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Search Results: 1 - 2 of 2 matches for " Ziortza Ispizua "
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Identification of a biomarker panel for colorectal cancer diagnosis
Amaia García-Bilbao, Rubén Arma?anzas, Ziortza Ispizua, Bego?a Calvo, Ana Alonso-Varona, I?aki Inza, Pedro Larra?aga, Guillermo López-Vivanco, Blanca Suárez-Merino, Mónica Betanzos
BMC Cancer , 2012, DOI: 10.1186/1471-2407-12-43
Abstract: A genomic study of human colorectal cancer has been carried out on a total of 31 tumoral samples, corresponding to different stages of the disease, and 33 non-tumoral samples. The study was carried out by hybridisation of the tumour samples against a reference pool of non-tumoral samples using Agilent Human 1A 60-mer oligo microarrays. The results obtained were validated by qRT-PCR. In the subsequent bioinformatics analysis, gene networks by means of Bayesian classifiers, variable selection and bootstrap resampling were built. The consensus among all the induced models produced a hierarchy of dependences and, thus, of variables.After an exhaustive process of pre-processing to ensure data quality--lost values imputation, probes quality, data smoothing and intraclass variability filtering--the final dataset comprised a total of 8, 104 probes. Next, a supervised classification approach and data analysis was carried out to obtain the most relevant genes. Two of them are directly involved in cancer progression and in particular in colorectal cancer. Finally, a supervised classifier was induced to classify new unseen samples.We have developed a tentative model for the diagnosis of colorectal cancer based on a biomarker panel. Our results indicate that the gene profile described herein can discriminate between non-cancerous and cancerous samples with 94.45% accuracy using different supervised classifiers (AUC values in the range of 0.997 and 0.955).Colorectal cancer (CRC), is the third most common form of cancer and the second leading cause of death among cancers worldwide, with approximately 1, 000, 000 new cases of CRC and 50, 000 deaths related to CRC each year [1,2]. Sporadic colon cancer represents the 70% of newly diagnosed cases, and it is believed to slowly develop via a progressive accumulation of multiple mutations that affect tumour suppressor genes, as well as oncogenes or mismatch repair genes (MMR) [3].Statistics concerning colon cancer survival show differen
A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study
Jér?me Durand, Catherine Bodénès, Emilie Chancerel, Jean-Marc Frigerio, Giovanni Vendramin, Federico Sebastiani, Anna Buonamici, Oliver Gailing, Hans-Peter Koelewijn, Fiorella Villani, Claudia Mattioni, Marcello Cherubini, Pablo G Goicoechea, Ana Herrán, Ziortza Ikaran, Cyril Cabané, Saneyoshi Ueno, Florian Alberto, Pierre-Yves Dumoulin, Erwan Guichoux, Antoine de Daruvar, Antoine Kremer, Christophe Plomion
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-570
Abstract: A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher.We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.Catalogues of Expressed Sequence Tags (ESTs) are developed from cDNA libraries to obtain expressional sequence information in contrasting environmental conditions or across developmental stages. When available, they also offer an inexpensive source of gene-based DNA markers, in particular SSRs [1]. Such collections of ESTs were produced in several plants providing a unique opportunity for searching SSR motifs and further develop the corresponding microsatellite markers [2]. Alternative and promising strategies to develop SSR markers from genome shotgun sequencing have recently emerged with the development of new generation sequencing tec
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