Cancer Research: Large-Scale Profiling of Archival Lymph Nodes Reveals Pervasive Remodeling of the Follicular Lymphoma Methylome

February 1, 2009

J. Keith Killian, Sven Bilke, Sean Davis, Robert L. Walker, M. Scott Killian, Erich B. Jaeger, Yidong Chen, Jason Hipp, Stefania Pittaluga, Mark Raffeld, Robert Cornelison, William I. Smith, Jr., Marina Bibikova, Jian-Bing Fan, Michael R. Emmert-Buck, Elaine S. Jaffe and Paul S. Meltzer Abstract Emerging technologies allow broad profiling of the cancer genome for differential DNA methylation relative to benign cells. Herein, bisulfite-modified DNA from lymph nodes with either reactive hyperplasia or follicular lymphoma (FL) were analyzed using a commercial C/UpG genotyping assay. Two hundred fifty-nine differentially methylated targets […]

Bioinformatics: GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

December 1, 2008

Yuelin Zhu, Sean Davis, Robert Stephens, Paul S. Meltzer, Yidong Chen Abstract The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data in GEO can be challenging. We have developed GEOmetadb in an attempt to make querying the GEO metadata both easier and more powerful. All GEO metadata records as well as […]

Cancer Research: Common familial colorectal cancer linked to chromosome 7q31: a genome-wide analysis

November 1, 2008

Deborah W Neklason 1, Richard A Kerber, David B Nilson, Hoda Anton-Culver, Ann G Schwartz, Constance A Griffin, Jan T Lowery, Joellen M Schildkraut, James P Evans, Gail E Tomlinson, Louise C Strong, Alexander R Miller, Jill E Stopfer, Dianne M Finkelstein, Prakash M Nadkarni, Carol H Kasten, Geraldine P Mineau, Randall W Burt Abstract Present investigations suggest that approximately 30% of colorectal cancer cases arise on the basis of inherited factors. We […]

Bioinformatics: A probe-density-based analysis method for array CGH data: simulation, normalization and centralization

October 1, 2008

Hung-I Harry Chen, Fang-Han Hsu, Yuan Jiang, Mong-Hsun Tsai, Pan-Chyr Yang, Paul S. Meltzer, Eric Y. Chuang, Yidong Chen Abstract Motivation: Genomic instability is one of the fundamental factors in tumorigenesis and tumor progression. Many studies have shown that copy-number abnormalities at the DNA level are important in the pathogenesis of cancer. Array comparative genomic hybridization (aCGH), developed based on expression microarray technology, […]

Journal of Biomolecular Screening: An analysis of normalization methods for Drosophila RNAi genomic screens and development of a robust validation scheme

September 13, 2008

Amy M Wiles 1, Dashnamoorthy Ravi, Selvaraj Bhavani, Alexander J R Bishop Abstract Genome-wide RNA interference (RNAi) screening allows investigation of the role of individual genes in a process of choice. Most RNAi screens identify a large number of genes with a continuous gradient in the assessed phenotype. Screeners must decide whether to examine genes with the most robust […]

Harvard Medical School, DRSC/TRiP Functional Genomics Resources: An Analysis of Normalization Methods for Drosophila RNAi Genomic Screens and Development of a Robust Validation Scheme

September 1, 2008

AMY M. WILES,* DASHNAMOORTHY RAVI,* SELVARAJ BHAVANI, and ALEXANDER J. R. BISHOP Genome-wide RNA interference (RNAi) screening allows investigation of the role of individual genes in a process of choice. Most RNAi screens identify a large number of genes with a continuous gradient in the assessed phenotype. Screeners must decide whether to examine genes with […]

Oncologist: Liver tumors in children

July 21, 2008

Jason B Litten 1, Gail E Tomlinson Abstract Malignant liver tumors account for slightly >1% of all pediatric malignancies, with roughly 150 new cases of liver tumors diagnosed in the U.S. annually. The embryonal tumor, hepatoblastoma, accounts for two-thirds of malignant liver tumors in children. Other liver malignancies in children include hepatocellular carcinoma, sarcomas, germ cell tumors, […]

Modern Pathology: A subset of cranial fasciitis is associated with dysregulation of the Wnt/beta-catenin pathway

June 27, 2008

Dinesh Rakheja 1, Jacqulin C Cunningham, Midori Mitui, Ashish S Patel, Gail E Tomlinson, Arthur G Weinberg Abstract Cranial fasciitis, an unusual fibroproliferative lesion that occurs in the scalp of infants, is considered a posttraumatic reactive process similar to nodular fasciitis. Its pathobiology has not been investigated. Over the last 15 years, we diagnosed cranial fasciitis in six children; in one […]

GATA factors and androgen receptor collaborate to transcriptionally activate the Rhox5 homeobox gene in Sertoli cells

April 28, 2008

Anjana Bhardwaj 1, Manjeet K Rao, Ramneet Kaur, Miriam R Buttigieg, Miles F Wilkinson Abstract How Sertoli-specific expression is initiated is poorly understood. Here, we address this issue using the proximal promoter (Pp) from the Rhox5 homeobox gene. Its Sertoli cell-specific expression is achieved, in part, through a negative regulatory element that inhibits Pp transcription in non-Sertoli cell lines. Complementing […]

Cancer: Twenty years of follow-up among survivors of childhood and young adult acute myeloid leukemia: a report from the Childhood Cancer Survivor Study

April 21, 2008

Daniel A Mulrooney 1, Douglas C Dover, Suwen Li, Yutaka Yasui, Kirsten K Ness, Ann C Mertens, Joseph P Neglia, Charles A Sklar, Leslie L Robison, Stella M Davies, Childhood Cancer Survivor Study Abstract Background: Limited data exist on the comprehensive assessment of late medical and social effects experienced by survivors of childhood and young adult acute myeloid leukemia (AML). Methods: This analysis included 272 5-year AML survivors […]