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lymphoma sequencing

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https://www.readbyqxmd.com/read/28644138/comparative-analysis-of-primary-versus-relapse-refractory-dlbcl-identifies-shifts-in-mutation-spectrum
#1
Danielle M Greenawalt, Winnie S Liang, Sakina Saif, Justin Johnson, Petar Todorov, Austin Dulak, Daniel Enriquez, Rebecca Halperin, Ambar Ahmed, Vladislav Saveliev, John Carpten, David Craig, J Carl Barrett, Brian Dougherty, Michael Zinda, Stephen Fawell, Jonathan R Dry, Kate Byth
Current understanding of the mutation spectrum of relapsed/refractory (RR) tumors is limited. We performed whole exome sequencing (WES) on 47 diffuse large B cell lymphoma (DLBCL) tumors that persisted after R-CHOP treatment, 8 matched to primary biopsies. We compared genomic alterations from the RR cohort against two treatment-naïve DLBCL cohorts (n=112). While the overall number and types of mutations did not differ significantly, we identified frequency changes in DLBCL driver genes. The overall frequency of MYD88 mutant samples increased (12% to 19%), but we noted a decrease in p...
June 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28640838/next-generation-sequencing-of-the-clonal-igh-rearrangement-detects-ongoing-mutations-and-interfollicular-trafficking-in-in-situ-follicular-neoplasia
#2
Perikles Kosmidis, Irina Bonzheim, Claudia Dufke, Sema Colak, Thomas Hentrich, Christopher Schroeder, Peter Bauer, Patrick Adam, Falko Fend
Follicular lymphoma (FL) is characterized genetically by a significant intraclonal diversity of rearranged immunoglobulin heavy chain (IGH) genes and a substantial cell migration activity (follicular trafficking). Recently, in situ follicular neoplasia (ISFN), characterized by accumulations of immunohistochemically strongly BCL2-positive, t(14;18)+ clonal B cells confined to germinal centers in reactive lymph nodes, has been identified as a precursor lesion of FL with low risk of progression to manifest FL...
2017: PloS One
https://www.readbyqxmd.com/read/28636991/non-invasive-detection-of-somatic-mutations-using-next-generation-sequencing-in-primary-central-nervous-system-lymphoma
#3
Maxime Fontanilles, Florent Marguet, Élodie Bohers, Pierre-Julien Viailly, Sydney Dubois, Philippe Bertrand, Vincent Camus, Sylvain Mareschal, Philippe Ruminy, Catherine Maingonnat, Stéphane Lepretre, Elena-Liana Veresezan, Stéphane Derrey, Hervé Tilly, Jean-Michel Picquenot, Annie Laquerrière, Fabrice Jardin
PURPOSE: Primary central nervous system lymphomas (PCNSL) have recurrent genomic alterations. The main objective of our study was to demonstrate that targeted sequencing of circulating cell-free DNA (cfDNA) released by PCNSL at the time of diagnosis could identify somatic mutations by next-generation sequencing (NGS). PATIENTS AND METHODS: PlasmacfDNA and matched tumor DNA (tDNA) from 25 PCNSL patients were sequenced using an Ion Torrent Personal Genome Machine (Life Technologies®)...
June 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28634614/detection-of-the-circulating-tumor-dnas-in-angioimmunoblastic-t-cell-lymphoma
#4
Mamiko Sakata-Yanagimoto, Rie Nakamoto-Matsubara, Daisuke Komori, Tran B Nguyen, Keiichiro Hattori, Toru Nanmoku, Takayasu Kato, Naoki Kurita, Yasuhisa Yokoyama, Naoshi Obara, Yuichi Hasegawa, Atsushi Shinagawa, Shigeru Chiba
Recent genetic studies identified that the disease-specific G17V RHOA mutation, together with mutations in TET2, DNMT3A, and IDH2, is a hallmark of angioimmunoblastic T cell lymphomas (AITL). The diagnostic value of these mutations is now being investigated. Circulating tumor DNAs (ctDNAs) may offer a non-invasive testing for diagnosis and disease monitoring of cancers. To investigate whether these mutations are useful markers for ctDNAs in AITL and its related lymphomas, we performed targeted sequencing for TET2, RHOA, DNMT3A, and IDH2 in paired tumors and cell-free DNAs from 14 patients at diagnosis...
June 20, 2017: Annals of Hematology
https://www.readbyqxmd.com/read/28631441/genetic-landscape-and-deregulated-pathways-in-b-cell-lymphoid-malignancies
#5
R Rosenquist, S Beà, M-Q Du, B Nadel, Q Pan-Hammarström
With the introduction of next-generation sequencing, the genetic landscape of the complex group of B-cell lymphoid malignancies has rapidly been unravelled in recent years. This has provided important information about recurrent genetic events and identified key pathways deregulated in each lymphoma subtype. In parallel, there has been intense search and development of novel types of targeted therapy that 'hit' central mechanisms in lymphoma pathobiology, such as BTK, PI3K or BCL2 inhibitors. In this review, we will outline the current view of the genetic landscape of selected entities: follicular lymphoma, diffuse large B-cell lymphoma, mantle cell lymphoma, chronic lymphocytic leukaemia and marginal zone lymphoma...
June 20, 2017: Journal of Internal Medicine
https://www.readbyqxmd.com/read/28630229/observing-clonal-dynamics-across-spatiotemporal-axes-a-prelude-to-quantitative-fitness-models-for-cancer
#6
Andrew W McPherson, Fong Chun Chan, Sohrab P Shah
The ability to accurately model evolutionary dynamics in cancer would allow for prediction of progression and response to therapy. As a prelude to quantitative understanding of evolutionary dynamics, researchers must gather observations of in vivo tumor evolution. High-throughput genome sequencing now provides the means to profile the mutational content of evolving tumor clones from patient biopsies. Together with the development of models of tumor evolution, reconstructing evolutionary histories of individual tumors generates hypotheses about the dynamics of evolution that produced the observed clones...
June 19, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28628241/aberrant-expression-of-cd10-and-bcl6-in-mantle-cell-lymphoma
#7
Marco Pizzi, Claudio Agostinelli, Simona Righi, Anna Gazzola, Claudia Mannu, Francesca Galuppini, Matteo Fassan, Andrea Visentin, Francesco Piazza, Gianpietro C Semenzato, Massimo Rugge, Elena Sabattini
AIMS: Mantle cell lymphoma (MCL) is characterized by distinctive histologic and molecular features. Aberrant expression of BCL6 and CD10 has occasionally been reported, but the biological features of such cases are largely unknown. This study aimed to define the epidemiologic, histologic and cytogenetic characteristics of BCL6 and CD10-positive MCLs, also investigating possible biological features. METHODS AND RESULTS: 165 cases of cyclin D1 and t(11;14)(q13;q34) positive MCLs were studied for CD10 and BCL6 immunohistochemical expression which was documented in 26/165 (15...
June 19, 2017: Histopathology
https://www.readbyqxmd.com/read/28627637/lentiviral-vector-mediated-co-overexpression-of-vegf-and-bcl-2-improves-mesenchymal-stem-cell-survival-and-enhances-paracrine-effects-in%C3%A2-vitro
#8
Xiaobin Ni, Caiwen Ou, Jingbin Guo, Bei Liu, Jianwu Zhang, Zhiye Wu, Hekai Li, Minsheng Chen
Mesenchymal stem cell (MSC) transplantation has emerged as a promising therapy for ischemic heart disease; however, the low survival rate of transplanted cells limits their therapeutic efficacy. The aim of this study was to investigate whether the dual genetic modification of vascular endothelial growth factor (VEGF) and B‑cell lymphoma‑2 (Bcl‑2) confers a higher expression level of the target genes, better survival and a stronger paracrine effect in MSCs in an adverse environment than the modification of the individual genes...
June 12, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28625332/considerations-of-developing-an-ngs-assay-for-clinical-applications-in-precision-oncology-the-nci-match-ngs-assay-experience
#9
Chih-Jian Lih, Naoko Takebe
Next generation sequencing (NGS) technologies have been widely adapted in clinical oncology by utilizing the profiled genetic mutation information to select patients and to guide the choice of target therapy. To fulfill the regulatory compliance, development of an NGS assay that will be used in clinical trials requires an analytical validation to meet its intend clinical use. NCI-MATCH trial is the largest precision oncology basket trial which uses a single NGS assay (NCI-MATHC NGS assay) to screen the actionable mutations in 6000 patients, who have relapsed/refractory solid tumors and lymphomas after standard systemic treatment, and assigns matched treatment...
May 2017: Current Problems in Cancer
https://www.readbyqxmd.com/read/28622960/treatment-of-peripheral-t-cell-lymphoma-in-community-settings
#10
Tatyana Feldman, Charles M Farber, Kelly Choi, Claudio Faria, Andre Goy, Jacqueline Connors, Dhakshila Paramanathan, Sukhi Kaur, Eric Schultz, Michael McGuire, Stuart L Goldberg
BACKGROUND: Peripheral T-cell lymphomas (PTCLs) represent a rare and heterogeneous group of malignancies that do not have consensus treatment recommendations. Strategies extrapolated from B-cell lymphoma have met with limited efficacy, although T-cell-specific salvage therapies have been recently developed. METHODS: To determine treatment patterns and associated outcomes in PTCL not otherwise specified (PTCL-NOS), anaplastic large T-cell lymphoma (ALCL), and angioimmunoblastic T-cell lymphoma (AITL), a retrospective analysis was undertaken at a large US community oncology network among patients treated between January 2010 and April 2015...
June 2017: Clinical Lymphoma, Myeloma & Leukemia
https://www.readbyqxmd.com/read/28608966/next-generation-sequencing-and-clinical-outcomes-of-patients-with-lung-adenocarcinoma-treated-with-stereotactic-body-radiotherapy
#11
Richard J Cassidy, Xinyan Zhang, Pretesh R Patel, Joseph W Shelton, Chase E Escott, Gabriel L Sica, Michael R Rossi, Charles E Hill, Conor E Steuer, Rathi N Pillai, Suresh S Ramalingam, Taofeek K Owonikoko, Madhusmita Behera, Seth D Force, Felix G Fernandez, Walter J Curran, Kristin A Higgins
BACKGROUND: Genetic aberrations are well characterized in lung adenocarcinomas (LACs) and clinical outcomes have been influenced by targeted therapies in the advanced setting. Stereotactic body radiotherapy (SBRT) is the standard-of-care therapy for patients with nonoperable, early-stage LAC, but to the authors' knowledge, no information is available regarding the impact of genomic changes in these patients. The current study sought to determine the frequency and clinical impact of genetic aberrations in this population...
June 13, 2017: Cancer
https://www.readbyqxmd.com/read/28607809/rapid-response-of-brain-metastasis-to-crizotinib-in-a-patient-with-klc1-alk-fusion-and-met-gene-amplification-positive-non-small-cell-lung-cancer-a-case-report
#12
Peng Wang, Pei Xiao, Yingnan Ye, Pengpeng Liu, Lei Han, Li Dong, Chunhua She, Jinpu Yu
Non-small cell lung cancer (NSCLC) ranks as the leading cause of cancer-related death in the world. Brain metastasis (BM) is a common complication of NSCLC, with 25%-40% of patients developing BM during the course of the disease. A significant strategy of local disease control in the central nervous system is radiation therapy. With the development of precision medicine, the concept of treating lung cancer BM has gradually changed. In this case, we performed a surgical procedure to obtain enough tumor tissue for the detection of the target gene and other related experiments after the patient was informed...
May 2017: Cancer Biology & Medicine
https://www.readbyqxmd.com/read/28607076/functional-proteogenomics-reveals-biomarkers-and-therapeutic-targets-in-lymphomas
#13
Delphine C M Rolland, Venkatesha Basrur, Yoon-Kyung Jeon, Carla McNeil-Schwalm, Damian Fermin, Kevin P Conlon, Yeqiao Zhou, Samuel Y Ng, Chih-Chiang Tsou, Noah A Brown, Dafydd G Thomas, Nathanael G Bailey, Gilbert S Omenn, Alexey I Nesvizhskii, David E Root, David M Weinstock, Robert B Faryabi, Megan S Lim, Kojo S J Elenitoba-Johnson
Identification of biomarkers and therapeutic targets is a critical goal of precision medicine. N-glycoproteins are a particularly attractive class of proteins that constitute potential cancer biomarkers and therapeutic targets for small molecules, antibodies, and cellular therapies. Using mass spectrometry (MS), we generated a compendium of 1,091 N-glycoproteins (from 40 human primary lymphomas and cell lines). Hierarchical clustering revealed distinct subtype signatures that included several subtype-specific biomarkers...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28606801/molecular-cloning-characterization-and-expression-analysis-of-b-cell-lymphoma-2-bcl-2-in-the-orange-spotted-grouper-epinephelus-coioides
#14
Sheng-Wei Luo, Huan Kang, Jing-Rong Kong, Ren-Chong Xie, Yuan Liu, Wei-Na Wang, Fu-Xing Xie, Cong Wang, Zuo-Ming Sun
Bcl-2 is a pro-survival member of Bcl-2 like superfamily, playing an important role in regulating the apoptotic process. In this study, the full-length Bcl-2 (EcBcl-2) was obtained, consisting of a 5'UTR of 290 bp, an ORF of 699 bp and a 3'UTR of 920 bp. EcBcl-2 gene encoded a polypeptide of 232 amino acids with an estimated molecular mass of 26.12 KDa and a predicted isoelectric point (pI) of 6.93. The deduced amino acid sequence analysis showed that EcBcl-2 consisted of the conserved residues and characteristic domains known to the critical functionality for Bcl-2...
June 9, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28606064/bacteremia-due-to-gordonia-polyisoprenivorans-case-report-and-review-of-literature
#15
Xiurong Ding, Yanhua Yu, Ming Chen, Chen Wang, Yanfang Kang, Hongman Li, Jinli Lou
BACKGROUND: Gordonia polyisoprenivorans is a ubiquitous aerobic actinomycetes bacterium that rarely cause infections in humans. Here, we report a case of G. polyisoprenivorans catheter-related bacteremia in an AIDS patient. CASE PRESENTATION: A 37-year-old man with a past medical history of AIDS-related lymphoma suffered bacteremia caused by a Gram-positive corynebacterium. The strain was identified as a Gordonia species by matrix-assisted laser desorption ionization-time of flight mass spectrometry and confirmed to G...
June 12, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28599078/non-lesional-atopic-dermatitis-skin-shares-similar-t-cell-clones-with-lesional-tissues
#16
Patrick M Brunner, Ryan O Emerson, Christopher Tipton, Sandra Garcet, Saakshi Khattri, Israel Coats, James G Krueger, Emma Guttman-Yassky
BACKGROUND: Atopic dermatitis (AD) is characterized by robust immune activation. Various T-cell subsets, including Th2/Th22 cells, are increased in lesional and non-lesional skin. However, there is conflicting literature on the diversity of the T-cell receptor (TCR) repertoire in lesional AD, and its relation to non-lesional skin remains unclear. METHODS: We performed high-throughput deep sequencing of the β-TCR repertoire in 29 lesional and 19 non-lesional AD biopsies, compared to 6 healthy control and 6 cutaneous T-cell lymphoma (CTCL) samples from previously published cohorts...
June 9, 2017: Allergy
https://www.readbyqxmd.com/read/28595732/the-novel-double-hit-t-8-22-q24-q11-myc-igl-and-t-14-15-q32-q24-igh-bcl2a1-in-diffuse-large-b-cell-lymphoma
#17
Takashi Akasaka, Chiyuki Kishimori, Katsuhiro Fukutsuka, Miho Nakagawa, Kayo Takeoka, Masahiko Hayashida, Gen Honjo, Hitoshi Ohno
An 82-year-old woman presented with generalized lymphadenopathy and skin involvement. Lymph node biopsy revealed diffuse large B-cell lymphoma with a high proliferation index. G-banding and fluorescence in situ hybridization showed a hypertetraploid karyotype with two copies of t(8;22)(q24;q11), generating the fusion of MYC and the immunoglobulin λ chain gene (IGL), and two copies of the novel immunoglobulin heavy chain gene (IGH) translocation, t(14;15)(q32;q24). A long-distance inverse polymerase chain reaction (PCR) using nested primer combinations designed for each constant gene of IGH showed that Cγ4 was juxtaposed to the downstream sequence of the BCL2A1 (BCL2-related protein A1) gene through the Sγ4 switch region...
August 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28589362/determining-the-origin-of-human-germinal-center-b-cell-derived-malignancies
#18
Marc Seifert, Ralf Küppers
Most human B cell lymphomas originate from germinal center (GC) B cells. This is partly caused by the high proliferative activity of GC B cells and the remodeling processes acting at the immunoglobulin (Ig) loci of these cells, i.e., somatic hypermutation and class-switching. Mistargeting of these processes can cause chromosomal translocations, and the hypermutation machinery may also target non-Ig genes. As somatic hypermutation is exclusively active in GC B cells, the presence of somatic mutations in rearranged IgV genes is a standard criterium for a GC or post-GC B cell origin of lymphomas...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28561693/age-and-sex-in-non-hodgkin-lymphoma-therapy-it-s-not-all-created-equal-or-is-it
#19
Michael Pfreundschuh
Age is the most prominent factor for survival in all patients diagnosed with lymphoma, and male sex implies an increased and independent risk for a worse progression-free survival (PFS) and overall survival (OS) in most lymphomas, possibly with the exception of mantle cell lymphoma (MCL). The worse outcome for elderly patients is only partially explained by decreased tolerance to treatment regimens associated with the increasing number and severity of comorbidities. Little is known about specific differences in lymphoma biology with respect to age and sex, and this is changing only slowly despite the recent rise in interest about these issues...
2017: American Society of Clinical Oncology Educational Book
https://www.readbyqxmd.com/read/28561224/variant-pik3r1-hypermorphic-mutation-and-clinical-phenotypes-in-a-family-with-short-statures-mild-immunodeficiency-and-lymphoma
#20
Fabian Hauck, Thomas Magg, Ana Krolo, Ivan Bilic, Tatjana Hirschmugl, Martin Laass, Angela Rösen-Wolff, Hella Luksch, Kaan Boztug, Joachim Roesler
Background Heterozygous point mutations in the GT splice donor consensus sequence of exon 11 of the PIK3R1 gene (coding for p85α, p55α, and p50α regulatory subunits of PI3K) lead to exon skipping and thereby to an aberrant protein that leaves PI3K hyperactivated. Several patients with this particular variant of PI3 kinase delta syndrome (APDS) suffering from sinopulmonary infections and lymphoproliferation have been described. Methods (Whole exome) sequencing, evaluation of cellular and clinical phenotypes...
May 2017: Klinische Pädiatrie
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