Search results for " microarray"

Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistic…

2008

Abstract Background Inferring cluster structure in microarray datasets is a fundamental task for the so-called -omic sciences. It is also a fundamental question in Statistics, Data Analysis and Classification, in particular with regard to the prediction of the number of clusters in a dataset, usually established via internal validation measures. Despite the wealth of internal measures available in the literature, new ones have been recently proposed, some of them specifically for microarray data. Results We consider five such measures: Clest, Consensus (Consensus Clustering), FOM (Figure of Merit), Gap (Gap Statistics) and ME (Model Explorer), in addition to the classic WCSS (Within Cluster…

Multiplex Amplicon Quantification (MAQ), a fast and efficient method for the simultaneous detection of copy number alterations in neuroblastoma

2010

Abstract Background Cancer genomes display characteristic patterns of chromosomal imbalances, often with diagnostic and prognostic relevance. Therefore assays for genome-wide copy number screening and simultaneous detection of copy number alterations in specific chromosomal regions are of increasing importance in the diagnostic work-up of tumors. Results We tested the performance of Multiplex Amplicon Quantification, a newly developed low-cost, closed-tube and high-throughput PCR-based technique for detection of copy number alterations in regions with prognostic relevance for neuroblastoma. Comparison with array CGH and the established Multiplex Ligation-dependent Probe Amplification method…

Prognostic value of partial genetic instability in neuroblastoma with ≤50% neuroblastic cell content

2011

Piqueras M, Navarro S, Canete A, Castel V & Noguera R (2011) Histopathology59, 22–30 Prognostic value of partial genetic instability in neuroblastoma with ≤50% neuroblastic cell content Aims:  Better understanding of neuroblastoma genetics will improve with genome-wide techniques. However, performing these analyses in samples with <60% neuroblast cells is not adequate. We evaluated the utility of fluorescence in situ hybridization (FISH) on tissue microarrays (TMA) in detecting partial genetic instability (PGI), focusing on samples with ≤50% neuroblast cells. Methods and results:  Alterations of 11q and 17q were detected by FISH on 369 neuroblastoma samples in TMA. Status of the MYCN gene a…

Prevalence and Clinical Outcomes for Patients With ALK Gene Rearrangement in Europe: Preliminary Results from the European Thoracic Oncology Platform…

2012

ABSTRACT Background The prevalence of ALK gene rearrangement (ALK+) in European patients with non-small cell lung cancer (NSCLC) is unknown. The Lungscape project provides a platform to evaluate its expression and clinical significance in a large cohort of patients with resected NSCLC from 13 European sites in 11 countries. Methods Participating sites retrospectively identified cases of NSCLC with clinical demographic and outcome data, and available tissue for research according to predefined protocol criteria. Local ethical and regulatory approvals were adhered to. Clinical data were entered to a central, secure database. Accepted cases on the basis of completeness of clinical data were as…

FUNCTIONAL GENOMIC APPROACHES TO ELUCIDATE BIOTIC AND ABIOTIC STRESS RESPONSES IN PLANTS

Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate

2007

Abstract Background The common marmoset monkey (Callithrix jacchus), a small non-endangered New World primate native to eastern Brazil, is becoming increasingly used as a non-human primate model in biomedical research, drug development and safety assessment. In contrast to the growing interest for the marmoset as an animal model, the molecular tools for genetic analysis are extremely limited. Results Here we report the development of the first marmoset-specific oligonucleotide microarray (EUMAMA) containing probe sets targeting 1541 different marmoset transcripts expressed in hippocampus. These 1541 transcripts represent a wide variety of different functional gene classes. Hybridisation of …