Search Results - "Laird, Peter W."

Interplay between the Cancer Genome and Epigenome by Shen, Hui, Laird, Peter W.

“…Cancer arises as a consequence of cumulative disruptions to cellular growth control with Darwinian selection for those heritable changes that provide the…”
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Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes by Zhou, Wanding, Laird, Peter W, Shen, Hui

“…Illumina Infinium DNA Methylation BeadChips represent the most widely used genome-scale DNA methylation assays. Existing strategies for masking Infinium probes…”
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The Landscape of Microsatellite Instability in Colorectal and Endometrial Cancer Genomes by Kim, Tae-Min, Laird, Peter W., Park, Peter J.

“…Microsatellites—simple tandem repeats present at millions of sites in the human genome—can shorten or lengthen due to a defect in DNA mismatch repair. We…”
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DNA methylation loss in late-replicating domains is linked to mitotic cell division by Zhou, Wanding, Dinh, Huy Q., Ramjan, Zachary, Weisenberger, Daniel J., Nicolet, Charles M., Shen, Hui, Laird, Peter W., Berman, Benjamin P.

“…DNA methylation loss occurs frequently in cancer genomes, primarily within lamina-associated, late-replicating regions termed partially methylated domains…”
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Low-level processing of Illumina Infinium DNA Methylation BeadArrays by Triche, Jr, Timothy J, Weisenberger, Daniel J, Van Den Berg, David, Laird, Peter W, Siegmund, Kimberly D

“…We propose a novel approach to background correction for Infinium HumanMethylation data to account for technical variation in background fluorescence signal…”
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Discovery of multi-dimensional modules by integrative analysis of cancer genomic data by Zhang, Shihua, Liu, Chun-Chi, Li, Wenyuan, Shen, Hui, Laird, Peter W, Zhou, Xianghong Jasmine

“…Recent technology has made it possible to simultaneously perform multi-platform genomic profiling (e.g. DNA methylation (DM) and gene expression (GE)) of…”
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The power and the promise of DNA methylation markers by Laird, Peter W

“…The past few years have seen an explosion of interest in the epigenetics of cancer. This has been a consequence of both the exciting coalescence of the…”
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Absolute quantification of somatic DNA alterations in human cancer by Carter, Scott L, Cibulskis, Kristian, Helman, Elena, McKenna, Aaron, Shen, Hui, Zack, Travis, Laird, Peter W, Onofrio, Robert C, Winckler, Wendy, Weir, Barbara A, Beroukhim, Rameen, Pellman, David, Levine, Douglas A, Lander, Eric S, Meyerson, Matthew, Getz, Gad

“…Tumors vary in their ratio of normal to cancerous cells and in their genomic copy number. Carter et al . describe an analytic method for inferring the purity…”
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Cell division drives DNA methylation loss in late-replicating domains in primary human cells by Endicott, Jamie L., Nolte, Paula A., Shen, Hui, Laird, Peter W.

“…DNA methylation undergoes dramatic age-related changes, first described more than four decades ago. Loss of DNA methylation within partially methylated domains…”
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Pan-cancer patterns of somatic copy number alteration by Zack, Travis I, Schumacher, Steven E, Carter, Scott L, Cherniack, Andrew D, Saksena, Gordon, Tabak, Barbara, Lawrence, Michael S, Zhang, Cheng-Zhong, Wala, Jeremiah, Mermel, Craig H, Sougnez, Carrie, Gabriel, Stacey B, Hernandez, Bryan, Shen, Hui, Laird, Peter W, Getz, Gad, Meyerson, Matthew, Beroukhim, Rameen

“…Rameen Beroukhim and colleagues analyzed somatic structural alterations in 12 tumor types. Whole-genome doubling was found in over a third of all cancers,…”
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DNA methylation as a biomarker for cardiovascular disease risk by Kim, Myungjin, Long, Tiffany I, Arakawa, Kazuko, Wang, Renwei, Yu, Mimi C, Laird, Peter W

“…Elevated serum homocysteine is associated with an increased risk of cardiovascular disease (CVD). This may reflect a reduced systemic remethylation capacity,…”
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Association Between Molecular Subtypes of Colorectal Cancer and Patient Survival by Phipps, Amanda I, Limburg, Paul J, Baron, John A, Burnett-Hartman, Andrea N, Weisenberger, Daniel J, Laird, Peter W, Sinicrope, Frank A, Rosty, Christophe, Buchanan, Daniel D, Potter, John D, Newcomb, Polly A

“…Background and Aims Colorectal cancer (CRC) is a heterogeneous disease that can develop via several pathways. Different CRC subtypes, identified based on tumor…”
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Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution by Kim, Hoon, Zheng, Siyuan, Amini, Seyed S, Virk, Selene M, Mikkelsen, Tom, Brat, Daniel J, Grimsby, Jonna, Sougnez, Carrie, Muller, Florian, Hu, Jian, Sloan, Andrew E, Cohen, Mark L, Van Meir, Erwin G, Scarpace, Lisa, Laird, Peter W, Weinstein, John N, Lander, Eric S, Gabriel, Stacey, Getz, Gad, Meyerson, Matthew, Chin, Lynda, Barnholtz-Sloan, Jill S, Verhaak, Roel G W

“…Glioblastoma (GBM) is a prototypical heterogeneous brain tumor refractory to conventional therapy. A small residual population of cells escapes surgery and…”
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Genome-scale analysis of aberrant DNA methylation in colorectal cancer by Hinoue, Toshinori, Weisenberger, Daniel J, Lange, Christopher P E, Shen, Hui, Byun, Hyang-Min, Van Den Berg, David, Malik, Simeen, Pan, Fei, Noushmehr, Houtan, van Dijk, Cornelis M, Tollenaar, Rob A E M, Laird, Peter W

“…Colorectal cancer (CRC) is a heterogeneous disease in which unique subtypes are characterized by distinct genetic and epigenetic alterations. Here we performed…”
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BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies by Zhou, Wanding, Johnson, Benjamin K, Morrison, Jacob, Beddows, Ian, Eapen, James, Katsman, Efrat, Semwal, Ayush, Habib, Walid Abi, Heo, Lyong, Laird, Peter W, Berman, Benjamin P, Triche, Timothy J, Shen, Hui

“…Abstract Data from both bulk and single-cell whole-genome DNA methylation experiments are under-utilized in many ways. This is attributable to inefficient…”
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Environmental epigenetics: prospects for studying epigenetic mediation of exposure–response relationships by Cortessis, Victoria K., Thomas, Duncan C., Levine, A. Joan, Breton, Carrie V., Mack, Thomas M., Siegmund, Kimberly D., Haile, Robert W., Laird, Peter W.

“…Changes in epigenetic marks such as DNA methylation and histone acetylation are associated with a broad range of disease traits, including cancer, asthma,…”
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DNA methylation in the human cerebral cortex is dynamically regulated throughout the life span and involves differentiated neurons by Siegmund, Kimberly D, Connor, Caroline M, Campan, Mihaela, Long, Tiffany I, Weisenberger, Daniel J, Biniszkiewicz, Detlev, Jaenisch, Rudolf, Laird, Peter W, Akbarian, Schahram

“…The role of DNA cytosine methylation, an epigenetic regulator of chromatin structure and function, during normal and pathological brain development and aging…”
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A Distinct DNA Methylation Shift in a Subset of Glioma CpG Island Methylator Phenotypes during Tumor Recurrence by de Souza, Camila Ferreira, Sabedot, Thais S., Malta, Tathiane M., Stetson, Lindsay, Morozova, Olena, Sokolov, Artem, Laird, Peter W., Wiznerowicz, Maciej, Iavarone, Antonio, Snyder, James, deCarvalho, Ana, Sanborn, Zachary, McDonald, Kerrie L., Friedman, William A., Tirapelli, Daniela, Poisson, Laila, Mikkelsen, Tom, Carlotti, Carlos G., Kalkanis, Steven, Zenklusen, Jean, Salama, Sofie R., Barnholtz-Sloan, Jill S., Noushmehr, Houtan

“…Glioma diagnosis is based on histomorphology and grading; however, such classification does not have predictive clinical outcome after glioblastomas have…”
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Comparison of Breast Cancer Molecular Features and Survival by African and European Ancestry in The Cancer Genome Atlas by Huo, Dezheng, Hu, Hai, Rhie, Suhn K, Gamazon, Eric R, Cherniack, Andrew D, Liu, Jianfang, Yoshimatsu, Toshio F, Pitt, Jason J, Hoadley, Katherine A, Troester, Melissa, Ru, Yuanbin, Lichtenberg, Tara, Sturtz, Lori A, Shelley, Carl S, Benz, Christopher C, Mills, Gordon B, Laird, Peter W, Shriver, Craig D, Perou, Charles M, Olopade, Olufunmilayo I

“…African Americans have the highest breast cancer mortality rate. Although racial difference in the distribution of intrinsic subtypes of breast cancer is…”
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Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns by Byun, Hyang-Min, Siegmund, Kimberly D., Pan, Fei, Weisenberger, Daniel J., Kanel, Gary, Laird, Peter W., Yang, Allen S.

“…DNA methylation is known to be associated with cell differentiation, aging, disease and cancer. There exists an expanding base of knowledge regarding…”
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