Search results for "ALGORITHM"
showing 10 items of 4887 documents
Clinical use of RNA sequencing and oncobox analytics to predict personalized targeted therapeutic efficacy.
2020
e13676 Background: Analysis of mutation profiles in cancer patients does not provide clinical benefits in 80-90% of cases in the US (Marquart et al., 2018). Gene expression analysis potentially complements standard detection of clinically relevant mutations. Methods: 239 adult late-stage cancer patients. RNA gene expression sequencing completed on solid tumor samples using FFPE blocks. Patient mRNA profiles were analyzed using Oncobox bioinformatics, prioritizing target drugs according to their personalized predicted efficacy. Summary reports were provided to oncologists and resulting treatment selection and outcomes were assessed. Results: As of February 2020, feedback was received from p…
Role of adjuvant imatinib dose in radically resected GIST harboring KIT exon 9 mutations
2020
11533 Background: Gastrointestinal stromal tumors (GIST) with a driver mutation in KIT exon 9 (Ex9) represent about 10% of all newly diagnosed cases. In the metastatic setting, Ex9-mutated GIST patients benefit from higher doses of imatinib (800 mg/day vs standard 400 mg/day). The additional therapeutic benefit from a higher dose of imatinib in the adjuvant setting in this molecular subgroup has not been confirmed. Methods: We retrospectively identified 105 patients (pts) with resected Ex9-mutated GIST treated with adjuvant imatinib (800 mg/day or 400 mg/day) in 15 different European centers. Disease-Free Survival (DFS) and Imatinib Failure-Free Survival (IFFS) were calculated and analyzed…
Functional analysis ofp53 gene and the prognostic impact of dominant-negativep53 mutation in endometrial cancer
2005
In addition to the loss of function, mutant p53 can possess a dominant-negative effect on wild-type p53 and may also exert gain-of-function activity. It is not clear whether the functional status of p53 mutation contributes to differences in outcome in endometrial cancer. We collected a total of 92 RNA samples of high quality from endometrial cancer tissues, and the samples were subjected to yeast functional assay and sequencing for p53 mutations. The detected mutant p53 genes were further investigated for their dominant-negative activity using a yeast-based transdominance assay. p53 mutation was found in 24 out of 92 (26.1%) tumors, of which 10 exhibited no dominant-negative activity (rece…
Phase 0/1 of Positron Emission Tomography (PET) imaging agent [18F]-ODS2004436 as a marker of EGFR mutation in patients with non-small cell lung canc…
2018
e24184Background: Multiple EGFR tyrosine kinase inhibitors (TKIs) are approved for treatment of NSCLC harboring EGFR activating mutations or secondary TKIs resistant mutation. We evaluate a new PET...
RNA-sequencing and bioinformatic analysis to pre-assess sensitivity to targeted therapeutics in recurrent glioblastoma.
2019
e13533 Background: This study developed molecular guided tools for individualized selection of chemotherapeutics for recurrent glioblastoma (rGB). A consortium involving clinical neurooncologists, molecular biologists and bioinformaticians identified gene expression patterns in rGB and quantitatively analyzed pathways involved in response to FDA approved oncodrugs. Methods: From2016 to 2018 biopsies from GB were collected using a multisampling approach. Biopsy material was used to isolate glioma stem-like cells and examined by RNA-sequencing. RNA-seq results were subjected to differential expression (DE) analysis and Oncobox analysis – a bioinformatic tool for quantitative pathway activati…
A Review of Mathematical and Computational Methods in Cancer Dynamics.
2022
Cancers are complex adaptive diseases regulated by the nonlinear feedback systems between genetic instabilities, environmental signals, cellular protein flows, and gene regulatory networks. Understanding the cybernetics of cancer requires the integration of information dynamics across multidimensional spatiotemporal scales, including genetic, transcriptional, metabolic, proteomic, epigenetic, and multi-cellular networks. However, the time-series analysis of these complex networks remains vastly absent in cancer research. With longitudinal screening and time-series analysis of cellular dynamics, universally observed causal patterns pertaining to dynamical systems, may self-organize in the si…
Fuzzy subgroup mining for gene associations
2004
When studying the therapeutic efficacy of potential new drugs, it would be much more efficient to use predictors in order to assess their toxicity before going into clinical trials. One promising line of research has focused on the discovery of sets of candidate gene profiles to be used as toxicity indicators in future drug development. In particular genomic microarrays may be used to analyze the causality relationship between the administration of the drugs and the so-called gene expression, a parameter typically used by biologists to measure its influence at gene level. This kind of experiments involves a high throughput analysis of noisy and particularly unreliable data, which makes the …
Genome-wide association scan of attention deficit hyperactivity disorder
2008
Contains fulltext : 70191.pdf (Publisher’s version ) (Closed access) Results of behavioral genetic and molecular genetic studies have converged to suggest that genes substantially contribute to the development of attention deficit/hyperactivity disorder (ADHD), a common disorder with an onset in childhood. Yet, despite numerous linkage and candidate gene studies, strongly consistent and replicable association has eluded detection. To search for ADHD susceptibility genes, we genotyped approximately 600,000 SNPs in 958 ADHD affected family trios. After cleaning the data, we analyzed 438,784 SNPs in 2,803 individuals comprising 909 complete trios using ADHD diagnosis as phenotype. We present t…
Whole-Genome Re-Sequencing Data to Infer Historical Demography and Speciation Processes in Land Snails: the Study of Two Candidula Sister Species
2021
Despite the global biodiversity of terrestrial gastropods and their ecological and economic importance, the genomic basis of ecological adaptation and speciation in land snail taxa is still largely unknown. Here, we combined whole-genome re-sequencing with population genomics to evaluate the historical demography and the speciation process of two closely related species of land snails from western Europe, Candidula unifasciata and C. rugosiuscula. Historical demographic analysis indicated fluctuations in the size of ancestral populations, probably driven by Pleistocene climatic fluctuations. Although the current population distributions of both species do not overlap, our approximate Bayesi…
Prototyping of Land-SAF leaf area index algorithm with VEGETATION and MODIS data over Europe
2009
Abstract The Satellite Application Facility on Land Surface Analysis (Land-SAF) aims to provide land surface variables for the meteorological and environmental science communities from EUMETSAT satellites. This study assesses the performance of a simplified (i.e. random distribution of vegetation is assumed) version of the Land-SAF algorithm for the estimation of Leaf Area Index (LAI) when prototyped with VEGETATION (processed in CYCLOPES program) and MODIS reflectances. The prototype estimates of LAI are evaluated both by comparison with validated CYCLOPES and MODIS LAI products derived from the same sensors and directly through comparison with ground-based estimates. Emphasis is given on …