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Dataset: Genomic approach in B-cell Chronic Lymphocytic Leukemia: molecularly distinct subgroups of patients with 13q14 deletion

B-cell chronic lymphocytic leukemia (B-CLL) is characterized by a highly variable clinical course that reflects its heterogeneous genomic...

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B-cell chronic lymphocytic leukemia (B-CLL) is characterized by a highly variable clinical course that reflects its heterogeneous genomic pattern. To better define molecular subtypes of the disease, we performed SNP and gene expression profiling microarray analyses in a panel of early stage (Binet A) patients. A clustering analysis of genomic profiles identified four significant groups mainly driven by del(13)(q14) and trisomy 12. Notably, patients with del(13)(q14) were grouped in two separate clusters based on the presence of a biallelic loss and the extension of the deletion. The shorter monoallelic deleted 13q14 region was found to be 635 kb in length, not encompassing the mir-15a/16-1 locus. Interestingly, the mir-15a and mir-16 expression was found to be significantly down-regulated only in patients with biallelic loss. Furthermore, a multiclass supervised analysis identified a different transcriptional signatures in the two genomic subgroups with del(13)(q14). Finally, an integrative approach identified 93 transcripts, mainly mapped to chromosome 12 and 13q12-q14.3, whose expression was significantly correlated with the DNA copy number. Overall, our data further support the notion that transcription deregulation in B-CLL could be mostly due to a gene dosage effect and underscore the presence of two distinct molecular types of 13q14 deleted patients with potential clinical relevance. Transcriptional analysis of 60 B-CLL patients, and genotyping analysis of 100 B-CLL patients, in early stage disease (Binet A). This series of microarray experiments contains the gene expression profiles of purified B-cell chronic lymphocytic leukemia (B-CLL) cells obtained from 60 newly diagnosed patients (Binet stage A). Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome. If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody treatment followed by magnetic beads. 3 micrograms of total RNA was processed and, in accordance with the manufacturer's protocols, 15 micrograms of fragmented biotin-labelled cRNA were hybridized on GeneChip Human Genome U133A Arrays (Affymetrix Inc.). The arrays were scanned using the GeneChip Scanner 3000 7G. The images were acquired using Affymetrix GeneChip Operating Software (GCOS version 1.4) and the probe level data converted to expression values using the Bioconductor function for the Robust Multi-Array average (RMA) procedure (Irizarry et al, 2003), in which perfect match intensities are background adjusted and quantile-quantile normalised. This series of microarray experiments contains the genome-wide profiles of purified B-cell chronic lymphocytic leukemia (B-CLL) cells obtained from 100 newly diagnosed patients (Binet stage A). Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple-positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome. If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody treatment followed by magnetic beads. 250 nanograms of genomic DNA was processed and, in accordance with the manufacturer's protocols, 90 micrograms of fragmented biotin-labeled DNA were hybridized on GeneChip Human Mapping 250K NspI Arrays (Affymetrix Inc.). The arrays were scanned using the GeneChip Scanner 3000 7G. The images were acquired using Affymetrix GeneChip Operating Software (GCOS version 1.4). The raw data for individual SNPs were extracted from CEL files and converted into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares using the Hidden Markov Model algorithm with a genomic smoothing window set to 0. After the pre-processing, piecewise constant estimates of the underlying local DNA copy number (CN) variation was calculated using the DNAcopy Bioconductor package, which looks for optimal breakpoints using circular binary segmentation (CBS).

Species:
human

Samples:
60

Source:
E-GEOD-16746

Updated:
Jan.20, 2015

Registered:
Jan.20, 2015


Factors: (via ArrayExpress)
Sample VH STATUS SEX
GSM419842 1 unmut
GSM419843 1 unmut
GSM419844 1 mut
GSM419845 1 mut
GSM419846 1 mut
GSM419847 1 mut
GSM419848 1 unmut
GSM419849 1 mut
GSM419850 1 mut
GSM419851 1 mut
GSM419852 1 mut
GSM419853 1 unmut
GSM419854 1 unmut
GSM419855 1 unmut
GSM419856 1 unmut
GSM419857 1 mut
GSM419858 1 unmut
GSM419859 1 unmut
GSM419860 1 mut
GSM419861 1 mut
GSM419862 1 unmut
GSM419863 1 unmut
GSM419864 1 unmut
GSM419865 1 unmut
GSM419866 1 mut
GSM419867 1 unmut
GSM419868 1 unmut
GSM419869 1 mut
GSM419870 1 mut
GSM419871 1 unmut
GSM419872 1 unmut
GSM419873 1 mut
GSM419874 1 mut
GSM419875 1 unmut
GSM419876 1 mut
GSM419877 1 unmut
GSM419878 1 unmut
GSM419879 1 mut
GSM419880 1 unmut
GSM419881 1 unmut
GSM419882 1 unmut
GSM419883 1 unmut
GSM419884 1 unmut
GSM419885 1 unmut
GSM419886 1 unmut
GSM419887 1 unmut
GSM419888 1 unmut
GSM419889 1 unmut
GSM419890 1 unmut
GSM419891 1 unmut
GSM419892 1 unmut
GSM419893 1 mut
GSM419894 1 unmut
GSM419895 1 mut
GSM419896 1 unmut
GSM419897 1 mut
GSM419898 1 mut
GSM419899 1 unmut
GSM419900 1 mut
GSM419901 1 unmut

Tags

  • b-cell chronic lymphocytic leukemia
  • cell
  • chromosome
  • disease
  • genome
  • leukemia
  • peripheral
  • segmentation

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