Search results for "profiling"
showing 10 items of 881 documents
Revised risk estimation and treatment stratification of low- and intermediate-risk neuroblastoma patients by integrating clinical and molecular progn…
2014
Abstract Purpose: To optimize neuroblastoma treatment stratification, we aimed at developing a novel risk estimation system by integrating gene expression–based classification and established prognostic markers. Experimental Design: Gene expression profiles were generated from 709 neuroblastoma specimens using customized 4 × 44 K microarrays. Classification models were built using 75 tumors with contrasting courses of disease. Validation was performed in an independent test set (n = 634) by Kaplan–Meier estimates and Cox regression analyses. Results: The best-performing classifier predicted patient outcome with an accuracy of 0.95 (sensitivity, 0.93; specificity, 0.97) in the validation coh…
Expression of cell cycle markers and human papillomavirus infection in oral squamous cell carcinoma: use of fuzzy neural networks.
2005
Our aim was to evaluate in oral squamous cell carcinoma (OSCC) the relationship between some cell cycle markers and HPV infection, conditionally to age, gender and certain habits of patients, and to assess the ability of fuzzy neural networks (FNNs) in building up an adequate predictive model based on logic inference rules. Eighteen cases of OSCC were examined by immunohistochemistry for MIB-1, PCNA and survivin expression; presence of HPV DNA was investigated in exfoliated oral mucosa cells by nested PCR (nPCR, MY09-MY11/GP5-GP6), and HPV genotype was determined by direct DNA sequencing. Data were analyzed by traditional statistics (TS) and FNNs. HPV DNA was found in 9/18 OSCCs (50.0 %) wi…
Intratumor CMS Heterogeneity Impacts Patient Prognosis in Localized Colon Cancer
2021
Abstract Purpose: The consensus molecular subtypes (CMS) represent a significant advance in the understanding of intertumor heterogeneity in colon cancer. Intratumor heterogeneity (ITH) is the new frontier for refining prognostication and understanding treatment resistance. This study aims at deciphering the transcriptomic ITH of colon cancer and understanding its potential prognostic implications. Experimental Design: We deconvoluted the transcriptomic profiles of 1,779 tumors from the PETACC8 trial and 155 colon cancer cell lines as weighted sums of the four CMSs, using the Weighted In Silico Pathology (WISP) algorithm. We assigned to each tumor and cell line a combination of up to three …
The EndoPredict Gene-Expression Assay in Clinical Practice - Performance and Impact on Clinical Decisions
2013
The validated EndoPredict assay is a novel tool to predict the risk of metastases of patients with estrogen receptor positive, HER2 negative breast cancer treated with endocrine therapy alone. It has been designed to integrate genomic and clinical information and includes clinico-pathological factors such as tumor size and nodal status. The test is feasible in a decentral setting in molecular pathology laboratories. In this project, we investigated the performance of this test in clinical practice, and performed a retrospective evaluation of its impact on treatment decisions in breast cancer. During one year, EndoPredict assays from 167 patients could be successfully performed. For retrospe…
Integrative clinical transcriptome analysis reveals TMPRSS2-ERG dependency of prognostic biomarkers in prostate adenocarcinoma.
2019
In prostate adenocarcinoma (PCa), distinction between indolent and aggressive disease is challenging. Around 50% of PCa are characterized by TMPRSS2‐ERG (T2E)‐fusion oncoproteins defining two molecular subtypes (T2E‐positive/negative). However, current prognostic tests do not differ between both molecular subtypes, which might affect outcome prediction. To investigate gene‐signatures associated with metastasis in T2E‐positive and T2E‐negative PCa independently, we integrated tumor transcriptomes and clinicopathological data of two cohorts (total n = 783), and analyzed metastasis‐associated gene‐signatures regarding the T2E‐status. Here, we show that the prognostic value of biomarkers in PCa…
Genome-wide association study identifies five loci associated with lung function
2009
Pulmonary function measures are heritable traits that predict morbidity and mortality and define chronic obstructive pulmonary disease (COPD). We tested genome-wide association with forced expiratory volume in 1 s (FEV(1)) and the ratio of FEV(1) to forced vital capacity (FVC) in the SpiroMeta consortium (n = 20,288 individuals of European ancestry). We conducted a meta-analysis of top signals with data from direct genotyping (n < or = 32,184 additional individuals) and in silico summary association data from the CHARGE Consortium (n = 21,209) and the Health 2000 survey (n < or = 883). We confirmed the reported locus at 4q31 and identified associations with FEV(1) or FEV(1)/FVC and co…
In response: Genomic profile of breast cancer.
2015
Response to: Plun-Favreau J, Svedman C, Valentine W, Rouzier R. Genomic profile of breast cancer. Expert Rev Pharmacoecon Outcomes Res 2015;15(3):393–94We would like to express our gratitude for th...
Detection of TP53 and PIK3CA Mutations in Circulating Tumor DNA Using Next-Generation Sequencing in the Screening Process for Early Breast Cancer Dia…
2019
Circulating tumor DNA (ctDNA) has emerged as a non-invasive &ldquo
Multi-party metering: An architecture for privacy-preserving profiling schemes
2013
Several privacy concerns about the massive deploy- ment of smart meters have been arisen recently. Namely, it has been shown that the fine-grained temporal traces generated by these meters can be correlated with different users behaviors. A new architecture, called multi-party metering, for enabling privacy-preserving analysis of high-frequency metering data without requiring additional complexity at the smart meter side is here proposed. The idea is to allow multiple entities to get a share of the high-frequency metering data rather than the real data, where this share does not reveal any information about the real data. By aggregating the shares provided by different users and publishing …
Comparative training procedures to learn odor descriptors: effects on profiling performance
1999
Three groups of ten naive assessors were recruited to perform an odor profiling of 10 orange juices using 8 odor descriptors, These panels differed on the way they learned each descriptor. Group 1R learned to match one descriptor with one external standard; group 3R learned to associate one descriptor with 3 external standards; group 0R defined by itself the 8 descriptors from a set of orange juices. Results showed that the use of one standard per descriptor seemed to be only efficient when the standard was typical of the odor perception in the orange juices. Learning one odor concept with 3 standards led to redundant use of discriminant descriptors and failed on the agreement among assesso…