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 […]

Community Genetics: Successful strategies for increasing African American participation in cancer genetic studies: hopeful signs for equalizing the benefits of genetic medicine

April 14, 2008

Annette R Patterson 1, Helen Davis, Kristin Shelby, Jerry McCoy, Linda D Robinson, Smita K Rao, Pia Banerji, Gail E Tomlinson Abstract Objective: To determine whether prior success in recruiting African Americans to an in-house cancer genetics registry could be duplicated when recruiting to a national registry requiring a significantly increased level of commitment. Additionally, to determine which recruitment sources and practices yielded the […]

American Journal of Human Genetics: Common breast cancer-predisposition alleles are associated with breast cancer risk in BRCA1 and BRCA2 mutation carriers

April 1, 2008

Antonis C Antoniou 1, Amanda B Spurdle, Olga M Sinilnikova, Sue Healey, Karen A Pooley, Rita K Schmutzler, Beatrix Versmold, Christoph Engel, Alfons Meindl, Norbert Arnold, Wera Hofmann, Christian Sutter, Dieter Niederacher, Helmut Deissler, Trinidad Caldes, Kati Kämpjärvi, Heli Nevanlinna, Jacques Simard, Jonathan Beesley, Xiaoqing Chen, Kathleen Cuningham Consortium for Research into Familial Breast Cancer; Susan L Neuhausen, Timothy R Rebbeck, Theresa Wagner, Henry T Lynch, Claudine Isaacs, Jeffrey Weitzel, Patricia A Ganz, Mary B Daly, Gail Tomlinson, Olufunmilayo I Olopade, Joanne L Blum, Fergus J Couch, Paolo Peterlongo, Siranoush […]

Cancer Research: Chromosomal Breakpoints in Primary Colon Cancer Cluster at Sites of Structural Variants in the Genome

March 1, 2008

Jordi Camps, Marian Grade, Quang Tri Nguyen, Patrick Hörmann, Sandra Becker, Amanda B. Hummon, Virginia Rodriguez, Settara Chandrasekharappa, Yidong Chen, Michael J. Difilippantonio, Heinz Becker, B. Michael Ghadimi and Thomas Ried Abstract Genomic aberrations on chromosome 8 are common in colon cancer and are associated with lymph node and distant metastases as well as with disease susceptibility. This prompted us to generate a high-resolution map of genomic imbalances of chromosome 8 in 51 primary colon carcinomas using a custom-designed genomic array […]