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Next generation sequencing leukemia

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https://www.readbyqxmd.com/read/29643105/a-next-generation-sequencing-based-assay-for-minimal-residual-disease-assessment-in-aml-patients-with-flt3-itd-mutations
#1
Mark J Levis, Alexander E Perl, Jessica K Altman, Christopher D Gocke, Erkut Bahceci, Jason Hill, Chaofeng Liu, Zhiyi Xie, Andrew R Carson, Valerie McClain, Timothy T Stenzel, Jeffrey E Miller
Internal tandem duplications in fms-like tyrosine kinase 3 ( FLT3- ITDs) are common in acute myeloid leukemia (AML) and confer a poor prognosis. A sensitive and specific assay for the detection of minimal residual disease (MRD) in FLT3- ITD mutated AML could guide therapy decisions. Existing assays for MRD in FLT3- ITD AML have not been particularly useful because of limited sensitivity. We developed a sensitive and specific MRD assay for FLT3- ITD mutations using next-generation sequencing. The initial validation of this assay was performed by spiking fixed amounts of mutant DNA into wild-type DNA to establish a sensitivity of detection equivalent to ≥1 FLT3- ITD-containing cell in 10 000, with a minimum input of 100 000 cell equivalents of DNA...
April 24, 2018: Blood Advances
https://www.readbyqxmd.com/read/29642462/new-challenges-in-targeting-signaling-pathways-in-acute-lymphoblastic-leukemia-by-ngs-approaches-an-update
#2
REVIEW
Adrián Montaño, Maribel Forero-Castro, Darnel Marchena-Mendoza, Rocío Benito, Jesús María Hernández-Rivas
The identification and study of genetic alterations involved in various signaling pathways associated with the pathogenesis of acute lymphoblastic leukemia (ALL) and the application of recent next-generation sequencing (NGS) in the identification of these lesions not only broaden our understanding of the involvement of various genetic alterations in the pathogenesis of the disease but also identify new therapeutic targets for future clinical trials. The present review describes the main deletions, amplifications, sequence mutations, epigenetic lesions, and new structural DNA rearrangements detected by NGS in B-ALL and T-ALL and their clinical importance for therapeutic procedures...
April 7, 2018: Cancers
https://www.readbyqxmd.com/read/29601269/molecular-minimal-residual-disease-in-acute-myeloid-leukemia
#3
Mojca Jongen-Lavrencic, Tim Grob, Diana Hanekamp, François G Kavelaars, Adil Al Hinai, Annelieke Zeilemaker, Claudia A J Erpelinck-Verschueren, Patrycja L Gradowska, Rosa Meijer, Jacqueline Cloos, Bart J Biemond, Carlos Graux, Marinus van Marwijk Kooy, Markus G Manz, Thomas Pabst, Jakob R Passweg, Violaine Havelange, Gert J Ossenkoppele, Mathijs A Sanders, Gerrit J Schuurhuis, Bob Löwenberg, Peter J M Valk
BACKGROUND: Patients with acute myeloid leukemia (AML) often reach complete remission, but relapse rates remain high. Next-generation sequencing enables the detection of molecular minimal residual disease in virtually every patient, but its clinical value for the prediction of relapse has yet to be established. METHODS: We conducted a study involving patients 18 to 65 years of age who had newly diagnosed AML. Targeted next-generation sequencing was carried out at diagnosis and after induction therapy (during complete remission)...
March 29, 2018: New England Journal of Medicine
https://www.readbyqxmd.com/read/29575541/simultaneous-detection-of-abl1-mutation-and-ikzf1-deletion-in-philadelphia-chromosome-positive-acute-lymphoblastic-leukemia-using-a-customized-target-enrichment-system-panel
#4
M Aoe, H Ishida, T Matsubara, S Karakawa, H Kawaguchi, K Fujiwara, K Kanamitsu, K Washio, K Okada, M Shibakura, A Shimada
INTRODUCTION: Recent clinical outcomes of pediatric Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph+ALL) vastly improved owing to tyrosine kinase inhibitor (TKI). However, the genetic status would be different in each case with ABL1 gene mutation or copy number variants (CNVs) such as IKZF1 deletion. In particular, the TKI resistant clone with ABL1 kinase mutation remains problematic. The comprehensive assessment of genetic status including mutation, insertion and deletion (indel) and CNVs is necessary...
March 25, 2018: International Journal of Laboratory Hematology
https://www.readbyqxmd.com/read/29563537/mutation-patterns-identify-adult-patients-with-de-novo-acute-myeloid-leukemia-aged-60-years-or-older-who-respond-favorably-to-standard-chemotherapy-an-analysis-of-alliance-studies
#5
Ann-Kathrin Eisfeld, Jessica Kohlschmidt, Krzysztof Mrózek, James S Blachly, Christopher J Walker, Deedra Nicolet, Shelley Orwick, Sophia E Maharry, Andrew J Carroll, Richard M Stone, Albert de la Chapelle, Eunice S Wang, Jonathan E Kolitz, Bayard L Powell, John C Byrd, Clara D Bloomfield
Thus far, only 5-15% of AML patients aged ≥60 years are cured with chemotherapy. Identification of patients who are less (more) likely to respond to standard chemotherapy might enable early risk stratification toward alternative treatment regimens. We used a next-generation sequencing panel of 80 cancer- and/or leukemia-associated genes to profile molecularly 423 older patients with de novo AML. Using variables identified in multivariable models and co-occurring mutations in NPM1-mutated AML, we classified the patients into good-, intermediate-, and poor-risk groups for complete remission (CR) attainment, disease-free (DFS), and overall survival (OS)...
February 25, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/29562441/-spectrum-of-somatic-mutations-and-their-prognostic-significance-in-adult-patients-with-b-cell-acute-lymphoblastic-leukemia
#6
J Feng, X Y Gong, Y J Jia, K Q Liu, Y Li, X B Dong, Q Y Fang, K Ru, Q H Li, H J Wang, X L Zhao, Y N Jia, Y Song, Z Tian, M Wang, K J Tang, J X Wang, Y C Mi
Objective: To investigate the spectrum of gene mutations in adult patients with B-acute lymphoblastic leukemia (B-ALL), and to analyze the influences of different gene mutations on prognosis. Methods: DNA samples from 113 adult B-ALL patients who administered from June 2009 to September 2015 were collected. Target-specific next generation sequencing (NGS) approach was used to analyze the mutations of 112 genes (focused on the specific mutational hotspots) and all putative mutations were compared against multiple databases to calculate the frequency spectrum...
February 14, 2018: Zhonghua Xue Ye Xue za Zhi, Zhonghua Xueyexue Zazhi
https://www.readbyqxmd.com/read/29559980/next-generation-sequencing-analysis-of-the-human-tcr%C3%AE-%C3%AE-t-cell-repertoire-reveals-shifts-in-v%C3%AE-and-v%C3%AE-usage-in-memory-populations-upon-aging
#7
Martine J Kallemeijn, François G Kavelaars, Michèle Y van der Klift, Ingrid L M Wolvers-Tettero, Peter J M Valk, Jacques J M van Dongen, Anton W Langerak
Immunological aging remodels the immune system at several levels. This has been documented in particular for the T-cell receptor (TCR)αβ+ T-cell compartment, showing reduced naive T-cell outputs and an accumulation of terminally differentiated clonally expanding effector T-cells, leading to increased proneness to autoimmunity and cancer development at older age. Even though TCRαβ+ and TCRγδ+ T-cells follow similar paths of development involving V(D)J-recombination of TCR genes in the thymus, TCRγδ+ T-cells tend to be more subjected to peripheral rather than central selection...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29544719/gene-knocked-out-chimeric-antigen-receptor-car-t-cells-tuning-up-for-the-next-generation-cancer-immunotherapy
#8
Hamid Reza Mirzaei, Hossein Pourghadamyari, Majid Rahmati, Abbas Mohammadi, Javid Sadri Nahand, Abbas Rezaei, Hamed Mirzaei, Jamshid Hadjati
Recently clinical trials utilizing genetically engineered T cells expressing a chimeric antigen receptor (CAR) that is half monoclonal antibody and half T-cell receptor have demonstrated remarkable response in patients with advanced cancers like relapsed or refractory acute lymphoblastic leukemia (ALL) and lymphoma. Moreover, emerging chimeric genome editing tools such as zinc-finger nucleases (ZNFs), transcription activator-like effector nucleases (TALENs) and clustered regulatory interspaced short palindromic repeat (CRISPR)/Cas composed of sequence-specific DNA binding module(s) linked to a non-specific DNA cleavage domain have made possible to dramatically expand the ability to manipulate cells aim to treat and/or study a wide range of diseases including cancer...
March 12, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29530751/rara-and-rarg-gene-downregulation-associated-with-ezh2-mutation-in-acute-promyelocytic-like-morphology-leukemia
#9
Nicoletta Coccaro, Antonella Zagaria, Paola Orsini, Luisa Anelli, Giuseppina Tota, Paola Casieri, Luciana Impera, Angela Minervini, Crescenzio F Minervini, Cosimo Cumbo, Elisa Parciante, Anna Mestice, Mario Delia, Claudia Brunetti, Giorgina Specchia, Francesco Albano
Most Acute Promyelocytic Leukemia (APL) patients express PML-RARA fusion; in rare cases RARA is rearranged with partner genes other than PML. To date, only two patients presenting features similar to APL showing the RARG gene rearrangement have been described. We report an Acute Myeloid Leukemia (AML) patient with morphology resembling APL without involvement of the RARA gene. Molecular and Fluorescent In Situ Hybridization (FISH) analyses excluded PML-RARA fusion and variant rearrangements involving RARA and RARG loci...
March 9, 2018: Human Pathology
https://www.readbyqxmd.com/read/29502313/epidemiology-of-malignant-lymphoma-and-recent-progress-in-research-on-adult-t-cell-leukemia-lymphoma-in-japan
#10
REVIEW
Hiroaki Miyoshi, Koichi Ohshima
The morbidity and mortality of disease vary according to the region and may also change over time. The morbidity and mortality of malignant lymphoma are also affected by differences in ethnicity, lifestyle habits, geographical area, and time period. Increasing research on malignant lymphoma has focused on its pathophysiology, diagnosis, and therapeutic treatment. Recent improvements in the accuracy of clinical study, technologies such as next-generation sequencing, and the development of targeted molecular agents have also resulted in a number of excellent studies...
March 3, 2018: International Journal of Hematology
https://www.readbyqxmd.com/read/29496691/genetic-landscape-of-acute-myeloid-leukemia-interrogated-by-next-generation-sequencing-a-large-cancer-center-experience
#11
Mohammad Omar Hussaini, Abu-Sayeef Mirza, Rami Komrokji, Jeffrey Lancet, Eric Padron, Jinming Song
BACKGROUND/AIM: Acute myeloid leukemia (AML) represents a heterogeneous disease with varying morphologic, immunophenotypic, and genetic features, along with varying patient outcomes. The genomic tractability of AML makes it amenable for targeted next-generation sequencing (NGS) testing clinically. MATERIALS AND METHODS: One hundred eights-seven unique patients with a diagnosis of acute myeloid leukemia between May 2011 and Oct 2014 and with mutational analysis by NGS were included in this study...
March 2018: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/29492206/mixed-phenotype-acute-leukemia-contains-heterogeneous-genetic-mutations-by-next-generation-sequencing
#12
Andrés E Quesada, Zhihong Hu, Mark J Routbort, Keyur P Patel, Rajyalakshmi Luthra, Sanam Loghavi, Zhuang Zuo, C Cameron Yin, Rashmi Kanagal-Shamanna, Sa A Wang, Jeffrey L Jorgensen, L Jeffrey Medeiros, Chi Young Ok
Mixed phenotype acute leukemia (MPAL) is an uncommon manifestation of acute leukemia. The aim of this study is to further characterize the genetic landscape of de novo cases of MPAL that fulfill the 2016 World Health Organization (WHO) classification criteria for this entity. We identified 14 cases examined by next generation sequencing (NGS) using 28 ( n = 10), 53 ( n = 3) or 81 ( n = 1) gene panels: 7 cases with a B-cell/myeloid (B/My) immunophenotype, 6 T-cell/myeloid (T/My) immunophenotype, and 1 B-cell/T-cell (B/T) immunophenotype...
February 2, 2018: Oncotarget
https://www.readbyqxmd.com/read/29491461/clinical-and-biological-implications-of-mutational-spectrum-in-acute-myeloid-leukemia-of-fab-subtypes-m4-and-m5
#13
Zhiheng Cheng, Kai Hu, Lei Tian, Yifeng Dai, Yifan Pang, Wei Cui, Hongmian Zhao, Tong Qin, Yu Han, Ning Hu, Li Chen, Chao Wang, Yijie Zhang, Depei Wu, Xiaoyan Ke, Jinlong Shi, Lin Fu
The mutational spectrum and molecular characteristics of acute myelomonocytic lineage leukemia, namely acute myeloid leukemia (AML) French-American-British (FAB) subtypes M4 and M5, are largely unknown. In order to explore the mutational spectrum and prognostic factors of FAB-M4 and -M5, next-generation sequencing (NGS) was performed to screen for mutated genes and fusion genes relevant to the pathogenesis of AML. Of the 63 patients enrolled in the study, 60% had more than three mutated genes. NPM1 had the highest mutation frequency, followed by DNMT3A, FLT3, NRAS, RUNX1, and TET2...
February 28, 2018: Cancer Gene Therapy
https://www.readbyqxmd.com/read/29481998/risk-stratification-of-oral-potentially-malignant-disorders-in-fanconi-anemia-patients-using-autofluorescence-imaging-and-cytology-on-a-chip-assay
#14
Timothy J Abram, Curtis R Pickering, Alexander K Lang, Nancy E Bass, Rameez Raja, Cynthia Meena, Amin M Alousi, Jeffrey N Myers, John T McDevitt, Ann M Gillenwater, Nadarajah Vigneswaran
Fanconi anemia (FA) is a hereditary genomic instability disorder with a predisposition to leukemia and oral squamous cell carcinomas (OSCCs). Hematopoietic stem cell transplantation (HSCT) facilitates cure of bone marrow failure and leukemia and thus extends life expectancy in FA patients; however, survival of hematologic malignancies increases the risk of OSCC in these patients. We developed a "cytology-on-a-chip" (COC)-based brush biopsy assay for monitoring patients with oral potentially malignant disorders (OPMDs)...
February 23, 2018: Translational Oncology
https://www.readbyqxmd.com/read/29476010/highly-multiplexed-and-quantitative-cell-surface-protein-profiling-using-genetically-barcoded-antibodies
#15
Samuel B Pollock, Amy Hu, Yun Mou, Alexander J Martinko, Olivier Julien, Michael Hornsby, Lynda Ploder, Jarrett J Adams, Huimin Geng, Markus Müschen, Sachdev S Sidhu, Jason Moffat, James A Wells
Human cells express thousands of different surface proteins that can be used for cell classification, or to distinguish healthy and disease conditions. A method capable of profiling a substantial fraction of the surface proteome simultaneously and inexpensively would enable more accurate and complete classification of cell states. We present a highly multiplexed and quantitative surface proteomic method using genetically barcoded antibodies called phage-antibody next-generation sequencing (PhaNGS). Using 144 preselected antibodies displayed on filamentous phage (Fab-phage) against 44 receptor targets, we assess changes in B cell surface proteins after the development of drug resistance in a patient with acute lymphoblastic leukemia (ALL) and in adaptation to oncogene expression in a Myc-inducible Burkitt lymphoma model...
February 23, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29473123/prognostic-factors-in-the-era-of-targeted-therapies-in-cll
#16
REVIEW
Prajwal Boddu, Alessandra Ferrajoli
PURPOSE OF REVIEW: Chronic lymphocytic leukemia is heterogeneous disease characterized by a variable clinical course that is greatly influenced by various patient and disease characteristics. Over the last two decades, advent of new diagnostic methodologies has led to the identification of several factors of prognostic and predictive relevance. Furthermore, recent advances in next-generation sequencing techniques has identified recurrent novel mutations in NOTCH1, SF3B1, BIRC3, and ATM genes whose role as prognostic and predictive markers is currently being investigated...
February 23, 2018: Current Hematologic Malignancy Reports
https://www.readbyqxmd.com/read/29467486/eric-recommendations-for-tp53-mutation-analysis-in-chronic-lymphocytic-leukemia-update-on-methodological-approaches-and-results-interpretation
#17
REVIEW
J Malcikova, E Tausch, D Rossi, L A Sutton, T Soussi, T Zenz, A P Kater, C U Niemann, D Gonzalez, F Davi, M Gonzalez Diaz, C Moreno, G Gaidano, K Stamatopoulos, R Rosenquist, S Stilgenbauer, P Ghia, S Pospisilova
In chronic lymphocytic leukemia (CLL), TP53 gene defects, due to deletion of the 17p13 locus and/or mutation(s) within the TP53 gene, are associated with resistance to chemoimmunotherapy and a particularly dismal clinical outcome. On these grounds, analysis of TP53 aberrations has been incorporated into routine clinical diagnostics to improve patient stratification and optimize therapeutic decisions. The predictive implications of TP53 aberrations have increasing significance in the era of novel targeted therapies, i...
February 2, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/29429887/assessment-of-capture-and-amplicon-based-approaches-for-the-development-of-a-targeted-next-generation-sequencing-pipeline-to-personalize-lymphoma-management
#18
Stacy S Hung, Barbara Meissner, Elizabeth A Chavez, Susana Ben-Neriah, Daisuke Ennishi, Martin R Jones, Hennady P Shulha, Fong Chun Chan, Merrill Boyle, Robert Kridel, Randy D Gascoyne, Andrew J Mungall, Marco A Marra, David W Scott, Joseph M Connors, Christian Steidl
Targeted next-generation sequencing panels are increasingly used to assess the value of gene mutations for clinical diagnostic purposes. For assay development, amplicon-based methods have been preferentially used on the basis of short preparation time and small DNA input amounts. However, capture sequencing has emerged as an alternative approach because of high testing accuracy. We compared capture hybridization and amplicon sequencing approaches using fresh-frozen and formalin-fixed, paraffin-embedded tumor samples from eight lymphoma patients...
February 7, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29427188/molecular-characteristic-of-acute-leukemias-with-t-16-21-fus-erg
#19
Elena Zerkalenkova, Agnesa Panfyorova, Anna Kazakova, Pavel Baryshev, Larisa Shelihova, Irina Kalinina, Galina Novichkova, Michael Maschan, Aleksey Maschan, Yulia Olshanskaya
T(16;21)(p11;q22)/FUS-ERG is a rare but recurrent translocation in acute leukemias and in some types of solid tumors. Due to multiple types of FUS-ERG transcripts, PCR-based minimal residual disease detection is impeded. In this study, we evaluated a cohort of pediatric patients with t(16;21)(p11;q22)/FUS-ERG and revealed fusion gene breakpoints. We implemented next-generation sequencing (NGS) on long PCR amplicons for the detection of fusion genes with unknown partners or DNA breakpoints. That allowed us to describe different fusion variants of FUS/ERG in different patients and to detect MRD on both RNA and DNA levels...
February 9, 2018: Annals of Hematology
https://www.readbyqxmd.com/read/29425073/sensitive-npm1-mutation-quantitation-in-acute-myeloid-leukemia-using-ultradeep-next-generation-sequencing-in-the-diagnostic-laboratory
#20
Piers Blombery, Kate Jones, Ken Doig, Georgina Ryland, Michelle McBean, Ella Thompson, Costas K Yannakou, David Westerman
CONTEXT: - Detection of measurable residual disease after therapy is an important predictor of outcome in acute myeloid leukemia. OBJECTIVE: - To investigate the feasibility of using next-generation sequencing (NGS) in the diagnostic laboratory to perform quantitative NPM1 mutation assessment using ultradeep (approximately 300 000×-500 000×) sequencing (NGS-q NPM1) as a method of assessing residual disease burden in patients with acute myeloid leukemia. DESIGN: - A flexible NGS-based assay for the detection and quantitation of NPM1 mutations was developed by polymerase chain reaction amplification of target DNA sequences, sequencing on an Illumina (San Diego, California) MiSeq, and analyzing data with an in-house-designed bioinformatic pipeline...
February 9, 2018: Archives of Pathology & Laboratory Medicine
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