Research Topics
| PETER LAIRDSummaryAffiliation: University of Southern California Country: USA Publications
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Publications
CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancerDaniel 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...- Modeling exposures for DNA methylation profilesKimberly 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... 
Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancerPaul 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....- Identification of a panel of sensitive and specific DNA methylation markers for lung adenocarcinomaJeffrey 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.... - Sensitivity and reproducibility of standardized-competitive RT-PCR for transcript quantification and its comparison with real time RT-PCRVincenzo Pagliarulo
Department of Pathology, University of Southern California, Keck School of Medicine, 2011 Zonal Ave, HMR 312C, Los Angeles, CA 90033, USA
Mol Cancer 3:5. 2004..The CT serves as an ideal internal control. The transcript numbers are expressed as copies per million transcripts of a control gene such as beta-actin (ACTB)... - Modeling measurement error in tumor characterization studiesCyril 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... - Cluster analysis for DNA methylation profiles having a detection thresholdPaul 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... 
Principles and challenges of genomewide DNA methylation analysisPeter W Laird
USC Epigenome Center, University of Southern California, Keck School of Medicine, Los Angeles, 90089 9601, USA
Nat Rev Genet 11:191-203. 2010..This Review discusses the different approaches and their relative merits and introduces considerations for data analysis...- The USC Epigenome CenterPeter W Laird
University of Southern California, Keck School of Medicine, USC Epigenome Center, 1450 Biggy Street, Los Angeles, CA 90089 99601, USA
Epigenomics 1:29-31. 2009..This unique facility promises to be a valuable resource for multidisciplinary research, education and training in genomics, epigenomics, bioinformatics, and translational medicine... - The power and the promise of DNA methylation markersPeter W Laird
University of Southern California, Norris Comprehensive Cancer Center, Room 6418, 1441 Eastlake Avenue, Los Angeles, California 90089 9176, USA
Nat Rev Cancer 3:253-66. 2003..The ubiquity of DNA methylation changes has opened the way to a host of innovative diagnostic and therapeutic strategies. Recent advances attest to the great promise of DNA methylation markers as powerful future tools in the clinic... - DNA methylation profiles of ovarian epithelial carcinoma tumors and cell linesSahar Houshdaran
Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, California, United States of America
PLoS ONE 5:e9359. 2010..This study applied recently developed methods for high-throughput DNA methylation profiling to characterize ovarian cancer cell lines and tumors, including representatives of three major histologies... - A comparison of cluster analysis methods using DNA methylation dataKimberly 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... - Hormone therapy, DNA methylation and colon cancerAnna 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... - Distinct DNA methylation profiles in malignant mesothelioma, lung adenocarcinoma, and non-tumor lungJeffrey 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... - DNA methylation profile of 28 potential marker loci in malignant mesotheliomaJeffrey 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.... - Smad3 deficiency promotes tumorigenesis in the distal colon of ApcMin/+ miceNicole M Sodir
Department of Surgery and Biochemistry, Norris Comprehensive Cancer Center, Los Angeles, CA 90089 9176, USA
Cancer Res 66:8430-8. 2006.... - DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLightDaniel J Weisenberger
Department of Surgery, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
Nucleic Acids Res 36:4689-98. 2008..Using digital MethyLight, we identified single-molecule, cancer-specific DNA hypermethylation events in the CpG islands of RUNX3, CLDN5 and FOXE1 present in plasma samples from breast cancer patients... - Unique DNA methylation patterns distinguish noninvasive and invasive urothelial cancers and establish an epigenetic field defect in premalignant tissueErika 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... - Long-term epigenetic therapy with oral zebularine has minimal side effects and prevents intestinal tumors in miceChristine B Yoo
Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California 90033 9181, USA
Cancer Prev Res (Phila) 1:233-40. 2008..Importantly, prolonged treatment of mice with epigenetic drugs resulted in only minor developmental and histologic changes... - DNA methyltransferase deficiency modifies cancer susceptibility in mice lacking DNA mismatch repairBinh N Trinh
Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089 9176, USA
Mol Cell Biol 22:2906-17. 2002.... - Analysis of the association between CIMP and BRAF in colorectal cancer by DNA methylation profilingToshinori Hinoue
USC Epigenome Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
PLoS ONE 4:e8357. 2009..Our data will be useful for future investigations toward understanding CIMP in colorectal cancer and gaining insights into the role of aberrant DNA hypermethylation in colorectal tumorigenesis... - Analysis of repetitive element DNA methylation by MethyLightDaniel J Weisenberger
Department of Surgery, Keck School of Medicine, USC/Norris Comprehensive Cancer Center, University of Southern California Los Angeles, CA, USA
Nucleic Acids Res 33:6823-36. 2005.... - Identification of a CpG island methylator phenotype that defines a distinct subgroup of gliomaHoutan Noushmehr
USC Epigenome Center, University of Southern California, Los Angeles, CA 90033, USA
Cancer Cell 17:510-22. 2010..Patients with G-CIMP tumors are younger at the time of diagnosis and experience significantly improved outcome. These findings identify G-CIMP as a distinct subset of human gliomas on molecular and clinical grounds... - Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patternsHyang 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... - Molecular characterization of MSI-H colorectal cancer by MLHI promoter methylation, immunohistochemistry, and mismatch repair germline mutation screeningJenny 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... - MethyLightMihaela Campan
Department of Surgery, University of Southern California, Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, CA, USA
Methods Mol Biol 507:325-37. 2009..We show that these control reactions perform as expected in a time-course experiment interrupting sodium bisulfite conversion at various timepoints... - Cooperativity between DNA methyltransferases in the maintenance methylation of repetitive elementsGangning Liang
USC/Norris Comprehensive Cancer Center, Department of Urology, Keck School of Medicine of the University of Southern California, Los Angeles, California 90089-9181, USA
Mol Cell Biol 22:480-91. 2002..Our results reveal a previously unrecognized degree of cooperativity among mammalian DNA methyltransferases in ES cells... - Association of breast cancer DNA methylation profiles with hormone receptor status and response to tamoxifenMartin 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.... - Complete genetic suppression of polyp formation and reduction of CpG-island hypermethylation in Apc(Min/+) Dnmt1-hypomorphic MiceCindy A Eads
Department of Biochemistry and Molecular Biology, University of Southern California, Keck School of Medicine, Norris Comprehensive Cancer Center, Room 6418, Los Angeles, California 90089 9176, USA
Cancer Res 62:1296-9. 2002.... - Rapid and quantitative method of allele-specific DNA methylation analysisHui-Lee Wong
University of Southern California, Los Angeles, CA 90089, USA
Biotechniques 41:734-9. 2006..Although we could reliably determine allele-specific methylation with our technique, additional studies will be required to confirm the ability of our assay to measure loss of imprinting... - Cancer epigeneticsPeter W Laird
Department of Surgery and Biochemistry and Molecular Biology, University of Southern California, 90086-9176, USA
Hum Mol Genet 14:R65-76. 2005..Sensitive detection technology has expanded from primarily blood-based cancer detection to include applications on a wide diversity of sample sources and is now also making inroads as a molecular risk assessment tool... - Widespread epigenetic abnormalities suggest a broad DNA methylation erasure defect in abnormal human spermSahar 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... - Diet, cancer and aging in DNA mismatch repair deficient miceJen 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... - DNA methylation in the human cerebral cortex is dynamically regulated throughout the life span and involves differentiated neuronsKimberly 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... - Sex differential in methylation patterns of selected genes in Singapore ChineseBarbara Sarter
Kenneth Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
Hum Genet 117:402-3. 2005..13 and 0.96, respectively). Our data suggest that gender is at least as strong a predictor of methylation level in the four genes under study as age, with males showing higher PMRs... - Role of methionine adenosyltransferase 2A and S-adenosylmethionine in mitogen-induced growth of human colon cancer cellsHui Chen
Division of Gastroenterology and Liver Diseases, University of Southern California Research Center for Liver Diseases, University of Southern California, Los Angeles, California 90033, USA
Gastroenterology 133:207-18. 2007..The role of MAT2A in colon cancer in unknown. The aims of this study were to examine whether MAT2A expression and SAMe and its metabolite methylthioadenosine (MTA) can modulate growth of colon cancer cells... - Analysis of complex methylation dataKimberly 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... - Combined bisulfite restriction analysis (COBRA)Cindy A Eads
Department of Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Los Angeles, CA, USA
Methods Mol Biol 200:71-85. 2002 - Dnmt1 deficiency leads to enhanced microsatellite instability in mouse embryonic stem cellsMyungjin Kim
Department of Surgery, University of Southern California, Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, CA 90089 9176, USA
Nucleic Acids Res 32:5742-9. 2004..The enhanced MSI was associated with higher levels of histone H3 acetylation and lower MeCP2 binding at regions near the assayed microsatellite, suggesting that Dnmt1 loss may decrease MMR efficiency by modifying chromatin structure... - 2'-Deoxy-N4-[2-(4-nitrophenyl)ethoxycarbonyl]-5-azacytidine: a novel inhibitor of DNA methyltransferase that requires activation by human carboxylesterase 1Hyang Min Byun
Division of Hematology, University of Southern California Norris Comprehensive Cancer Center, 1441 Eastlake Avenue, Room 6428, Los Angeles, CA, USA
Cancer Lett 266:238-48. 2008..Theses differences between decitabine and NPEOC-DAC are dependent on the cleavage of the carboxylester bond, and could be potentially exploited pharmacologically... - DNA methylation profiles of gastric carcinoma characterized by quantitative DNA methylation analysisGyeong Hoon Kang
Department of Pathology, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
Lab Invest 88:161-70. 2008..Through our large-scale screening of 170 CpG island loci, we found 17 new DNA methylation markers of GC, which may serve as useful markers that may identify a distinct subset of GC... - Correlation of pathologic features with CpG island methylator phenotype (CIMP) by quantitative DNA methylation analysis in colorectal carcinomaShuji Ogino
Department of Pathology, Brigham and Women s Hospital, Boston, MA 02115, USA
Am J Surg Pathol 30:1175-83. 2006..Both MSI and CIMP appear to play a role in the pathogenesis of specific morphologic patterns of colorectal carcinoma... - Hierarchical clustering of lung cancer cell lines using DNA methylation markersArvind 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... - Gene-specific methylation and subsequent risk of colorectal adenomas among participants of the polyp prevention trialKaren Woodson
Cancer Prevention Studies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
Cancer Epidemiol Biomarkers Prev 14:1219-23. 2005..No association between CDKN2A, PTGS2, or PGR methylation and adenoma recurrence was observed. These data suggest that ESR1 methylation may play a role in subsequent adenoma recurrence... - Hypomethylation and hypermethylation of DNA in Wilms tumorsMelanie Ehrlich
Tulane Cancer Center and Human Genetics Program, Tulane Medical School, New Orleans, Louisiana, LA 70112, USA
Oncogene 21:6694-702. 2002..This suggests that the DNA hypomethylation contributes independently to oncogenesis or tumor progression... - Sensitive detection of DNA methylationSusan E Cottrell
Epigenomics, Inc, Seattle, Washington 98101, USA
Ann N Y Acad Sci 983:120-30. 2003..Once these technical concerns have been addressed, the sensitive detection of methylation will provide a powerful diagnostic and prognostic tool, especially for the early detection of preneoplastic and neoplastic lesions... - Distinct methylation profiles of glioma subtypesKaren Uhlmann
, , , Berlin, Germany
Int J Cancer 106:52-9. 2003..Our results show that glioma subtypes have characteristic methylation profiles and, with the exception of pilocytic astrocytomas, show both locus specific hyper- as well as hypomethylation... - DNA hypomethylation and ovarian cancer biologyMartin Widschwendter
Department of Obstetrics and Gynecology, Medical University Innsbruck, Innsbruck, Austria
Cancer Res 64:4472-80. 2004.... - Kaiso contributes to DNA methylation-dependent silencing of tumor suppressor genes in colon cancer cell linesEloisi C Lopes
Department of Molecular Pharmacology and Chemistry, Memorial Sloan Kettering Cancer Center, New York, New York, USA
Cancer Res 68:7258-63. 2008..Because Kaiso inactivation sensitized colon cancer cell lines to chemotherapy, it is possible that therapeutic targeting of Kaiso could improve the efficacy of current treatment regimens... - Comprehensive genomic characterization defines human glioblastoma genes and core pathwaysRoger McLendon
Nature 455:1061-8. 2008..Together, these findings establish the feasibility and power of TCGA, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer... - Promoter hypermethylation: a new therapeutic target emerges in urothelial cancerRichard J Cote
J Clin Oncol 23:2879-81. 2005 - Promoter hypermethylation of tumor suppressor genes in urine from patients with cervical neoplasiaQinghua Feng
Department of Pathology, School of Medicine, University of Washington, Seattle, WA 98109, USA
Cancer Epidemiol Biomarkers Prev 16:1178-84. 2007..This study shows the potential feasibility of using molecular markers detected in urine for cervical cancer screening... - The role of DNA methylation in the development and progression of lung adenocarcinomaKeith M Kerr
Department of Pathology, Aberdeen Royal Infirmary, Link Building, Foresterhill, Aberdeen, AB25 2ZN, UK
Dis Markers 23:5-30. 2007.... - Epigenetic stem cell signature in cancerMartin Widschwendter
Department of Gynecological Oncology, Institute for Women s Health, University College London, London WC1E 6DH, UK
Nat Genet 39:157-8. 2007.... - Breast cancer DNA methylation profiles in cancer cells and tumor stroma: association with HER-2/neu status in primary breast cancerHeidi Fiegl
Department of Obstetrics and Gynecology, Innsbruck Medical University, Innsbruck, Austria
Cancer Res 66:29-33. 2006..04). These data support the view that in addition to HER-2/neu-associated signaling, epigenetic changes in cancer as well as in tumor stroma cells might attribute to the specific biological features of HER-2/neu-positive cancers... - Precision and performance characteristics of bisulfite conversion and real-time PCR (MethyLight) for quantitative DNA methylation analysisShuji Ogino
Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, 75 Francis St, Boston, MA 02115, USA
J Mol Diagn 8:209-17. 2006..In conclusion, sodium bisulfite conversion and quantitative MethyLight assays have good precision and linearity and can be effectively used for high-throughput DNA methylation analysis on paraffin-embedded tissue...
Research Grants
- SUPPRESSION OF NEOPLASIA BY DNA HYPOMETHYLATIONPETER LAIRD; Fiscal Year: 2006..abstract_text> ..
- DNA Methylation Markers in Esophageal AdenocarcinomaPETER LAIRD; Fiscal Year: 2006..We will also investigate whether factors known to increase the risk of adenocarcinoma of the esophagus, increase the risk of DNA methylation in normal tissue, or in the resulting adenocarcinoma. ..
- DNA Methylation Markers in Ovarian CancerPETER LAIRD; Fiscal Year: 2006..Finally, we propose to use the most promising biomarkers to evaluate the capacity to detect preclinical relapse of disease, as a function of time before clinical diagnosis of relapse. ..
- SUPPRESSION OF NEOPLASIA BY DNA HYPOMETHYLATIONPETER LAIRD; Fiscal Year: 2007..abstract_text> ..
- CpG Island Methylator Phenotype in Human Colorectal CancerPETER LAIRD; Fiscal Year: 2007..This study will investigate how some colorectal tumors acquire an unusually high number of epigenetic changes, with the long-term goal of using this knowledge to block or reverse these types of deleterious changes. ..
- CpG Island Methylator Phenotype in Human Colorectal CancerPeter W Laird; Fiscal Year: 2010..This study will investigate how some colorectal tumors acquire an unusually high number of epigenetic changes, with the long-term goal of using this knowledge to block or reverse these types of deleterious changes. ..
- SUPPRESSION OF NEOPLASIA BY DNA HYPOMETHYLATIONPETER LAIRD; Fiscal Year: 2000..He proposes to use a tissue culture selection assay to determine the effect of DNA methylation on chromosome stability. ..
- SUPPRESSION OF NEOPLASIA BY DNA HYPOMETHYLATIONPETER LAIRD; Fiscal Year: 2003..abstract_text> ..
- Environmental EpigenomicsPETER LAIRD; Fiscal Year: 2004..At the end of the planning period, they intend to submit an application to establish a Center for Environmental Epigenomics, to be affiliated with the Environmental Genome Project. ..
- Visualizing the effect of epigenetic modifications on transcription and mutationPeter W Laird; Fiscal Year: 2010....