Identifying susceptibility genes by using joint tests of association and linkage and accounting for epistasis. BMC Genet. 2005 Dec 30; 6 Suppl 1:S147. View in: PubMed

Testing association and linkage using affected-sib-parent study designs. Genet Epidemiol. 2005 Nov; 29(3):225-33. View in: PubMed

Prognostic relevance of methylation markers in patients with non-muscle invasive bladder carcinoma. Eur J Cancer. 2005 Nov; 41(17):2769-78. View in: PubMed

Age-related human small intestine methylation: evidence for stem cell niches. BMC Med. 2005 Jun 23; 3:10. View in: PubMed

Lower cancer incidence in Amsterdam-I criteria families without mismatch repair deficiency: familial colorectal cancer type X. JAMA. 2005 Apr 27; 293(16):1979-85. View in: PubMed

XRCC1 and XRCC3 polymorphisms and their role as effect modifiers of unsaturated fatty acids and antioxidant intake on colorectal adenomas risk. Cancer Epidemiol Biomarkers Prev. 2005 Mar; 14(3):609-15. View in: PubMed

Distinct DNA methylation profiles in malignant mesothelioma, lung adenocarcinoma, and non-tumor lung. Lung Cancer. 2005 Feb; 47(2):193-204. View in: PubMed

Detection of methylated apoptosis-associated genes in urine sediments of bladder cancer patients. Clin Cancer Res. 2004 Nov 15; 10(22):7457-65. View in: PubMed

A comparison of cluster analysis methods using DNA methylation data. Bioinformatics. 2004 Aug 12; 20(12):1896-904. View in: PubMed

Association of breast cancer DNA methylation profiles with hormone receptor status and response to tamoxifen. Cancer Res. 2004 Jun 01; 64(11):3807-13. View in: PubMed

A case-control study of cyclin D1 CCND1 870A-->G polymorphism and bladder cancer. Carcinogenesis. 2003 Oct; 24(10):1645-50. View in: PubMed

Diet, cancer and aging in DNA mismatch repair deficient mice. Carcinogenesis. 2002 Nov; 23(11):1807-10. View in: PubMed

Analysis of complex methylation data. Methods. 2002 Jun; 27(2):170-8. View in: PubMed

Ascertainment bias in family-based case-control studies. Am J Epidemiol. 2002 May 01; 155(9):875-80. View in: PubMed

Hierarchical clustering of lung cancer cell lines using DNA methylation markers. Cancer Epidemiol Biomarkers Prev. 2002 Mar; 11(3):291-7. View in: PubMed

Stratified case sampling and the use of family controls. Genet Epidemiol. 2001 Apr; 20(3):316-27. View in: PubMed

Association tests in nuclear families. Hum Hered. 2001; 52(2):66-76. View in: PubMed

Testing linkage disequilibrium in sibships. Am J Hum Genet. 2000 Jul; 67(1):244-8. View in: PubMed

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