Research Paper

IEEE: Stochastic Modeling of the Relationship between Copy Number and Gene Expression Based on Transcriptional Logic

October 24, 2011

Fang-Han Hsu; Erchin Serpedin; Yidong Chen; Edward R. Dougherty Abstract: DNA copy number alterations (CNAs) can cause genetic diseases, and studies have revealed a relationship between CNAs and gene expression; however, the manner in which CNAs relate to gene expression and what regulatory mechanisms underlying the relationship remain unclear. In many instances, real data have revealed a nonlinear […]

Molecular Profiling: Genome-Wide Methylation Profiling in Archival Formalin-Fixed Paraffin-Embedded Tissue Samples

October 21, 2011

J. Keith Killian, Robert L. Walker, Sven Bilke, Yidong Chen, Sean Davis, Robert Cornelison, William I. Smith, Paul S. Meltzer Abstract New technologies allow for the genome-scale measurement of DNA methylation. In an effort to increase the clinical utility of DNA methylation as a biomarker, we have adapted a commercial bisulfite epigenotype assay for genome-wide methylation profiling in archival formalin-fixed paraffin-embedded pathology specimens. This […]

Proteome Science: Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks

October 14, 2011

Jia Meng, Jianqiu (Michelle) Zhang, Yidong Chen & Yufei Huang Abstract Background Transcriptional regulation by a transcription factor (TF) controls the time and abundance of mRNA transcription. Due to the limitation of current proteomics technologies, large scale measurements of protein level activities of TFs is usually infeasible, making computational reconstruction of the transcriptional regulatory network a difficult task. Results […]

BMC Research Notes: A model-based circular binary segmentation algorithm for the analysis of array CGH data

October 10, 2011

Fang-Han Hsu, Hung-I H Chen, Mong-Hsun Tsai, Liang-Chuan Lai, Chi-Cheng Huang, Shih-Hsin Tu, Eric Y Chuang & Yidong Chen Abstract Background Circular Binary Segmentation (CBS) is a permutation-based algorithm for array Comparative Genomic Hybridization (aCGH) data analysis. CBS accurately segments data by detecting change-points using a maximal-t test, but an extensive computational burden is involved for evaluating the significance of change-points using permutations. […]

BMC Cancer: Activating mutation in MET oncogene in familial colorectal cancer

October 4, 2011

Deborah W Neklason 1, Michelle W Done, Nykole R Sargent, Ann G Schwartz, Hoda Anton-Culver, Constance A Griffin, Dennis J Ahnen, Joellen M Schildkraut, Gail E Tomlinson, Louise C Strong, Alexander R Miller, Jill E Stopfer, Randall W Burt Abstract Background: In developed countries, the lifetime risk of developing colorectal cancer (CRC) is 5%, and it is the second leading cause of death from cancer. The presence of family […]

Carcinogenesis: Candidate gene association analysis of acute lymphoblastic leukemia identifies new susceptibility locus at 11p15 (LMO1)

September 21, 2011

Joke Beuten 1, Jonathan A L Gelfond, Duangjai Piwkham, Brad H Pollock, Naomi J Winick, Anderson B Collier 3rd, Gail E Tomlinson Abstract To determine the contribution of susceptibility loci in explaining the genetic basis of acute lymphoblastic leukemia (ALL), we genotyped 29 high-potential candidate genes with 672 tagged single-nucleotide polymorphisms (SNPs) in a sample (163 cases and 251 healthy controls) of […]

Molecular & Cellular Biology: A Conditional Mouse Model for Measuring the Frequency of Homologous Recombination Events In Vivo in the Absence of Essential Genes

August 10, 2011

Adam D. Brown, Alison B. Claybon, Alexander J. R. Bishop ABSTRACT The ability to detect and repair DNA damage is crucial to the prevention of various diseases. The loss of function of genes involved in these processes is known to result in significant developmental defects and/or predisposition to cancer. One such DNA repair mechanism, homologous recombination, has […]

Cancer Epidemiology Biomarkers & Prevevention: Genetic variation in IGF2 and HTRA1 and breast cancer risk among BRCA1 and BRCA2 carriers

August 1, 2011

Susan L Neuhausen 1, Sean Brummel, Yuan Chun Ding, Linda Steele, Katherine L Nathanson, Susan Domchek, Timothy R Rebbeck, Christian F Singer, Georg Pfeiler, Henry T Lynch, Judy E Garber, Fergus Couch, Jeffrey N Weitzel, Andrew Godwin, Steven A Narod, Patricia A Ganz, Mary B Daly, Claudine Isaacs, Olufunmilayo I Olopade, Gail E Tomlinson, Wendy S Rubinstein, Nadine Tung, Joanne L Blum, Daniel L Gillen Abstract Background: BRCA1 and BRCA2 mutation carriers have a lifetime breast cancer risk of 40% […]

Cancer Research: Modification of BRCA1-Associated Breast and Ovarian Cancer Risk by BRCA1-Interacting Genes

July 28, 2011

Timothy R Rebbeck 1, Nandita Mitra, Susan M Domchek, Fei Wan, Tara M Friebel, Teo V Tran, Christian F Singer, Muy-Kheng Maria Tea, Joanne L Blum, Nadine Tung, Olufunmilayo I Olopade, Jeffrey N Weitzel, Henry T Lynch, Carrie L Snyder, Judy E Garber, Antonis C Antoniou, Susan Peock, D Gareth Evans, Joan Paterson, M John Kennedy, Alan Donaldson, Huw Dorkins, Douglas F Easton, Epidemiological Study of BRCA1 and BRCA2 Mutation Carriers (EMBRACE); Wendy S Rubinstein, Mary B Daly, Claudine Isaacs, Heli Nevanlinna, Fergus J […]

JAMA Network: Clinically relevant changes in family history of cancer over time

July 13, 2011

Argyrios Ziogas 1, Nora K Horick, Anita Y Kinney, Jan T Lowery, Susan M Domchek, Claudine Isaacs, Constance A Griffin, Patricia G Moorman, Karen L Edwards, Deirdre A Hill, Jonathan S Berg, Gail E Tomlinson, Hoda Anton-Culver, Louise C Strong, Carol H Kasten, Dianne M Finkelstein, Sharon E Plon Abstract Context: Knowledge of family cancer history is important for assessing cancer risk and guiding screening recommendations. Objective: To quantify how often throughout adulthood clinically […]