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Towards an integrated framework for clinico-biological data management and analysis: The case of Chronic Lymphocytic Leukemia

Evangelia Minga, Athanasios Gkoufas, Anna Vardi, Evangelia Stalika, Anastasia Hadzidimitriou, Kostas Stamatopoulos, Nicos Maglaveras, Ioanna Chouvarda
2013 13th IEEE International Conference on BioInformatics and BioEngineering  
The proposed concepts are applied in the case of Chronic Lymphocytic Leukemia, a paradigmatic age-related hematologic cancer, and the steps for data integration and information analysis are illustrated  ...  In this respect we propose an approach for the integrated management and analysis of large quantities of clinicobiological data, including high-throughput sequencing data.  ...  Comparing identical categories of data coming from different medical centers, we have come up against Towards an Integrated Framework for Clinico-Biological Data Management and Analysis: the Case of  ... 
doi:10.1109/bibe.2013.6701690 dblp:conf/bibe/MingaGVSHSMC13 fatcat:ju2kixoqbneq5nly6sly3ih72a

Navigating Multi-scale Cancer Systems Biology towards Model-driven Personalized Therapeutics [article]

Mahnoor Naseer Gondal, Safee Ullah Chaudhary
2021 bioRxiv   pre-print
The review concludes by highlighting that the absence of a generic, zero-code, panomics-based multi-scale modeling pipeline and associated software framework, impedes the development and seamless deployment  ...  (iii) associated simulation software for development of personalized cancer therapeutics, and (iv) translational attempts to pipeline multi-scale panomics data for data-driven in silico clinical oncology  ...  In this review, we will evaluate the emergence, evolution, and integration of multiscale cancer data towards building coherent and biologically plausible in silico models and their integrative analysis  ... 
doi:10.1101/2021.05.17.444410 fatcat:vbfvmtb5irdapglgkmh5na73je

Landscape of Big Medical Data: A Pragmatic Survey on Prioritized Tasks [article]

Zhifei Zhang, Wanling Gao, Fan Zhang, Yunyou Huang, Shaopeng Dai, Fanda Fan, Jianfeng Zhan, Mengjia Du, Silin Yin, Longxin Xiong, Juan Du, Yumei Cheng, Xiexuan Zhou, Rui Ren (+2 others)
2019 arXiv   pre-print
Third, do the state-of-the-practice and state-of-the-art algorithms perform good jobs? Fourth, are there any benchmarks for measuring algorithms and systems for big medical data?  ...  Fifth, what are the performance gaps of state-of-the-practice and state-of-the-art systems handling big medical data currently or in future?  ...  IMG [186] is an integrated microbial genomes database and comparative analysis system. For medical text data, Neamatullah et al.  ... 
arXiv:1901.00642v1 fatcat:fak46q7bgzesll6y4h7i6mcysi

Immunophenotyping in acute leukaemia, myelodysplastic syndromes and hairy cell leukaemia. The use of monoclonal antibodies against myeloid differentiation antigens

J S Kristensen
1994 Danish medical bulletin  
Data management: With the number of samples steadily accumulating in the study and a large number of parameters to be stored for each analysis, the construction of a database quickly became necessary.  ...  CDI Ic (LEU-MS) expression characterizes a B- cell chronic lymphoproliferative disorder with feature of both chronic lymphocytic leukemia and hairy cell leukemia.  ... 
pmid:8187565 fatcat:or7zxnicc5duzokvusug7rpkfe

XVI Congress of the Italian Society of Experimental Hematology, Napoli, Italy, October 15-17, 2020

The authors
2020 Haematologica  
The integration of mutational and expression data from a large cohort of adult pan myeloid leukemia cases enabled the definition of subtypes and constellations of mutations and have prognostic significance  ...  Despite the unprecedented efficacy observed with Bcr-Abl tyrosine kinase inhibitors (TKIs) in the management of chronic myeloid leukemia (CML), resistance and intolerance towards first-, second-and third-generation  ...  Patients with IDH1 Introduction: In Chronic lymphocytic leukemia (CLL) the worst prognosis is associated with TP53 defects (mutations an deletion) and IGHV gene somatic hyper-mutation status (SHM) with  ... 
doi:10.3324/haematol.2020.s2 pmid:33410314 fatcat:diew3clymfh2nl3gewoxl7nkvm

The (epi)genomic landscape of splenic marginal zone lymphoma, biological implications, clinical utility, and future questions

Carolina Jaramillo Oquendo, Helen Parker, David Oscier, Sarah Ennis, Jane Gibson, Jonathan C. Strefford
2021 Journal of Translational Genetics and Genomics  
Our understanding of the mutational landscape of SMZL is built on a limited number of index cases, but has highlighted recurrent mutations in KLF2, NOTCH2 and TP53, and a spectrum of genes that cluster  ...  This review will provide an overview of our current understanding of the molecular basis of SMZL, and how this information impacts patient outcomes.  ...  These data will then be integrated with genome-wide mutational and CNA data, telomere dynamics, and for key biological subgroups, the proliferative history based on methylation arrays, transcriptomic and  ... 
doi:10.20517/jtgg.2021.04 fatcat:bgsxzs4o4zea5ljggc6yg725su

Landscape of Big Medical Data: A Pragmatic Survey on Prioritized Tasks

Zhifei Zhang, Wanling Gao, Fan Zhang, Yunyou Huang, Shaopeng Dai, Fanda Fan, Jianfeng Zhan, Mengjia Du, Silin Yin, Longxin Xiong, Juan Du, Yumei Cheng (+4 others)
2019 IEEE Access  
Third, do the state-of-the-practice and state-of-the-art algorithms perform good jobs? Fourth, are there any benchmarks for measuring algorithms and systems for big medical data?  ...  Fifth, what are the performance gaps of the state-of-the-practice and state-of-the-art systems handling big medical data currently or in the future?  ...  IMG [186] is an integrated microbial genomes database and comparative analysis system. For medical text data, Neamatullah et al.  ... 
doi:10.1109/access.2019.2891948 fatcat:d7yabam6zbdpxdojd4vfeth2rq

Vaccine therapies [chapter]

2010 The Lymphoid Neoplasms 3ed  
While all reasonable efforts have been made to publish reliable data and information, neither the author[s] nor the publisher can accept any legal responsibility or liability for any errors or omissions  ...  of the publishers.  ...  chronic lymphocytic leukemia.  ... 
doi:10.1201/b13424-103 fatcat:xummiahdkfhuffjwqway6shahu

Cancer biomarker discovery and validation

Nicolas Goossens, Shigeki Nakagawa, Xiaochen Sun, Yujin Hoshida
2015 Translational Cancer Research  
We also discuss regulatory issues and future perspectives in the era of big data analysis and precision medicine.  ...  With the emergence of genomic profiling technologies and selective molecular targeted therapies, biomarkers play an increasingly important role in the clinical management of cancer patients.  ...  Acknowledgements Funding: This work was supported by the FLAGS foundation, the Nuovo-Soldati Cancer Research Foundation and an advanced training grant from Geneva University Hospital to NG and NIH/NIDDK  ... 
doi:10.3978/j.issn.2218-676x.2015.06.04 pmid:26213686 pmcid:PMC4511498 fatcat:y5nfoa66vvd7jbtgwf6zzfcqnm

High-resolution representational oligonucleotide microarray analysis and fluorescence in situ hybridization analysis of aneuploid and diploid breast tumors

J Hicks, V Grubor, N Navin, P Lundin, S Månér, T Hägerström, L Skoog, M Wigler, A Zetterberg
2005 Breast Cancer Research  
Our data do not support the hypothesis that TGF-β signaling in mammary carcinoma cells is important for invasion and metastasis, at least in this model system.  ...  There is compelling evidence from transgenic mouse studies and analysis of mutations in human carcinomas indicating that the TGF-β signal transduction pathway is tumor suppressive.  ...  the systematic integration of the biological and clinical data.  ... 
doi:10.1186/bcr1069 fatcat:2phq3m5fkzakjg6c4r4xst6nhq

Hematopathology

2014 Modern Pathology  
All 100 samples had morphology with corresponding FC analysis, 95 had an evaluable aspirate smear and 86 had myeloma FISH.  ...  Statistical analysis was performed using Fisher's exact tests. Results: 35% of PCM cases (14/40) were positive for surface expression of CXCR4, while nearly all control plasma cells were positive.  ...  Of the HCL cases, mutational status by PCR was available for 19 cases and all were concordant with IHC results.  ... 
doi:10.1038/modpathol.2014.17 fatcat:tq7ooe2lwzfnpampu6naxbhpd4

Abstracts from the XXIX Conferenza Nazionale di Citometria

2011 Cytometry Part A  
Results: Our data showed that TMZ, independent of MGMT expression, inhibited glioblastoma cell growth via an irreversible G2 block in MGMT depleted or the induction of apoptosis in MGMT expressing cells  ...  Cell cycle analysis and apoptosis were evaluated by Flow Cytometry (FCM). Cell cycle molecules were detected by Western blot and co-immunoprecipitation assay.  ...  Regulatory T-cells (Tregs) constitute a small subset of cells involved in antitumour immunity and are generally increased in patients with chronic lymphocytic leukemia (CLL), for the diagnosis of which  ... 
doi:10.1002/cyto.a.21155 fatcat:hikuikbbczgypnhvda5e3goxb4

61st Annual Conference of Indian Society of Hematology & Blood Transfusion (ISHBT) November 2020

2020 Indian Journal of Hematology and Blood Transfusion  
A web interface for integrative meta-analysis, Integrative Meta-Analysis of Expression Data tool was used for the meta-analysis along with the Cytoscape tool for the hub gene analysis.  ...  Results: Of the 142 cases of CLPD diagnosed during this period, chronic lymphocytic leukemia (CLL) was the most common (84%).  ...  The samples were processed for different MFC panels (acute leukemia, CLPD, myeloma, lymphocyte subset) depending on clinical suspicion.  ... 
doi:10.1007/s12288-020-01384-8 fatcat:3jwz62e32zh4tm776izpy2jf54

Cord blood transplantation and cord blood banking

Shunichi Kato
2005 Hematology  
The molecular basis for aggressive transformation of multiple myeloma (MM) and other cancers is not completely understood.  ...  In particular, over-expression of CKS1B , which maps to an amplicon at 1q21 in myeloma and regulates SCF Skp2 -mediated ubquitination and proteolysis of the cyclin dependent kinase inhibitor p27 Kip1 was  ...  Acknowledgements We are indebted to members of the Donna D. and Donald M.  ... 
pmid:16285114 fatcat:oxdtmc242jbiritbbfj4kdrxxe

XVI meeting of the European Association for Haematopathology 2012 Abstracts

2012 Journal of Hematopathology  
We further screened 228 mature Bcell neoplasms with VE1 and detected one positive case of B-lymphocytic leukemia. Sequencing confirmed the presence of a BRAF V600E mutation.  ...  Conclusions: In conclusion we demonstrate the high sensitivity and specificity of VE1 immunohistochemistry for HCL.  ...  Aim of the study: We report a very rare case of metastatic chronic lymphocytic leukemia/small lymphocytic lymphoma to mature cystic teratoma of the ovary.  ... 
doi:10.1007/s12308-012-0160-x fatcat:6ycbkrfj2vfmvghul4lhkuc2by
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