{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"technology_type":["Illumina Genome Analyzer IIx, Illumina Genome Analyzer II, Affymetrix U219"],"study_type":["Other"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001000374"],"host":["EGA"],"description":["EGA study EGAS00001000374"],"dataset_title":["Deep RNA sequencing in CLL","Title not provided","Recurrent Somatic Mutations in CLL"],"category":["restricted"],"repository":["EGA"],"pubmed_abstract":["Chronic lymphocytic leukemia (CLL) has heterogeneous clinical and biological behavior. Whole-genome and -exome sequencing has contributed to the characterization of the mutational spectrum of the disease, but the underlying transcriptional profile is still poorly understood. We have performed deep RNA sequencing in different subpopulations of normal B-lymphocytes and CLL cells from a cohort of 98 patients, and characterized the CLL transcriptional landscape with unprecedented resolution. We detected thousands of transcriptional elements differentially expressed between the CLL and normal B cells, including protein-coding genes, noncoding RNAs, and pseudogenes. Transposable elements are globally derepressed in CLL cells. In addition, two thousand genes-most of which are not differentially expressed-exhibit CLL-specific splicing patterns. Genes involved in metabolic pathways showed higher expression in CLL, while genes related to spliceosome, proteasome, and ribosome were among the most down-regulated in CLL. Clustering of the CLL samples according to RNA-seq derived gene expression levels unveiled two robust molecular subgroups, C1 and C2. C1/C2 subgroups and the mutational status of the immunoglobulin heavy variable (IGHV) region were the only independent variables in predicting time to treatment in a multivariate analysis with main clinico-biological features. This subdivision was validated in an independent cohort of patients monitored through DNA microarrays. Further analysis shows that B-cell receptor (BCR) activation in the microenvironment of the lymph node may be at the origin of the C1/C2 differences."],"pubmed_title":["Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia."],"pubmed_authors":["Ferreira Pedro G PG, Jares Pedro P, Rico Daniel D, Gómez-López Gonzalo G, Martínez-Trillos Alejandra A, Villamor Neus N, Ecker Simone S, González-Pérez Abel A, Knowles David G DG, Monlong Jean J, Johnson Rory R, Quesada Victor V, Djebali Sarah S, Papasaikas Panagiotis P, López-Guerra Mónica M, Colomer Dolors D, Royo Cristina C, Cazorla Maite M, Pinyol Magda M, Clot Guillem G, Aymerich Marta M, Rozman Maria M, Kulis Marta M, Tamborero David D, Gouin Anaïs A, Blanc Julie J, Gut Marta M, Gut Ivo I, Puente Xose S XS, Pisano David G DG, Martin-Subero José Ignacio JI, López-Bigas Nuria N, López-Guillermo Armando A, Valencia Alfonso A, López-Otín Carlos C, Campo Elías E, Guigó Roderic R"],"additional_accession":[]},"is_claimable":false,"name":"Deep RNA sequencing in CLL","description":"Chronic lymphocytic leukemia (CLL) is a B-cell neoplasm with a heterogeneous clinical and biological behavior.  We have performed deep RNA sequencing in different subpopulations of B-lymphocytes from healthy individuals and CLL cells from a cohort of 98 patients, and characterized the CLL transcriptional landscape with unprecedented resolution. The transcriptomic architecture of CLL uncovered here refines the biological characterization of the disease and opens new perspectives for the clinical management of patients.","dates":{"updated":"2019-10-31 12:52:10"},"accession":"EGAS00001000374","cross_references":{"TAXONOMY":["9606"],"pubmed":["24265505"],"EGA":["EGAD00001000258","EGAD00001000083","EGAD00010000472","EGAC00001000010"]}}