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Next generation sequencing leukemia

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https://www.readbyqxmd.com/read/28626218/molecular-characterization-of-ezh2-mutant-patients-with-myelodysplastic-myeloproliferative-neoplasms
#1
J Rinke, J P Müller, M F Blaess, A Chase, M Meggendorfer, V Schäfer, N Winkelmann, C Haferlach, N C P Cross, A Hochhaus, T Ernst
Mutations in the epigenetic regulator gene EZH2 are frequently observed in patients with myelodysplastic/myeloproliferative neoplasms (MDS/MPN; 10-13%) and are associated with a poor outcome. To gain more insight into EZH2 pathology we sought to genetically characterize a cohort of 41 EZH2-mutated MDS/MPN patients using targeted deep next generation sequencing (NGS), colony forming progenitor assays and transcriptome analysis. Stable shRNA-mediated downregulation of EZH2 was performed in MDS derived F-36P, MOLM-13 and OCI-M2 cells to study EZH2 specific changes...
June 19, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28608976/tp53-mutation-does-not-confer-a-poor-outcome-in-adult-patients-with-acute-lymphoblastic-leukemia-who-are-treated-with-frontline-hyper-cvad-based-regimens
#2
Rashmi Kanagal-Shamanna, Preetesh Jain, Koichi Takahashi, Nicholas J Short, Guilin Tang, Ghayas C Issa, Farhad Ravandi, Guillermo Garcia-Manero, Cameron C Yin, Rajyalakshmi Luthra, Keyur P Patel, Joseph D Khoury, Guillermo Montalban-Bravo, Koji Sasaki, Tapan M Kadia, Gautam Borthakur, Marina Konopleva, Nitin Jain, Rebecca Garris, Sherry Pierce, William Wierda, Zeev Estrov, Jorge Cortes, Susan O'Brien, Hagop Kantarjian, Elias Jabbour
BACKGROUND: Tumor protein 53 (TP53) mutations are uncommon in adult patients with acute lymphoblastic leukemia (ALL) and predict a poor outcome. METHODS: TP53 mutation analysis was performed in 164 newly diagnosed adult patients with ALL using a combination of targeted amplicon-based next-generation sequencing and Sanger sequencing. RESULTS: TP53 mutations were detected in 25 patients (15%), with a median allelic frequency of 42.2% (range, 5...
June 13, 2017: Cancer
https://www.readbyqxmd.com/read/28605290/early-response-based-therapy-stratification-improves-survival-in-adult-early-thymic-precursor-acute-lymphoblastic-leukemia-a-group-for-research-on-adult-acute-lymphoblastic-leukemia-study
#3
Jonathan Bond, Carlos Graux, Ludovic Lhermitte, Diane Lara, Thomas Cluzeau, Thibaut Leguay, Agata Cieslak, Amélie Trinquand, Cedric Pastoret, Mohamed Belhocine, Salvatore Spicuglia, Véronique Lheritier, Stéphane Leprêtre, Xavier Thomas, Françoise Huguet, Norbert Ifrah, Hervé Dombret, Elizabeth Macintyre, Nicolas Boissel, Vahid Asnafi
Purpose Early thymic precursor (ETP) acute lymphoblastic leukemia (ALL) is an immunophenotypically defined subgroup of T-cell ALL (T-ALL) associated with high rates of intrinsic treatment resistance. Studies in children have shown that the negative prognostic impact of chemotherapy resistance is abrogated by the implementation of early response-based intensification strategies. Comparable data in adults are lacking. Patients and Methods We performed comprehensive clinicobiologic, genetic, and survival analyses of a large cohort of 213 adult patients with T-ALL, including 47 patients with ETP-ALL, treated in the GRAALL (Group for Research on Adult Acute Lymphoblastic Leukemia) -2003 and -2005 studies...
June 12, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28598576/semi-automated-cancer-genome-analysis-using-high-performance-computing
#4
Giuliano Crispatzu, Pranav Kulkarni, Mohammad R Toliat, Peter Nürnberg, Marco Herling, Carmen D Herling, Peter Frommolt
Next-Generation Sequencing (NGS) has turned from a new and experimental technology into a standard procedure for cancer genome studies and clinical investigation. While a multitude of software packages for cancer genome data analysis have been made available, these need to be combined into efficient analytical workflows that cover multiple aspects relevant to a clinical environment and that deliver handy results within a reasonable time frame. Here, we introduce QuickNGS Cancer as a new suite of bioinformatics pipelines which is focused on cancer genomics and significantly reduces the analytical hurdles that still limit a broader applicability of NGS technology, particularly to clinically driven research...
June 9, 2017: Human Mutation
https://www.readbyqxmd.com/read/28596278/hla-drb1-07-01-hla-dqa1-02-01-hla-dqb1-02-02-haplotype-is-associated-with-a-high-risk-of-asparaginase-hypersensitivity-in-acute-lymphoblastic-leukemia
#5
Nóra Kutszegi, Xiaoqin Yang, András Gézsi, Géza Schermann, Dániel J Erdélyi, Ágnes F Semsei, Krisztina M Gábor, Judit C Sági, Gábor T Kovács, András Falus, Hongyun Zhang, Csaba Szalai
Hypersensitivity reactions are the most frequent dose-limiting adverse reactions to Escherichia coli-derived asparaginase in pediatric acute lymphoblastic leukemia patients. The aim of the present study was to identify associations between sequence-based Human Leukocyte Antigen Class II region alleles and asparaginase hypersensitivity in a Hungarian acute lymphoblastic leukemia population. Four-digit typing of HLA-DRB1 and HLA-DQB1 loci was performed in 359 pediatric acute lymphoblastic leukemia patients by using next-generation sequencing method...
June 8, 2017: Haematologica
https://www.readbyqxmd.com/read/28596259/morphologic-and-molecular-characteristics-of-de-novo-aml-with-jak2-v617f-mutation
#6
Juliana E Hidalgo-López, Rashmi Kanagal-Shamanna, L Jeffrey Medeiros, Zeev Estrov, C Cameron Yin, Srdan Verstovsek, Sergej Konoplev, Jeffrey L Jorgensen, Mohammad M Mohammad, Roberto N Miranda, Chong Zhao, John Lee, Zhuang Zuo, Carlos E Bueso-Ramos
Background:JAK2 V617F mutation (mut) in acute myeloid leukemia (AML) is rare. We describe the clinicopathologic findings of a single-institution series of 11 de novo AML cases with JAK2 V617. Methods: We identified cases of de novo AML with JAK2 V617F over a 10-year period. We reviewed diagnostic peripheral blood and bone marrow (BM) morphologic, cytogenetic, and molecular studies, including next-generation sequencing. The control group consisted of 12 patients with JAK2 wild-type (wt) AML matched for age, sex, and diagnosis...
June 2017: Journal of the National Comprehensive Cancer Network: JNCCN
https://www.readbyqxmd.com/read/28592762/chronic-lymphocytic-leukemia-pathophysiology-and-current-therapy
#7
Jun Takizawa
Chronic lymphocytic leukemia (CLL) is the most frequent adult leukemia in western countries, but it is rare in Japan. Several mutations have been identified in patients with CLL using next-generation sequencing, but disease-specific mutations were not found. Some mutations, such as those in TP53, NOTCH1, SF3B, and BIRC3 are useful for risk stratification and prognosis prediction in patients with CLL. Strategies for treating CLL are rapidly evolving, with targeted agents such as the B-cell receptor signaling pathway inhibitors (ibrutinib, idelalisib), novel anti-CD20 monoclonal antibody (obinutuzumab), and Bcl-2 inhibitor (venetoclax) being approved by the US Food and Drug Administration...
2017: [Rinshō Ketsueki] the Japanese Journal of Clinical Hematology
https://www.readbyqxmd.com/read/28588253/nucleotide-excision-repair-ner-is-a-potential-therapeutic-target-in-multiple-myeloma
#8
R Szalat, M K Samur, M Fulciniti, M Lopez, P Nanjappa, A Cleynen, K Wen, S Kumar, T Perrini, A S Calkins, E Reznichenko, D Chauhan, Y-T Tai, M Shammas, J-P Fermand, B Arnulf, H Avet-Loiseau, J-B Lazaro, N C Munshi
Nucleotide excision repair is active in multiple myeloma cells.Inhibition of NER increases sensitivity to alkylating agent.NER is a potential target for multiple myeloma treatment. Despite the development of novel drugs, alkylating agents remain an important component of therapy in multiple myeloma (MM). DNA repair processes contribute towards sensitivity to alkylating agents, therefore we here evaluate the role of nucleotide excision repair (NER) which is involved in the removal of bulky adducts and DNA crosslinks in MM...
June 7, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28558674/learning-rule-sets-from-survival-data
#9
Łukasz Wróbel, Adam Gudyś, Marek Sikora
BACKGROUND: Survival analysis is an important element of reasoning from data. Applied in a number of fields, it has become particularly useful in medicine to estimate the survival rate of patients on the basis of their condition, examination results, and undergoing treatment. The recent developments in the next generation sequencing open new opportunities in survival study as they allow vast amount of genome-, transcriptome-, and proteome-related features to be investigated. These include single nucleotide and structural variants, expressions of genes and microRNAs, DNA methylation, and many others...
May 30, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28555081/genomic-determinants-of-chronic-myelomonocytic-leukemia
#10
B Patel, B Przychodzen, S Thota, T Radivoyevitch, V Visconte, T Kuzmanovic, M Clemente, C Hirsch, A Morawski, R Souaid, C Saygin, A Nazha, B Demarest, T LaFramboise, H Sakaguchi, S Kojima, H Carraway, S Ogawa, H Makishima, M Sekeres, J Maciejewski
The biology, clinical phenotype and progression rate of chronic myelomonocytic leukemia (CMML) are highly variable due to diverse initiating and secondary clonal genetic events. To determine the effects of molecular features including clonal hierarchy in CMML, we studied whole exome and targeted next generation sequencing data from 150 patients with robust clinical and molecular annotation assessed cross-sectionally and at serial time points of disease evolution. To identify molecular lesions unique to CMML we compared it to related myeloid neoplasms (N=586), including JMML, MDS, and primary monocytic AML and discerned distinct molecular profiles despite similar patho-morphologic features...
May 30, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28548121/ebv-negative-aggressive-nk-cell-leukemia-lymphoma-a-clinical-and-pathological-study-from-a-single-institution
#11
Juehua Gao, Amir Behdad, Peng Ji, Kristy L Wolniak, Olga Frankfurt, Yi-Hua Chen
Aggressive natural killer (NK)-cell leukemia/lymphoma is a systemic NK-cell neoplasm that preferentially affects Asians with a fulminant clinical course and is almost always associated with Epstein-Barr virus (EBV). The data on EBV-negative aggressive NK-cell leukemia/lymphoma are limited. Here we report a series of three patients (two Caucasians, one African-American) with EBV-negative aggressive NK-cell leukemia/lymphoma from a single institution, including a case diagnosed on post-mortem examination. Similar to EBV-positive aggressive NK-cell leukemia/lymphoma, our patients presented with constitutional symptoms and hepatosplenomegaly, and followed a highly aggressive clinical course...
May 26, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28535805/first-case-of-b-all-with-kmt2a-maml2-rearrangement-a-case-report
#12
Estelle Menu, Nathalie Beaufils, Fabrice Usseglio, Estelle Balducci, Marina Lafage Pochitaloff, Regis Costello, Jean Gabert
BACKGROUND: A large number of chromosomal translocations of the human KMT2A gene, better known as the MLL gene, have so far been characterized. Genetic rearrangements involving KMT2A gene are frequently involved in lymphoid, myeloid and mixed lineage leukemia. One of its rare fusion partners, the mastermind like 2 (MAML2) gene has been reported in four cases of myeloid neoplasms after chemotherapy so far: two acute myeloid leukemias (AML) and two myelodysplasic syndrome (MDS), and two cases of secondary T-cell acute lymphoblastic leukemia (T-ALL)...
May 23, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28533818/a-novel-bcr-abl1-fusion-gene-with-genetic-heterogeneity-indicates-a-good-prognosis-in-a-chronic-myeloid-leukemia-case
#13
Fen Zhou, Runming Jin, Yu Hu, Heng Mei
BACKGROUND: Chronic myelogenous leukemia (CML) is a pluripotent hematopoietic stem cell disorder caused by the fusion of the BCR and ABL1 genes. Quantitative RT-PCR (qRT-PCR) is a routinely performed screening technique to identify BCR-ABL1 fusion genes, but a limitation of this method is its inability to recognize novel fusions that have not been previously characterized. Next-generation sequencing (NGS) is an effective and sensitive detection method for the determination of novel BCR-ABL1 fusion genes as well as previously characterized ones...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/28529810/molecular-profiling-a-case-of-zbtb16-rara-acute-promyelocytic-leukemia
#14
Stephen E Langabeer, Lisa Preston, Johanna Kelly, Matt Goodyer, Ezzat Elhassadi, Amjad Hayat
Several variant RARA translocations have been reported in acute promyelocytic leukemia (APL) of which the t(11;17)(q23;q21), which results in a ZBTB16-RARA fusion, is the most widely identified and is largely resistant to therapy with all-trans retinoic acid (ATRA). The clinical course together with the cytogenetic and molecular characterization of a case of ATRA-unresponsive ZBTB16-RARA APL is described. Additional mutations potentially cooperating with the translocation fusion product in leukemogenesis have been hitherto unreported in ZBTB16-RARA APL and were sought by application of a next-generation sequencing approach to detect those recurrently found in myeloid malignancies...
2017: Case Reports in Hematology
https://www.readbyqxmd.com/read/28502479/megakaryocytes-in-myeloproliferative-neoplasms-have-unique-somatic-mutations
#15
Belinda B Guo, Richard J Allcock, Bob Mirzai, Jacques A Malherbe, Fizzah A Choudry, Mattia Frontini, Hun Chuah, James Liang, Simon E Kavanagh, Rebecca Howman, Willem H Ouwehand, Kathryn A Fuller, Wendy N Erber
Myeloproliferative neoplasms (MPNs) are a group of related clonal hemopoietic stem cell disorders associated with hyperproliferation of myeloid cells. They are driven by mutations in the hemopoietic stem cell, most notably JAK2(V617F), CALR, and MPL. Clinically, they have the propensity to progress to myelofibrosis and transform to acute myeloid leukemia. Megakaryocytic hyperplasia with abnormal features are characteristic, and it is thought that these cells stimulate and drive fibrotic progression. The biological defects underpinning this remain to be explained...
July 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/28479420/cbp-catenin-antagonists-targeting-lscs-achilles-heel
#16
REVIEW
Yong-Mi Kim, Eun-Ji Gang, Michael Kahn
Cancer stem cells (CSCs), including leukemia stem cells (LSCs), exhibit self-renewal capacity and differentiation potential and have the capacity to maintain or renew and propagate a tumor/leukemia. The initial isolation of CSCs/LSCs was in adult myelogenous leukemia, although more recently, the existence of CSCs in a wide variety of other cancers has been reported. CSCs, in general, and LSCs, specifically with respect to this review, are responsible for initiation of disease, therapeutic resistance and ultimately disease relapse...
May 4, 2017: Experimental Hematology
https://www.readbyqxmd.com/read/28475434/enhancing-acute-myeloid-leukemia-therapy-monitoring-response-using-residual-disease-testing-as-a-guide-to-therapeutic-decision-making
#17
REVIEW
Benjamin Tomlinson, Hillard M Lazarus
Current standards for monitoring the response of acute myeloid leukemia (AML) are based on morphologic assessments of the bone marrow and recovery of peripheral blood counts. A growing experience is being developed to enhance the detection of small amounts of AML, or minimal residual disease (MRD). Areas covered: Available techniques include multi-color flow cytometry (MFC) of leukemia associated immunophenotypes (LAIP), quantitative reverse transcriptase polymerase chain reaction (QRT-PCR) for detecting fusion and mutated genes (RUNX1-RUNX1T1, CBFB-MYH11, and NPM1), overexpression of genes such as WT1, and next generation sequencing (NGS) for MRD...
June 2017: Expert Review of Hematology
https://www.readbyqxmd.com/read/28469373/the-use-of-next-generation-sequencing-in-the-identification-of-a-fastidious-pathogen-a-lesson-from-a-clinical-setup
#18
Amr Tm Saeb, Mohamed Abouelhoda, Manojkumar Selvaraju, Sahar I Althawadi, Maysoon Mutabagani, Mohammad Adil, Abdullah Al Hokail, Hamsa T Tayeb
Clostridium haemolyticum is the causal agent of bacillary hemoglobinuria in cattle, goat, sheep, and ruminants. In this study, we report the first recorded human-infecting C. haemolyticum strain collected from an 18-year-old woman diagnosed with acute lymphoblastic leukemia. After failure of traditional techniques, only next-generation sequencing (NGS) technology in combination with bioinformatics, phylogenetic, and pathogenomics analyses revealed that our King Faisal Specialist Hospital and Research Center (KFSHRC) bacterial isolate belongs to C...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28467808/a-systematic-approach-for-peptide-characterization-of-b-cell-receptor-in-chronic-lymphocytic-leukemia-cells
#19
Paula Díez, Nieves Ibarrola, Rosa M Dégano, Quentin Lécrevisse, Arancha Rodriguez-Caballero, Ignacio Criado, Wendy G Nieto, Rafael Góngora, Marcos González, Julia Almeida, Alberto Orfao, Manuel Fuentes
A wide variety of immunoglobulins (Ig) is produced by the immune system thanks to different mechanisms (V(D)J recombination, somatic hypermutation, and antigen selection). The profiling of Ig sequences (at both DNA and peptide levels) are of great relevance to developing targeted vaccines or treatments for specific diseases or infections. Thus, genomics and proteomics techniques (such as Next-Generation Sequencing (NGS) and mass spectrometry (MS)) have notably increased the knowledge in Ig sequencing and serum Ig peptide profiling in a high-throughput manner...
April 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28452038/is-next-generation-sequencing-the-way-to-go-for-residual-disease-monitoring-in-acute-lymphoblastic-leukemia
#20
REVIEW
Michaela Kotrova, Jan Trka, Michael Kneba, Monika Brüggemann
Minimal residual disease (MRD) is the most important independent prognostic factor in acute lymphoblastic leukemia (ALL). Since it has been implemented into in treatment stratification strategies, cure rates have improved significantly for all age groups. Real time quantitative (RQ)-PCR of clonal immunoglobulin and T-cell receptor gene rearrangements using allele-specific primers is currently regarded as the gold standard for MRD analysis in ALL, as it is not only highly sensitive and specific but also provides accurate MRD quantification...
April 27, 2017: Molecular Diagnosis & Therapy
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