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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Mutational analysis of CLL patient samples

ABSTRACT: High genomic complexity (HGC) is linked to poor prognosis in chronic lymphocytic leukaemia (CLL), but its independent prognostic value remains uncertain amid emerging biomarkers. Therefore we analysed copy number alterations in 495 treatment-naïve patients from three randomized trials (CLL4, ADMIRE, ARCTIC), incorporating IGHV status, telomere length (TL), targeted sequencing, and DNA-methylation subtypes.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: helen Parker

PROVIDER: E-MTAB-15598 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Copy number profiling of CLL patient samples

Project description:High genomic complexity (HGC) is linked to poor prognosis in chronic lymphocytic leukaemia (CLL), but its independent prognostic value remains uncertain amid emerging biomarkers. Therefore we analysed copy number alterations in 495 treatment-naïve patients from three randomized trials (CLL4, ADMIRE, ARCTIC), incorporating IGHV status, telomere length (TL), targeted sequencing, and DNA-methylation subtypes.

2026-04-01 | E-MTAB-15600 | biostudies-arrayexpress

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Methylation Profiling of IGHV Unmutated vs mutated CLL

Project description:In the present study, the methylation profiling (MeDIP) was carried out in 14 treatment-naive, early stage (Rai stage 0-2) CLL patients and pooled 19+ normal controls. To find an association of methylation with IGHV mutation status, CLL patients were further segregated into IGHV unmutated (n=9) and IGHV mutated (n=5) subgroups. The methylation signature obtained for CLL versus nornal controls and; unmutated versus mutated CLL was integrated with gene expression profile of these patients and the results were correlated with clinical outcome.

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Project description:In the present study, the gene expression profiling was carried out in 21 early stage CLL patients. A gene expression signature was generated for CLL patients as compared to normal controls; CLL patients were further seggregated into IGHV unmutated (n=10) and IGHV mutated (n=11) subgroups. The expression pattern was confirmed using real time quantitative PCR and the results were correlated with clinical outcome.

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INCISE Mutational Data Subset

Project description:This study used formalin-fixed paraffin-embedded (FFPE) human tissue collected for the Integrated teChnologies for Improved polyp SurveillancE (INCISE) collaborative from polypectomies performed within the Scottish BCSP in the NHS Greater Glasgow and Clyde health board between 2009-2016 in patients who underwent further colonoscopy between 6 months and 6 years after the index colonoscopy. The extracted DNA was then passed to the Genomics Innovation Alliance (formerly Glasgow Precision Oncology Laboratory; GPOL) for genomic sequencing using their bespoke Cancer Plus panel. The output from the sequencing is FASTQ files and VCF files.

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Expression data from chronic lymphocytic leukemia (CLL) cells

Project description:We compared gene expression profiles of CLL patients with and without MYD88 L265P mutations, taking into consideration IGHV mutation status.

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Gene expression study in WT and NOTCH1 mutated CLL cells.

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mutated IGHV3-23 CLL

Project description:Expression of stereotyped B cell receptors (BCR), i.e. non-random combinations of immunoglobulin heavy-chain variable (IGHV) genes, complementarity-determining region-3 (HCDR3), and IGV light chains, identifies discrete clusters and represents a peculiar feature of chronic lymphocytic leukemia (CLL). Expression of IGHV3-23 characterized a CLL subset with peculiar molecular and clinical features.

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lncRNA and mRNA Expression Profiling in Early Stage UM CLL

Project description:Predicting disease progression in chronic lymphocytic leukemia (CLL) remains challenging particularly in patients with Rai Stage 0/I disease that have an unmutated immunoglobulin heavy chain variable region (UM IGHV). Even though patients with UM IGHV have a poor prognosis and generally require earlier treatment, not all UM IGHV patients experience more rapid disease progression with some remaining treatment free for many years. This observation suggests biologic characteristics other than known prognostic factors influence disease progression. Alterations in long non-coding RNA (lncRNA) expression levels have been implicated in diagnosis and prognosis of various cancers, however, their role in disease progression of early Rai stage UM CLL is unknown. Here we use microarray analysis to compare lncRNA and mRNA profiles of Rai 0/I UM IGHV patients who progressed in <2 years relative to patients who had not progressed for >5 years. Over 1300 lncRNAs and 940 mRNAs were differentially expressed (fold change ≥ 2.0; p-value ≤ 0.05). Of interest, the differentially expressed lncRNAs G047155, TCAM1P, and uc.436, have known associated genes that have been linked to CLL. Thus, our study reveals differentially expressed lncRNAs in progressive early stage CLL requiring therapy versus indolent early Rai stage UM CLL. These lncRNAs have the potential to impact relevant biological processes and pathways that influence clinical outcome in CLL.

2018-11-29 | GSE123075 | GEO

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