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https://www.readbyqxmd.com/read/28102226/chronic-lymphocytic-leukaemia
#1
Thomas J Kipps, Freda K Stevenson, Catherine J Wu, Carlo M Croce, Graham Packham, William G Wierda, Susan O'Brien, John Gribben, Kanti Rai
Chronic lymphocytic leukaemia (CLL) is a malignancy of CD5(+) B cells that is characterized by the accumulation of small, mature-appearing lymphocytes in the blood, marrow and lymphoid tissues. Signalling via surface immunoglobulin, which constitutes the major part of the B cell receptor, and several genetic alterations play a part in CLL pathogenesis, in addition to interactions between CLL cells and other cell types, such as stromal cells, T cells and nurse-like cells in the lymph nodes. The clinical progression of CLL is heterogeneous and ranges from patients who require treatment soon after diagnosis to others who do not require therapy for many years, if at all...
January 19, 2017: Nature Reviews. Disease Primers
https://www.readbyqxmd.com/read/28096240/coevolution-of-leukemia-and-host-immune-cells-in-chronic-lymphocytic-leukemia
#2
Noelia Purroy, C J Wu
Cumulative studies on the dissection of changes in driver genetic lesions in cancer across the course of the disease have provided powerful insights into the adaptive mechanisms of tumors in response to the selective pressures of therapy and environmental changes. In particular, the advent of next-generation-sequencing (NGS)-based technologies and its implementation for the large-scale comprehensive analyses of cancers have greatly advanced our understanding of cancer as a complex dynamic system wherein genetically distinct subclones interact and compete during tumor evolution...
January 17, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28075457/high-resolution-melting-analysis-for-rapid-and-sensitive-notch1-screening-in-chronic-lymphocytic-leukemia
#3
Jing-Jing Xu, Fei-Rong Yao, Min Jiang, You-Tao Zhang, Feng Guo
Chronic lymphocytic leukemia (CLL) is a biological and clinical heterogeneous disease. Activating mutations of NOTCH1 have been implicated to be associated with adverse prognosis in CLL. The objective of the present study was to develop an effective high-resolution melting (HRM) assay for detecting NOTCH1 mutations. Genomic DNA (gDNA) extracted from 133 CLL patients was screened by HRM assay, and the results were compared with the data obtained using direct sequencing. The relative sensitivity of the HRM assay and direct sequencing was evaluated using diluted gDNA with different NOTCH1 mutational frequencies...
February 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28069558/from-genome-to-proteome-looking-beyond-dna-and-rna-in-chronic-lymphocytic-leukemia
#4
Lauren A Thurgood, Karen M Lower, Bryone J Kuss, Tim K Chataway
Chronic lymphocytic leukemia (CLL) remains the most common leukemia in the Western world. Whilst its disease course is extremely heterogeneous (ranging from indolent to aggressive), current methods are unable to accurately predict the clinical journey of each patient. There is clearly a pressing need for both improved prognostication and treatment options for patients with this disease.Whilst molecular studies have analyzed both genetic mutations and gene expression profiles of these malignant B-cells, and as a result have shed light on the pathogenesis of CLL, proteomic studies have been largely overlooked to date...
January 6, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28004597/functional-proteomic-insights-in-b-cell-chronic-lymphocytic-leukemia
#5
Paula Díez, Rafael Góngora, Alberto Orfao, Manuel Fuentes
B cell chronic lymphocytic leukemia (B-CLL) is a hematological malignancy considered as the most common leukemia in the Western world. The understanding of B cell differentiation is crucial for the diagnosis, prognosis, and treatment of the disease. Areas covered: In this review, B-cell ontogeny and its relation with the CLL development, in combination with the proteomic approaches which could provide a deep characterization of the disease through the characterization of the cellular signaling pathways involved in the pathological cells is described...
February 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27982015/evolution-of-multiple-cell-clones-over-a-29-year-period-of-a-cll-patient
#6
Zhikun Zhao, Lynn Goldin, Shiping Liu, Liang Wu, Weiyin Zhou, Hong Lou, Qichao Yu, Shirley X Tsang, Miaomiao Jiang, Fuqiang Li, MaryLou McMaster, Yang Li, Xinxin Lin, Zhifeng Wang, Liqin Xu, Gerald Marti, Guibo Li, Kui Wu, Meredith Yeager, Huanming Yang, Xun Xu, Stephen J Chanock, Bo Li, Yong Hou, Neil Caporaso, Michael Dean
Chronic lymphocytic leukaemia (CLL) is a frequent B-cell malignancy, characterized by recurrent somatic chromosome alterations and a low level of point mutations. Here we present single-nucleotide polymorphism microarray analyses of a single CLL patient over 29 years of observation and treatment, and transcriptome and whole-genome sequencing at selected time points. We identify chromosome alterations 13q14-, 6q- and 12q+ in early cell clones, elimination of clonal populations following therapy, and subsequent appearance of a clone containing trisomy 12 and chromosome 10 copy-neutral loss of heterogeneity that marks a major population dominant at death...
December 16, 2016: Nature Communications
https://www.readbyqxmd.com/read/27959900/genomic-profile-of-chronic-lymphocytic-leukemia-in-korea-identified-by-targeted-sequencing
#7
Jung-Ah Kim, Byungjin Hwang, Si Nae Park, Sunghoon Huh, Kyongok Im, Sungbin Choi, Hye Yoon Chung, JooRyung Huh, Eul-Ju Seo, Je-Hwan Lee, Duhee Bang, Dong Soon Lee
Chronic lymphocytic leukemia (CLL) is extremely rare in Asian countries and there has been one report on genetic changes for 5 genes (TP53, SF3B1, NOTCH1, MYD88, and BIRC3) by Sanger sequencing in Chinese CLL. Yet studies of CLL in Asian countries using Next generation sequencing have not been reported. We aimed to characterize the genomic profiles of Korean CLL and to find out ethnic differences in somatic mutations with prognostic implications. We performed targeted sequencing for 87 gene panel using next-generation sequencing along with G-banding and fluorescent in situ hybridization (FISH) for chromosome 12, 13q14...
2016: PloS One
https://www.readbyqxmd.com/read/27928896/genomic-data-integration-in-chronic-lymphocytic-leukemia
#8
Juan Luis Fernández-Martínez, Enrique J deAndrés-Galiana, Stephen T Sonis
BACKGROUND: B-cell Chronic Lymphocytic Leukemia (CLL) is a heterogeneous disease and the most common adult leukemia in western countries. IgVH mutational status distinguishes two major types of CLL, which were associated with different prognosis and survival. Sequencing identified NOTCH1 and SF3B1 as the two main recurrent mutations. We described a novel method to elucidate how these mutations affect gene expression by finding small-scale signatures to predict the IgVH, NOTCH1 and SF3B1 mutations...
December 8, 2016: Journal of Gene Medicine
https://www.readbyqxmd.com/read/27777635/global-dna-methylation-profiling-reveals-new-insights-into-epigenetically-deregulated-protein-coding-and-long-noncoding-rnas-in-cll
#9
Santhilal Subhash, Per-Ola Andersson, Subazini Thankaswamy Kosalai, Chandrasekhar Kanduri, Meena Kanduri
BACKGROUND: Methyl-CpG-binding domain protein enriched genome-wide sequencing (MBD-Seq) is a robust and powerful method for analyzing methylated CpG-rich regions with complete genome-wide coverage. In chronic lymphocytic leukemia (CLL), the role of CpG methylated regions associated with transcribed long noncoding RNAs (lncRNA) and repetitive genomic elements are poorly understood. Based on MBD-Seq, we characterized the global methylation profile of high CpG-rich regions in different CLL prognostic subgroups based on IGHV mutational status...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27652313/mutational-landscape-and-underlying-mutational-processes-in-chronic-lymphocytic-leukemia
#10
S Kasar, J R Brown
Sequencing studies have been instrumental in understanding the genetic basis of chronic lymphocytic leukemia (CLL). Our recent whole-genome sequencing study focusing on lower cytogenetic risk CLL demonstrated that CLL mutations can be attributed to 3 key mutational processes-2 types of activation induced-cytidine deaminase (AID) signatures and an aging signature-that operate at different times throughout CLL evolution.
July 2016: Molecular & Cellular Oncology
https://www.readbyqxmd.com/read/27633522/extensive-next-generation-sequencing-analysis-in-chronic-lymphocytic-leukemia-at-diagnosis-clinical-and-biological-correlations
#11
Gian Matteo Rigolin, Elena Saccenti, Cristian Bassi, Laura Lupini, Francesca Maria Quaglia, Maurizio Cavallari, Sara Martinelli, Luca Formigaro, Enrico Lista, Maria Antonella Bardi, Eleonora Volta, Elisa Tammiso, Aurora Melandri, Antonio Urso, Francesco Cavazzini, Massimo Negrini, Antonio Cuneo
BACKGROUND: In chronic lymphocytic leukemia (CLL), next-generation sequencing (NGS) analysis represents a sensitive, reproducible, and resource-efficient technique for routine screening of gene mutations. METHODS: We performed an extensive biologic characterization of newly diagnosed CLL, including NGS analysis of 20 genes frequently mutated in CLL and karyotype analysis to assess whether NGS and karyotype results could be of clinical relevance in the refinement of prognosis and assessment of risk of progression...
September 15, 2016: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/27588518/atm-function-and-its-relationship-with-atm-gene-mutations-in-chronic-lymphocytic-leukemia-with-the-recurrent-deletion-11q22-3-23-2
#12
Y Jiang, H-C Chen, X Su, P A Thompson, X Liu, K-A Do, W Wierda, M J Keating, W Plunkett
Approximately 10-20% of chronic lymphocytic leukemia (CLL) patients exhibit del(11q22-23) before treatment, this cohort increases to over 40% upon progression following chemoimmunotherapy. The coding sequence of the DNA damage response gene, ataxia-telangiectasia-mutated (ATM), is contained in this deletion. The residual ATM allele is frequently mutated, suggesting a relationship between gene function and clinical response. To investigate this possibility, we sought to develop and validate an assay for the function of ATM protein in these patients...
September 2, 2016: Blood Cancer Journal
https://www.readbyqxmd.com/read/27524613/genetic-predisposition-to-chronic-lymphocytic-leukemia-is-mediated-by-a-bmf-super-enhancer-polymorphism
#13
Radhika Kandaswamy, Georgina P Sava, Helen E Speedy, Sílvia Beà, José I Martín-Subero, James B Studd, Gabriele Migliorini, Philip J Law, Xose S Puente, David Martín-García, Itziar Salaverria, Jesús Gutiérrez-Abril, Carlos López-Otín, Daniel Catovsky, James M Allan, Elías Campo, Richard S Houlston
Chronic lymphocytic leukemia (CLL) is an adult B cell malignancy. Genome-wide association studies show that variation at 15q15.1 influences CLL risk. We deciphered the causal variant at 15q15.1 and the mechanism by which it influences tumorigenesis. We imputed all possible genotypes across the locus and then mapped highly associated SNPs to areas of chromatin accessibility, evolutionary conservation, and transcription factor binding. SNP rs539846 C>A, the most highly associated variant (p = 1.42 × 10(-13), odds ratio = 1...
August 23, 2016: Cell Reports
https://www.readbyqxmd.com/read/27503198/survival-of-del17p-cll-depends-on-genomic-complexity-and-somatic-mutation
#14
Lijian Yu, Haesook T Kim, Siddha N Kasar, Parul Benien, Wei Du, Kevin Hoang, Andrew Aw, Bethany Tesar, Reina Improgo, Stacey M Fernandes, Saranya Radhakrishnan, Josephine L Klitgaard, Charles Lee, Gad Getz, Sunita R Setlur, Jennifer R Brown
PURPOSE: Chronic lymphocytic leukemia (CLL) with 17p deletion typically progresses quickly and is refractory to most conventional therapies. However, some del(17p) patients do not progress for years, suggesting that del(17p) is not the only driving event in CLL progression. We hypothesize that other concomitant genetic abnormalities underlie the clinical heterogeneity of del(17p) CLL. EXPERIMENTAL DESIGN: We profiled the somatic mutations and copy number alterations (CNA) in a large group of del(17p) CLLs as well as wild-type CLL and analyzed the genetic basis of their clinical heterogeneity...
August 8, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27486974/telomere-status-in-chronic-lymphocytic-leukemia-with-tp53-disruption
#15
Romain Guièze, Mélanie Pages, Lauren Véronèse, Patricia Combes, Richard Lemal, Mathilde Gay-Bellile, Martine Chauvet, Mary Callanan, Fabrice Kwiatkowski, Bruno Pereira, Philippe Vago, Jacques-Olivier Bay, Olivier Tournilhac, Andreï Tchirkov
In chronic lymphocytic leukemia (CLL), telomere dysfunction is associated with poor outcomes. TP53 is involved in cellular responses to dysfunctional telomeres, and its inactivation is the strongest adverse prognostic factor for CLL. Given the biological relationship between TP53 and telomeres, and their prognostic value, it is important to improve our understanding of the impact of TP53 alterations on telomeres. We performed a comprehensive study of the deletions and mutations of the TP53 gene and telomere parameters, including hTERT and the shelterin complex, in 115 CLL patients...
30, 2016: Oncotarget
https://www.readbyqxmd.com/read/27469216/genomic-characterization-of-high-count-mbl-cases-indicates-that-early-detection-of-driver-mutations-and-subclonal-expansion-are-predictors-of-adverse-clinical-outcome
#16
S Barrio, T D Shanafelt, J Ojha, K G Chaffee, C Secreto, K M Kortüm, S Pathangey, D L Van-Dyke, S L Slager, R Fonseca, N E Kay, E Braggio
High-count monoclonal B-cell lymphocytosis (MBL) is an asymptomatic expansion of clonal B cells in the peripheral blood without other manifestations of chronic lymphocytic leukemia (CLL). Yearly, 1% of MBLs evolve to CLL requiring therapy; thus being critical to understand the biological events that determine which MBLs progress to intermediate/advanced CLL. In this study, we performed targeted deep sequencing on 48 high-count MBLs, 47 of them with 2-4 sequential samples analyzed, exploring the mutation status of 21 driver genes and evaluating clonal evolution...
January 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/27461342/hypomethylation-coordinates-antagonistically-with-hypermethylation-in-cancer-development-a-case-study-of-leukemia
#17
Garima Kushwaha, Mikhail Dozmorov, Jonathan D Wren, Jing Qiu, Huidong Shi, Dong Xu
BACKGROUND: Methylation changes are frequent in cancers, but understanding how hyper- and hypomethylated region changes coordinate, associate with genomic features, and affect gene expression is needed to better understand their biological significance. The functional significance of hypermethylation is well studied, but that of hypomethylation remains limited. Here, with paired expression and methylation samples gathered from a patient/control cohort, we attempt to better characterize the gene expression and methylation changes that take place in cancer from B cell chronic lymphocyte leukemia (B-CLL) samples...
2016: Human Genomics
https://www.readbyqxmd.com/read/27346425/chromatin-accessibility-maps-of-chronic-lymphocytic-leukaemia-identify-subtype-specific-epigenome-signatures-and-transcription-regulatory-networks
#18
André F Rendeiro, Christian Schmidl, Jonathan C Strefford, Renata Walewska, Zadie Davis, Matthias Farlik, David Oscier, Christoph Bock
Chronic lymphocytic leukaemia (CLL) is characterized by substantial clinical heterogeneity, despite relatively few genetic alterations. To provide a basis for studying epigenome deregulation in CLL, here we present genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients measured by the ATAC-seq assay. We also performed ChIPmentation and RNA-seq profiling for ten representative samples. Based on the resulting data set, we devised and applied a bioinformatic method that links chromatin profiles to clinical annotations...
June 27, 2016: Nature Communications
https://www.readbyqxmd.com/read/27341486/fishing-in-the-dark-how-the-combination-of-fish-and-conventional-karyotyping-improves-the-diagnostic-yield-in-cpg-stimulated-chronic-lymphocytic-leukemia
#19
Adrian M Dubuc, Matthew S Davids, Mirela Pulluqi, Olja Pulluqi, Kevin Hoang, Jesus M Hernandez-Sánchez, Cathy Schlich, Jesus M Hernández-Rivas, Jennifer R Brown, Paola Dal Cin
Despite significant advances in molecular genetic approaches, fluorescence in situ hybridization (FISH) remains the gold standard for the diagnostic evaluation of genomic aberrations in patients with chronic lymphocytic leukemia (CLL). Efforts to improve the diagnostic utility of molecular cytogenetic testing have led to the expansion of the traditional 4-probe CLL FISH panel. Not only do these efforts increase the cost of testing, they remain hindered by the inherent limitations of FISH studies - namely the inability to evaluate genomic changes outside of the targeted loci...
October 2016: American Journal of Hematology
https://www.readbyqxmd.com/read/27302925/phenotypic-alteration-of-cd8-t-cells-in-chronic-lymphocytic-leukemia-is-associated-with-epigenetic-reprogramming
#20
Jiazhu Wu, Xiaojing Xu, Eun-Joon Lee, Austin Y Shull, Lirong Pei, Farrukh Awan, Xiaoling Wang, Jeong-Hyeon Choi, Libin Deng, Hong-Bo Xin, Wenxun Zhong, Jinhua Liang, Yi Miao, Yujie Wu, Lei Fan, Jianyong Li, Wei Xu, Huidong Shi
Immunosuppression is a prevalent clinical feature in chronic lymphocytic leukemia (CLL) patients, with many patients demonstrating increased susceptibility to infections as well as increased failure of an antitumor immune response. However, much is currently not understood regarding the precise mechanisms that attribute to this immunosuppressive phenotype in CLL. To provide further clarity to this particular phenomenon, we analyzed the T-cell profile of CLL patient samples within a large cohort and observed that patients with an inverted CD4/CD8 ratio had a shorter time to first treatment as well as overall survival...
June 28, 2016: Oncotarget
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