Adam B Olshen

..g. those involved in mitosis, replication, repair, and telomeres) are rarely mutated in chromosomally unstable sporadic tumors, even though such mutations are associated with some heritable cancer prone syndromes...

..435,632 SNPs overlapped and met annotation criteria in the two groups...

..The method is evaluated by simulation and is demonstrated on cell line data with known copy number alterations and on a breast cancer cell line data set...

....

..This study also demonstrates that EC cells can serve as robust models to investigate early lineage choices during both embryonic and extra-embryonic human development...

..The data analysis workflow we propose provides a unified and computationally scalable framework to harness the full potential of large-scale integrated cancer genomic data for integrative subtype discovery...

..Currently, patients are risk-stratified on the basis of clinical presentation and serum tumor markers. The introduction of molecular markers could improve outcome prediction...

..AVAILABILITY: Bioconductor (http://bioconductor.org/packages/release/bioc/html/Clonality.html) and http://www.mskcc.org/mskcc/html/13287.cfm...

..In order to identify important cancer genes CNAs and CNVs must be distinguished. Although the Database of Genomic Variants (DGV) contains a list of all known CNVs, there is no standard methodology to use the database effectively...

..The raw data from such experiments are two-dimensional, but are unphased. Consequently, inference based on them necessitates development of new analytic methods...

..Thus, the response of DLBCL in vivo and in vitro is defined by several distinct molecular and genetic pathways which is, perhaps, not surprising given the heterogeneous clinical, morphologic and genetic nature of DLBCL...

..Our data analyses show that in many cases a strong clonal signal emerges. Sensitivity analyses show that most of the diagnoses are robust when the data are of high quality...

....

..A more statistically powerful approach would incorporate all data types simultaneously and generate a single integrated cluster assignment...

..This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster algorithm...

..MET, a tyrosine kinase that is constitutively active in tumor cells with MET oncogene amplification, has recently been identified as another HSP-90 client...

..Furthermore, the differential expression of core stem cell genes may explain the differences in pluripotency between embryonal carcinomas and seminomas...

..This study suggests that BMP-2-induced differentiation of NT2/D1 cells provides a powerful assay to study early human epithelial and smooth muscle development...

..These mice might therefore be useful models for discovering changes in gene expression during cancer development...

....

..Thus, racial disparities in clinical outcomes are unlikely to reflect differences in gene expression and may instead be attributable to other epidemiologic, clinical, or pathologic factors...

..These data provide a rationale for the novel therapeutic targeting of CD32B using the humanized 2B6 MoAb in patients with systemic AL-amyloidosis...

..Our study attests to the power of combining descriptive tumor genomics with functional screens and reveals EPHA7(TR) as tumor suppressor with immediate therapeutic potential...

..Defining how malignant plasma cell growth is regulated in the bone marrow versus at extramedullary sites will help to delineate the mechanisms underlying the dependence of tumour cell growth on angiogenesis and cell adhesion...

..Gene expression profiling of mesotheliomas is an important discovery tool, but its power in clinical prognostication has been overestimated...

..Others contribute to aggressive growth selectively in the lung. Many encode extracellular proteins and are of previously unknown relevance to cancer metastasis...

..Our findings also have important implications for future peptide biomarker discovery efforts...

..Overall, array-CGH identified relatively small genomic regions associated with outcome, which, along with follow-up expression studies, may reveal target genes important in DLBCL clinical behavior...

....

..Thus, the expression-based classifier accurately assigned a single predominant histology to mixed NSGCTs, and identified transcripts differentially expressed between histologic components with relevance to NSGCT differentiation...

..These findings suggest that gene expression profiling can potentially contribute to the clinical classification and management of intermediate-risk endometrial cancers...

..These results suggest that Hsp90 inhibitors can effectively suppress Akt activity in animal models of human cancer at nontoxic doses, thus sensitizing tumor cells to proapoptotic stimuli...

..Candidate genes in the 6q22.33 region include ECHDC1, which encodes a protein involved in mitochondrial fatty acid oxidation, and also RNF146, which encodes a ubiquitin protein ligase, both known pathways in breast cancer pathogenesis...

..AVAILABILITY: The software and supplementary information are available freely to researchers at academic and non-profit institutions at http://cc.ucsf.edu/jain/public..

....

..To summarize, the ultimate goals of approaches we provide is to predict phenotype, typically untoward or not, within a specific window of time. Our approach is neither through linkage nor from finding haplotype frequencies per se...

..75), suggesting that these copy number increases contribute to activation of PI3K signaling in SqCas of the lung...

..These results indicate that array-based CGH is capable of diagnosing the vast majority of renal cell carcinomas based on their genetic profiles...