New England Journal of Medicine: MicroRNA Expression, Survival, and Response to Interferon in Liver Cancer

October 8, 2009

Junfang Ji, PhD, Jiong Shi, MD, Anuradha Budhu, PhD, Zhipeng Yu, B.S., Marshonna Forgues, B.S., Stephanie Roessler, PhD, Stefan Ambs, PhD, M.P.H., Yidong Chen, PhD, Paul S. Meltzer, MD, Carlo M. Croce, MD, Lun-Xiu Qin, MD, PhD, Kwan Man, MD, PhD, Abstract BACKGROUND Hepatocellular carcinoma is a common and aggressive cancer that occurs mainly in men. We examined microRNA expression patterns, survival, and response to interferon […]

Cancer Research: Modification of ovarian cancer risk by BRCA1/2-interacting genes in a multicenter cohort of BRCA1/2 mutation carriers

July 1, 2009

Timothy R Rebbeck 1, Nandita Mitra, Susan M Domchek, Fei Wan, Shannon Chuai, Tara M Friebel, Saarene Panossian, Amanda Spurdle, Georgia Chenevix-Trench, kConFab; Christian F Singer, Georg Pfeiler, Susan L Neuhausen, Henry T Lynch, Judy E Garber, Jeffrey N Weitzel, Claudine Isaacs, Fergus Couch, Steven A Narod, Wendy S Rubinstein, Gail E Tomlinson, Patricia A Ganz, Olufunmilayo I Olopade, Nadine Tung, Joanne L Blum, Roger Greenberg, Katherine L Nathanson, Mary B Daly Abstract Inherited BRCA1/2 mutations confer elevated ovarian cancer risk. Knowledge of […]

Pediatric Blood & Cancer: Small cell undifferentiated variant of hepatoblastoma: adverse clinical and molecular features similar to rhabdoid tumors

March 1, 2009

Angela D Trobaugh-Lotrario 1, Gail E Tomlinson, Milton J Finegold, Lia Gore, James H Feusner Abstract Background: Small cell undifferentiated (SCU) histology in patients with stage I hepatoblastoma (HB) predicts an increased risk of relapse. We sought to determine the significance of SCU histology in patients with unresectable HB. Procedure: Patients enrolled in the pediatric Intergroup (INT0098) trial for HB and patients […]

UT Health SA Newsroom: Noted childhood cancer researchers to meet in San Antonio

February 9, 2009

About 100 scientists from noted cancer centers will gather in downtown San Antonio Feb. 26-27 to share findings and exchange ideas at the Genetics and Biology of Childhood Cancer 2009 symposium. It is the first scientific meeting sponsored by The Greehey Children’s Cancer Research Institute at The University of Texas Health Science Center at San […]

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 […]