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Next generation sequencing leukemia

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https://www.readbyqxmd.com/read/29035575/hetfhmm-a-novel-approach-to-infer-tumor-heterogeneity-using-factorial-hidden-markov-models
#1
Mohammad S Rahman, Ann E Nicholson, Gholamreza Haffari
Cancer arises from successive rounds of mutations, resulting in tumor cells with different somatic mutations known as clones. Drug responsiveness and therapeutics of cancer depend on the accurate detection of clones in a tumor sample. Recent research has considered inferring clonal composition of a tumor sample using computational models based on short read data of the sample generated using next-generation sequencing (NGS) technology. Short reads (segmented DNA parts of different tumor cells) are noisy; therefore, inferring the clones and their mutations from the data is a difficult and complex problem...
October 16, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29032017/editorial-next-generation-sequencing-technology-a-new-tool-for-killer-cell-immunoglobulin-like-receptor-allele-typing-in-hematopoietic-stem-cell-transplantation
#2
B Maniangou, C Retière, K Gagne
Killer cell Immunoglobulin-like Receptor (KIR) genes are a family of genes located together within the leukocyte receptor cluster on human chromosome 19q13.4. To date, 17 KIR genes have been identified including nine inhibitory genes (2DL1/L2/L3/L4/L5A/L5B, 3DL1/L2/L3), six activating genes (2DS1/S2/S3/S4/S5, 3DS1) and two pseudogenes (2DP1, 3DP1) classified into group A (KIR A) and group B (KIR B) haplotypes. The number and the nature of KIR genes vary between the individuals. In addition, these KIR genes are known to be polymorphic at allelic level (907 alleles described in July 2017)...
October 11, 2017: Transfusion Clinique et Biologique: Journal de la Société Française de Transfusion Sanguine
https://www.readbyqxmd.com/read/29027628/the-prognostic-significance-of-measurable-minimal-residual-disease-in-acute-myeloid-leukemia
#3
REVIEW
Francesco Buccisano, Christopher S Hourigan, Roland B Walter
PURPOSE OF REVIEW: The purpose of this review was to evaluate recent literature on detection methodologies for, and prognostic significance of, measurable ("minimal") residual disease (MRD) in acute myeloid leukemia (AML). RECENT FINDINGS: There is no "one-fits-all" approach to MRD testing in AML. Most exploited to date are methods relying on immunophenotypic aberrancies (identified via multiparameter flow cytometry) or genetic abnormalities (identified via PCR-based assays)...
October 13, 2017: Current Hematologic Malignancy Reports
https://www.readbyqxmd.com/read/28978836/mds-recent-progress-in-molecular-pathogenesis-and-clinical-aspects
#4
Hironori Harada
Myelodysplastic syndromes (MDS) are defined as hematopoietic stem cell disorders caused by various gene abnormalities. Recent analysis using next generation sequencing has provided great progress in identifying relationships between gene mutations and clinical phenotypes of MDS. It is estimated that one or more gene mutations occur in greater than 90% of MDS patients. More than 50 gene mutations affecting RNA splicing machinery, DNA methylation, histone modifications, transcription factors, signal transduction proteins, and components of the cohesion complex participate in the pathogenesis of MDS...
2017: [Rinshō Ketsueki] the Japanese Journal of Clinical Hematology
https://www.readbyqxmd.com/read/28978834/molecular-biology-and-treatment-of-cml
#5
Shinya Kimura
Since the development of imatinib mesylate, an ABL tyrosine kinase inhibitor (TKI), the treatment of chronic myeloid leukemia (CML) has made remarkable progress. Second and third generation TKIs have also become available for clinical use. Considering the improved treatment outcomes, chronic phase CML has become manageable, with a low mortality rate. Furthermore, clinical trials such as STIM and DADI have shown that TKI can be discontinued safely in certain CML patients. However, some CML patients, especially those in accelerated phase (AP) or blast phase (BP), require more aggressive forms of treatment such as allogenic hematopoietic stem cell transplantation...
2017: [Rinshō Ketsueki] the Japanese Journal of Clinical Hematology
https://www.readbyqxmd.com/read/28978832/clinical-sequencing-in-leukemia-with-the-assistance-of-artificial-intelligence
#6
Arinobu Tojo
Next generation sequencing (NGS) of cancer genomes is now becoming a prerequisite for accurate diagnosis and proper treatment in clinical oncology. Because the genomic regions for NGS expand from a certain set of genes to the whole exome or whole genome, the resulting sequence data becomes incredibly enormous and makes it quite laborious to translate the genomic data into medicine, so-called annotation and curation. We organized a clinical sequencing team and established a bidirectional (bed-to-bench and bench-to-bed) system to integrate clinical and genomic data for hematological malignancies...
2017: [Rinshō Ketsueki] the Japanese Journal of Clinical Hematology
https://www.readbyqxmd.com/read/28967088/uncommon-somatic-mutations-in-metastatic-nut-midline-carcinoma
#7
Stefano Cavalieri, Anastasios Stathis, Alessandra Fabbri, Angelica Sonzogni, Federica Perrone, Elena Tamborini, Giuseppe Pelosi, Filippo de Braud, Marco Platania
INTRODUCTION: NUT midline carcinoma (NMC) is a rare and aggressive epithelial cancer arising from median organs. It is driven by chromosomal translocation t(15;19) involving the rearrangement of NUT (nuclear protein in testis) and BRD4 (bromodomain 4) genes leading to fusion oncoprotein BRD4-NUT. CASE PRESENTATION: We report the case of a woman who was previously treated with induction chemotherapy, surgery, radiotherapy and adjuvant trastuzumab for HER-2 positive invasive ductal carcinoma of the breast...
September 25, 2017: Tumori
https://www.readbyqxmd.com/read/28933999/minimal-residual-disease-assessment-in-lymphoma-methods-and-applications
#8
Alex F Herrera, Philippe Armand
Standard methods for disease response assessment in patients with lymphoma, including positron emission tomography and computed tomography scans, are imperfect. In other hematologic malignancies, particularly leukemias, the ability to detect minimal residual disease (MRD) is increasingly influencing treatment paradigms. However, in many subtypes of lymphoma, the application of MRD assessment techniques, like flow cytometry or polymerase chain reaction-based methods, has been challenging because of the absence of readily detected circulating disease or canonic chromosomal translocations...
September 21, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28933735/clinical-outcomes-and-co-occurring-mutations-in-patients-with-runx1-mutated-acute-myeloid-leukemia
#9
Maliha Khan, Jorge Cortes, Tapan Kadia, Kiran Naqvi, Mark Brandt, Sherry Pierce, Keyur P Patel, Gautam Borthakur, Farhad Ravandi, Marina Konopleva, Steven Kornblau, Hagop Kantarjian, Kapil Bhalla, Courtney D DiNardo
(1) Runt-related transcription factor 1 (RUNX1) mutations in acute myeloid leukemia (AML) are often associated with worse prognosis. We assessed co-occurring mutations, response to therapy, and clinical outcomes in patients with and without mutant RUNX1 (mRUNX1); (2) We analyzed 328 AML patients, including 177 patients younger than 65 years who received intensive chemotherapy and 151 patients >65 years who received hypomethylating agents. RUNX1 and co-existing mutations were identified using next-generation sequencing; (3) RUNX1 mutations were identified in 5...
July 26, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28927162/myelodysplastic-syndrome-unclassifiable-mds-u-with-1-blasts-is-a-distinct-subgroup-of-mds-u-with-a-poor-prognosis
#10
Elizabeth Margolskee, Robert P Hasserjian, Duane Hassane, Wayne Tam, Susan Mathew, Chi Young Ok, Sa A Wang, Jean Oak, Daniel A Arber, Attilio Orazi
Objectives: Three situations qualify as myelodysplastic syndrome, unclassifiable (MDS-U): (1) refractory cytopenia with dysplasia and 1% blasts in peripheral blood (BL), (2) pancytopenia with unilineage dysplasia (Pan), and (3) persistent cytopenia, less than 5% bone marrow blasts, and less than 10% dysplastic cells and presence of MDS-defining cytogenetic abnormalities (CG). We compared the clinicopathologic features and mutational profiles for these three groups. Methods: MDS-U cases were reviewed at four major academic institutions...
July 1, 2017: American Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28925935/technical-advances-in-the-measurement-of-residual-disease-in-acute-myeloid-leukemia
#11
REVIEW
Gregory W Roloff, Catherine Lai, Christopher S Hourigan, Laura W Dillon
Outcomes for those diagnosed with acute myeloid leukemia (AML) remain poor. It has been widely established that persistent residual leukemic burden, often referred to as measurable or minimal residual disease (MRD), after induction therapy or at the time of hematopoietic stem cell transplant (HSCT) is highly predictive for adverse clinical outcomes and can be used to identify patients likely to experience clinically evident relapse. As a result of inherent genetic and molecular heterogeneity in AML, there is no uniform method or protocol for MRD measurement to encompass all cases...
September 19, 2017: Journal of Clinical Medicine
https://www.readbyqxmd.com/read/28924241/clinical-impact-of-the-subclonal-architecture-and-mutational-complexity-in-chronic-lymphocytic-leukemia
#12
F Nadeu, G Clot, J Delgado, D Martín-García, T Baumann, I Salaverria, S Beà, M Pinyol, P Jares, A Navarro, H Suárez-Cisneros, M Aymerich, M Rozman, N Villamor, D Colomer, M González, M Alcoceba, M J Terol, B Navarro, E Colado, Á R Payer, X S Puente, C López-Otín, A López-Guillermo, A Enjuanes, E Campo
Genome studies of chronic lymphocytic leukemia (CLL) have revealed the remarkable subclonal heterogeneity of the tumors, but the clinical implications of this phenomenon are not well known. We assessed the mutational status of 28 CLL driver genes by deep-targeted next-generation sequencing and copy number alterations (CNA) in 406 previously untreated patients and 48 sequential samples. We detected small subclonal mutations (0.6-25% of cells) in nearly all genes (26/28), and they were the sole alteration in 22% of the mutated cases...
September 19, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28923882/mutational-profiling-of-acute-myeloid-leukemia-with-normal-cytogenetics-in-brazilian-patients-the-value-of-next-generation-sequencing-for-genomic-classification
#13
Thiago Rodrigo de Noronha, Miguel Mitne-Neto, Maria de Lourdes Chauffaille
Karyotype (KT) aberrations are important prognostic factors for acute myeloid leukemia (AML); however, around 50% of cases present normal results. Single nucleotide polymorphism array can detect chromosomal gains, losses or uniparental disomy that are invisible to KT, thus improving patients' risk assessment. However, when both tests are normal, important driver mutations can be detected by the use of next-generation sequencing (NGS). Fourteen adult patients with AML with normal cytogenetics were investigated by NGS for 19 AML-related genes...
September 18, 2017: Journal of Investigative Medicine: the Official Publication of the American Federation for Clinical Research
https://www.readbyqxmd.com/read/28913558/only-setbp1-hotspot-mutations-are-associated-with-refractory-disease-in-myeloid-malignancies
#14
Nils Winkelmann, Vivien Schäfer, Jenny Rinke, Alexander Kaiser, Philipp Ernst, Sebastian Scholl, Andreas Hochhaus, Thomas Ernst
INTRODUCTION: SETBP1 mutations have been established as a diagnostic marker in myeloid malignancies and are associated with inferior survival. Since there is limited data on their clinical impact and stability during disease progression, we sought to investigate the relationship between SETBP1 mutations and disease evolution. METHODS: Bidirectional Sanger sequencing of the SETBP1 gene was performed for 442 unselected patients with World Health Organization (WHO) defined myeloid disorders...
September 14, 2017: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28883284/pediatric-acute-myeloid-leukemia-with-genetic-alterations
#15
Akira Shimada
Annually, it is estimated that approximately 150-200 children aged 0-16 years are diagnosed with acute myeloid leukemia (AML). In Japan, clinical studies with ANLL91, AML99, CCLSG-AML9805, and JPLSG-AML05 protocols were performed historically, and the risk stratification with a combination of chemotherapy and hematopoietic stem cell transplantation resulted in the improvement of clinical outcomes. Regarding the onset of pediatric AML at the molecular level, mutations in FLT3-ITD or KIT (Class I mutation) showed a poor prognosis, but the ratio of mutations in Class III-V genes was smaller than that in adult AML...
2017: [Rinshō Ketsueki] the Japanese Journal of Clinical Hematology
https://www.readbyqxmd.com/read/28875545/targeted-next-generation-sequencing-in-myelodysplastic-syndromes-and-prognostic-interaction-between-mutations-and-ipss-r
#16
Ayalew Tefferi, Terra L Lasho, Mrinal M Patnaik, Lyla Saeed, Mythri Mudireddy, Dame Idossa, Christy Finke, Rhett P Ketterling, Animesh Pardanani, Naseema Gangat
A 27-gene panel was used for next-generation sequencing (NGS) in 179 patients (median age 73 years) with primary myelodysplastic syndromes (MDS); risk distribution according to the revised International Prognostic Scoring System (IPSS-R) was 11% very high, 18% high, 17% intermediate, 38% low and 16% very low. At least one mutation/variant was detected in 147 (82%) patients; 23% harbored three or more mutations/variants. The most frequent mutations/variants included ASXL1 (30%), TET2 (25%), SF3B1 (20%), U2AF1 (16%), SRSF2 (16%), TP53 (13%), RUNX1 (11%) and DNMT3A (10%)...
September 5, 2017: American Journal of Hematology
https://www.readbyqxmd.com/read/28860343/antigen-receptor-sequencing-of-paired-bone-marrow-samples-shows-homogeneous-distribution-of-acute-lymphoblastic-leukemia-subclones
#17
Prisca M J Theunissen, David van Zessen, Andrew P Stubbs, Malek Faham, Michel Zwaan, Jacques J M van Dongen, Vincent H J Van der Velden
In B-cell precursor acute lymphoblastic leukemia, the initial leukemic cells share the same antigen receptor gene rearrangements. However, due to ongoing rearrangement processes, leukemic cells with different gene rearrangement patterns can develop, resulting in subclone formation. We studied leukemic subclones and their distribution in the bone marrow and peripheral blood at diagnosis. Antigen receptor gene rearrangements (IGH, IGK, TRG, TRD, TRB) were analyzed by next-generation sequencing in seven paired bone marrow samples and five paired bone marrow-blood samples...
August 31, 2017: Haematologica
https://www.readbyqxmd.com/read/28837890/fragment-analysis-represents-a-suitable-approach-for-the-detection-of-hotspot-c-7541_7542delct-notch1-mutation-in-chronic-lymphocytic-leukemia
#18
Eva Vavrova, Barbara Kantorova, Barbara Vonkova, Jitka Kabathova, Hana Skuhrova-Francova, Eva Diviskova, Ondrej Letocha, Jana Kotaskova, Yvona Brychtova, Michael Doubek, Jiri Mayer, Sarka Pospisilova
The hotspot c.7541_7542delCT NOTCH1 mutation has been proven to have a negative clinical impact in chronic lymphocytic leukemia (CLL). However, an optimal method for its detection has not yet been specified. The aim of our study was to examine the presence of the NOTCH1 mutation in CLL using three commonly used molecular methods. Sanger sequencing, fragment analysis and allele-specific PCR were compared in the detection of the c.7541_7542delCT NOTCH1 mutation in 201 CLL patients. In 7 patients with inconclusive mutational analysis results, the presence of the NOTCH1 mutation was also confirmed using ultra-deep next generation sequencing...
August 7, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28805986/histiocytic-sarcoma-new-insights-into-fna-cytomorphology-and-molecular-characteristics
#19
Yin P Hung, Scott B Lovitch, Xiaohua Qian
BACKGROUND: Histiocytic sarcoma (HS) is a rare malignant neoplasm showing morphologic and immunophenotypic features of histiocytes. Molecular characteristics of HS and fine-needle aspiration (FNA) criteria for its diagnosis have not been established. METHODS: A case series of HS in 8 FNA samples from 6 patients was reviewed along with histopathologic and clinical data. Immunohistochemistry was performed on cell blocks (3 cases), core biopsies (5 cases), and surgical specimens (4 cases)...
August 2017: Cancer
https://www.readbyqxmd.com/read/28804123/integrating-genomic-alterations-in-diffuse-large-b-cell-lymphoma-identifies-new-relevant-pathways-and-potential-therapeutic-targets
#20
K Karube, A Enjuanes, I Dlouhy, P Jares, D Martin-Garcia, F Nadeu, G R Ordóñez, J Rovira, G Clot, C Royo, A Navarro, B Gonzalez-Farre, A Vaghefi, G Castellano, C Rubio-Perez, D Tamborero, J Briones, A Salar, J M Sancho, S Mercadal, E Gonzalez-Barca, L Escoda, H Miyoshi, K Ohshima, K Miyawaki, K Kato, K Akashi, A Mozos, L Colomo, M Alcoceba, A Valera, A Carrió, D Costa, N Lopez-Bigas, R Schmitz, L M Staudt, I Salaverria, A López-Guillermo, E Campo
Genome studies of diffuse large B-cell lymphoma (DLBCL) have revealed a large number of somatic mutations and structural alterations. However, the clinical significance of these alterations is still not well defined. In this study, we have integrated the analysis of targeted next-generation sequencing of 106 genes and genomic copy number alterations (CNA) in 150 DLBCL. The clinically significant findings were validated in an independent cohort of 111 patients. Germinal center B-cell and activated B-cell DLBCL had a differential profile of mutations, altered pathogenic pathways and CNA...
August 14, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
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