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Journal articles on the topic 'For SNVQ Intermediate'

Author: Grafiati

Published: 4 June 2021

Last updated: 27 July 2025

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1

Tu, Kailing, Keying Lu, Qilin Zhang, Wei Huang, and Dan Xie. "Accurate single-cell genotyping utilizing information from the local genome territory." Nucleic Acids Research 49, no. 10 (2021): e57-e57. http://dx.doi.org/10.1093/nar/gkab106.

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Abstract Single-nucleotide variant (SNV) detection in the genome of single cells is affected by DNA amplification artefacts, including imbalanced alleles and early PCR errors. Existing single-cell genotyper accuracy often depends on the quality and coordination of both the target single-cell and external data, such as heterozygous profiles determined by bulk data. In most single-cell studies, information from different sources is not perfectly matched. High-accuracy SNV detection with a limited single data source remains a challenge. We developed a new variant detection method, SCOUT (Single C

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Massey, Steven E., Adrian Jones, Daoyu Zhang, Yuri Deigin, and Steven C. Quay. "Unwarranted Exclusion of Intermediate Lineage A-B SARS-CoV-2 Genomes Is Inconsistent with the Two-Spillover Hypothesis of the Origin of COVID-19." Microbiology Research 14, no. 1 (2023): 448–53. http://dx.doi.org/10.3390/microbiolres14010033.

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Pekar et al. (2022) propose that SARS-CoV-2 was a zoonotic spillover that first infected humans in the Huanan Seafood Market in Wuhan, China. They propose that there were two separate spillovers of the closely related lineages A and lineage B in a short period of time. The two lineages are differentiated by two SNVs; hence, a single-SNV A-B intermediate must have occurred in an unsampled animal host if the two-spillover hypothesis is correct. Consequently, confirmation of the existence of an intermediate A-B genome from humans would falsify their hypothesis of two spillovers. Pekar et al. iden

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Stopka, Tomas, Karin Vargova, Vojtech Kulvait, Nina Dusilkova, and Anna T. Jonasova. "Somatic Mutation-Detecting Algorithm Enables Analysis of MDS Patients during Azacitidine Therapy." Blood 124, no. 21 (2014): 5600. http://dx.doi.org/10.1182/blood.v124.21.5600.5600.

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Abstract Introduction: Somatic mutation detection in myelodysplastic syndrome (MDS) is very important in deciphering clonal pathogenesis of every patient and if determined correctly will become useful tool in followup studies such as testing individual susceptibility to epigenetic therapy with azacitidine (AZA). While some patients respond to AZA by restoring hematologic parameters, others progress to AML. Recent identification of quite heterogeneous sets of mutated genes (Bejar R et al. 2013) suggested that: patients with specific mutation pattern/s may respond to epigenetic therapy different

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Bernasconi, Claude F., Rodney J. Ketner, Xin Chen, and Zvi Rappoport. "Detection and kinetic characterization of SNV intermediates. Reactions of thiomethoxybenzylidene Meldrum's acid with thiolate ions, alkoxide ions, OH-, and water in aqueous DMSO." Canadian Journal of Chemistry 77, no. 5-6 (1999): 584–94. http://dx.doi.org/10.1139/v99-009.

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The reaction of thiomethoxybenzylidene Meldrum's acid (5-SMe) with thiolate and alkoxide ion nucleophiles is shown to proceed by the two-step addition-elimination SNV mechanism in which the tetrahedral intermediate accumulates to detectable levels. For the reactions with thiolate ions, rate constants for nucleophilic addition (k1RX), its reverse (k-1RX), and for conversion of the intermediate to products (k2RX) were determined. For the reactions with alkoxide ions, only k1RX and k-1RX could be obtained; the intermediate in these reactions did not yield the expected substitution products, and h

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5

Dubois, Frank, Ofer Shapira, Noah Greenwald, et al. "HGG-41. STRUCTURAL VARIANT DRIVERS IN PEDIATRIC HIGH-GRADE GLIOMA." Neuro-Oncology 22, Supplement_3 (2020): iii351. http://dx.doi.org/10.1093/neuonc/noaa222.322.

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Abstract BACKGROUND Driver single nucleotide variants (SNV) and somatic copy number aberrations (SCNA) of pediatric high-grade glioma (pHGGs), including Diffuse Midline Gliomas (DMGs) are characterized. However, structural variants (SVs) in pHGGs and the mechanisms through which they contribute to glioma formation have not been systematically analyzed genome-wide. METHODS Using SvABA for SVs as well as the latest pipelines for SCNAs and SNVs we analyzed whole-genome sequencing from 174 patients. This includes 60 previously unpublished samples, 43 of which are DMGs. Signature analysis allowed u

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Tabori, Uri, Scott Ryall, Michal Zapotocky, et al. "LGG-50. INTEGRATED MOLECULAR AND CLINICAL ANALYSIS OF 1,000 PEDIATRIC LOW-GRADE GLIOMAS UNCOVERS NOVEL SUBGROUPS FOR CLINICAL RISK STRATIFICATION." Neuro-Oncology 22, Supplement_3 (2020): iii375—iii376. http://dx.doi.org/10.1093/neuonc/noaa222.428.

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Abstract Pediatric low-grade gliomas (pLGG) are primarily driven by genetic alterations in the RAS/MAPK pathway, most commonly involving BRAF of NF1. Despite their molecular convergence, pLGG often show unexplained variability in their clinical outcome. To address this, we molecularly characterized a cohort of &gt;1,000 clinically annotated pLGG. 84% of cases harbored a detectable driver mutation. The remaining 16% of patients nonetheless showed RAS/MAPK pathway up-regulation at the RNA level. The clinical presentation and outcome of pLGG appeared highly variable and linked to the alterati

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Nicolò, Eleonora, Lorenzo Gerratana, Lorenzo Foffano, et al. "Abstract PO3-06-05: Association of tumor-derived extracellular vesicles with circulating tumor DNA alterations in metastatic breast cancer patients: exploring differences in inflammatory breast cancer." Cancer Research 84, no. 9_Supplement (2024): PO3–06–05—PO3–06–05. http://dx.doi.org/10.1158/1538-7445.sabcs23-po3-06-05.

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Abstract Background: Liquid biopsy provides a real-time assessment of metastatic breast cancer (MBC). Recently, the complementary prognostic value of tumor-derived extracellular vesicles (tdEVs) and circulating tumor cells (CTCs) has been reported. We have previously confirmed the strong prognostic significance of CTCs and tdEVs in inflammatory breast cancer (IBC). While previous studies have reported the association of CTCs with circulating tumor DNA (ctDNA) alterations in MBC, no evidence is available for tdEVs. This study aimed to analyze the association of tdEVs with ctDNA alterations, to

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Karni, Miriam, Claude F. Bernasconi, and Zvi Rappoport. "Role of Negative Hyperconjugation and Anomeric Effects in the Stabilization of the Intermediate in SNV Reactions." Journal of Organic Chemistry 73, no. 8 (2008): 2980–94. http://dx.doi.org/10.1021/jo7017476.

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9

Couch, Fergus, Huaizhi Huang, Tina Pesaran, et al. "Saturation genome editing-based functional evaluation and clinical classification of BRCA2 single nucleotide variants." Journal of Clinical Oncology 42, no. 16_suppl (2024): 10511. http://dx.doi.org/10.1200/jco.2024.42.16_suppl.10511.

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10511 Background: Germline BRCA2 loss-of function (LOF) variants identified by clinical genetic testing predispose to breast, ovarian, prostate and pancreatic cancer. However, variants of uncertain significance (VUS) (n > 4000) limit the clinical use of testing results. Thus, there is an urgent need for functional characterization and clinical classification of all BRCA2 variants. Here we report on comprehensive saturation genome editing (SGE)-based functional characterization of 97% of all possible single nucleotide variants (SNVs) in the BRCA2 DNA Binding Domain hotspot encoded by exons 1

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10

van Belzen, Ianthe A. E. M., Marc van Tuil, Shashi Badloe, et al. "Molecular Characterization Reveals Subclasses of 1q Gain in Intermediate Risk Wilms Tumors." Cancers 14, no. 19 (2022): 4872. http://dx.doi.org/10.3390/cancers14194872.

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Chromosomal alterations have recurrently been identified in Wilms tumors (WTs) and some are associated with poor prognosis. Gain of 1q (1q+) is of special interest given its high prevalence and is currently actively studied for its prognostic value. However, the underlying mutational mechanisms and functional effects remain unknown. In a national unbiased cohort of 30 primary WTs, we integrated somatic SNVs, CNs and SVs with expression data and distinguished four clusters characterized by affected biological processes: muscle differentiation, immune system, kidney development and proliferation

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Bernasconi, Claude F., Aquiles E. Leyes та Zvi Rappoport. "Kinetics of the Reaction of β-Methoxy-α-nitrostilbene with Cyanamide in 50 DMSO−50 Water. Failure to Detect the SNV Intermediate". Journal of Organic Chemistry 64, № 8 (1999): 2897–902. http://dx.doi.org/10.1021/jo990044u.

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12

Hsieh, Kang-Lin, Sankar Maity, Ganiraju Manya, Bradley Broom, Christopher Logothetis, and Patrick Pilie. "Abstract 1061: Post-doctoral fellow." Cancer Research 85, no. 8_Supplement_1 (2025): 1061. https://doi.org/10.1158/1538-7445.am2025-1061.

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Introduction: Prostate cancer research spans genetics, proteomics, metabolomics, cell signaling, and tumor microenvironment domains. While this data is valuable, integrating clinical and basic research findings presents challenges. The Prostate Cancer Cartography Initiative (PCCI) offers a unified data model for efficient research across clinical, co-clinical, and mechanistic studies. The data model divides cases into anatomic and biological groups, facilitating cross-domain knowledge translation and hypothesis generation through efficient data integration. Materials & Methods: Our databas

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Incorvaia, Lorena, Giuseppe Badalamenti, Daniele Fanale, et al. "Not all KIT 557/558 codons mutations have the same prognostic influence on recurrence-free survival: breaking the exon 11 mutations in gastrointestinal stromal tumors (GISTs)." Therapeutic Advances in Medical Oncology 13 (January 2021): 175883592110497. http://dx.doi.org/10.1177/17588359211049779.

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Background: Although the gastrointestinal stromal tumor (GIST) genotype is not currently included in risk-stratification systems, a growing body of evidence shows that the pathogenic variant (PV) type and codon location hold a strong prognostic influence on recurrence-free survival (RFS). This information has particular relevance in the adjuvant setting, where an accurate prognostication could help to better identify high-risk tumors and guide clinical decision-making. Materials and Methods: Between January 2005 and December 2020, 96 patients with completely resected GISTs harboring a KIT prot

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Zhang, Jingxian, Ruijie Zhang, Shikui Song, et al. "Whole-Genome Analysis of Mycobacterium neoaurum DSM 1381 and the Validation of Two Key Enzymes Affecting C22 Steroid Intermediates in Sterol Metabolism." International Journal of Molecular Sciences 24, no. 7 (2023): 6148. http://dx.doi.org/10.3390/ijms24076148.

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Mycobacterium neoaurum DSM 1381 originated from Mycobacterium neoaurum ATCC 25790 by mutagenesis screening is a strain of degrading phytosterols and accumulating important C22 steroid intermediates, including 22-hydroxy-23, 24-bisnorchola-4-en-3-one (4-HP) and 22-hydroxy-23, 24-bisnorchola-1,4-dien-3-one (HPD). However, the metabolic mechanism of these C22 products in M. neoaurum DSM 1381 remains unknown. Therefore, the whole-genome sequencing and comparative genomics analysis of M. neoaurum DSM 1381 and its parent strain M. neoaurum ATCC 25790 were performed to figure out the mechanism. As a

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15

Mori, Takuto, Kazuyuki Shimada, Kaito Mimura, et al. "Whole-Genome Analysis Revealed the Genetic Landscape of Intravascular Large B-Cell Lymphoma." Blood 144, Supplement 1 (2024): 2983. https://doi.org/10.1182/blood-2024-204466.

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Introduction Intravascular large B-cell lymphoma (IVLBCL) is a rare subtype of aggressive lymphoma characterized by selective growth of large malignant cells within small vessels in multiple organs. Previous studies using targeted sequencing and exome sequencing of IVLBCLs revealed a similar mutational landscape with that of activated B-cell (ABC) type of DLBCLs. However, the mechanism of exclusive localization of lymphoma cells within blood vessels and molecular pathogenesis of tumor development in IVLBCL remains unclear. Recent reports showed the usefulness of cell-free DNA (cfDNA) for genet

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Gupta, Aditya K., Tong Wang, Avantika Mann, Vincent Piguet, Anuradha Chowdhary, and Wayne L. Bakotic. "Mechanisms of resistance against allylamine and azole antifungals in Trichophyton: A renewed call for innovative molecular diagnostics in susceptibility testing." PLOS Pathogens 21, no. 2 (2025): e1012913. https://doi.org/10.1371/journal.ppat.1012913.

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The emergence of antifungal resistance calls for continued research efforts to better guide healthcare providers in treatment selection and outcomes. Unlike bacterial infections, treatment of superficial fungal infections is mainly limited to allylamines (terbinafine) and azoles (itraconazole). Here, we aim to update our current understanding of resistance mechanisms against allylamine and azole antifungals in the Trichophyton genus. Resistance development has been demonstrated in vitro by challenging Trichophyton isolates with allylamines or azoles at levels below the minimum inhibitory conce

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Bernasconi, Claude F., Shoshana D. Brown, Irina Eventova та Zvi Rappoport. "Spectroscopic and Kinetic Evidence for an Accumulating Intermediate in an SNV Reaction with Amine Nucleophiles. Reaction of Methyl β-Methylthio-α-nitrocinnamate with Piperidine and Morpholine". Journal of Organic Chemistry 72, № 9 (2007): 3302–10. http://dx.doi.org/10.1021/jo062602s.

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18

Bernasconi, Claude F., Rodney J. Ketner, Xin Chen, and Zvi Rappoport. "Kinetics of the Reactions of Methoxybenzylidene Meldrum's Acid with Thiolate Ions, Alkoxide Ions, OH-, and Water in Aqueous DMSO. Detection and Kinetic Characterization of the SNV Intermediate." Journal of the American Chemical Society 120, no. 30 (1998): 7461–68. http://dx.doi.org/10.1021/ja9743102.

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19

Lopez-Diaz, Fernando, Lauryn Keeler, Sally Agersborg, Lawrence Weiss, and Vincent Funari. "240 Identification of lung cancer mutational signatures and tumor drivers associated with specific bimodal PD-L1/TMB status." Journal for ImmunoTherapy of Cancer 8, Suppl 3 (2020): A258. http://dx.doi.org/10.1136/jitc-2020-sitc2020.0240.

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BackgroundPD-L1 expression and Tumor Mutation Burden (TMB) have independently emerged as prospective biomarkers of response to anti PD1-/PDL1 checkpoint inhibitors and even combined use of TMB, PD-L1 protein levels has been proposed. However, how the tumor genomic landscape interplays with the tumor microenvironment (TME) in defining particular predictive therapy response statuses is not clear.Methods424 FFPE clinical samples from lung cancer patients were analyzed using a CLIA-validated NGS-based assay that interrogates SNVs, indels using a 323 gene panel and by IHC for PD-L1 using the FDA ap

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Vinayak, Bhandari, Lydia Liu, Shadrielle Espirritu, et al. "The molecular hallmarks and clinical consequences of tumor hypoxia in prostate cancer." Journal of Clinical Oncology 37, no. 7_suppl (2019): 81. http://dx.doi.org/10.1200/jco.2019.37.7_suppl.81.

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81 Background: Localised prostate cancers are classified into risk-groups using clinical measurements like grade and stage to inform treatment decisions. However, these groupings are imprecise: ~30% of intermediate-risk patients suffer relapse of their disease despite precision image-guided radiotherapy or radical prostatectomy. One reason for this variability in response to treatment is the underlying cellular and molecular heterogeneity of tumours. Prostate tumour cells exist within a microenvironment characterized by gradients of oxygen levels and prostate tumours with low levels of oxygen

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Črepinšek, Klementina, Nika Klobučar, Tine Tesovnik, et al. "PAX5 Alterations in a Consecutive Childhood B-Cell Acute Lymphoblastic Leukemia Cohort Treated Using the ALL IC-BFM 2009 Protocol." Cancers 16, no. 6 (2024): 1164. http://dx.doi.org/10.3390/cancers16061164.

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In this study, we aimed to identify patients within our B-ALL cohort with altered PAX5. Our objective was to use a comprehensive analysis approach to characterize the types of genetic changes, determine their origin (somatic/germline), and analyze the clinical outcomes associated with them. A consecutive cohort of 99 patients with B-ALL treated at the Children’s Hospital of the UMC Ljubljana according to the ALL IC-BFM 2009 protocol was included in our study. We used RNA sequencing data for gene expression analysis, fusion gene detection and single nucleotide variant identification, multiplex-

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Chen, Haiyan, Mark J. Cowan, Jeffrey D. Hasday, Stefanie N. Vogel та Andrei E. Medvedev. "SMOKING INHIBITS EXPRESSION OF PROINFLAMMATORY CYTOKINES AND ACTIVATION OF IRAK-1, p38 AND NF-κB IN ALVEOLAR MACROPHAGES STIMULATED WITH TLR2 AND TLR4 AGONISTS (40.6)". Journal of Immunology 178, № 1_Supplement (2007): S28. http://dx.doi.org/10.4049/jimmunol.178.supp.40.6.

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Abstract Bronchiolitis is common in smokers and we hypothesized that this may be due to impaired sensing of bacterial components via TLR2 and TLR4 by smokers’ alveolar macrophages (AM). AM and PBMC obtained from smokers and non-smoking volunteers were stimulated with TLR2 and TLR4 agonists, Pam3Cys and LPS, and expression of cytokines and activation of intracellular intermediates were examined. Smokers’ AM exhibited suppressed gene expression and secretion of pro-inflammatory cytokines TNF-α, IL-1β, IL-6, IFN-γ and chemokines IL-8 and RANTES upon stimulation with LPS and Pam3Cys, whereas expre

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Satbir, Thakur, Son Tran, Mohit Jain, et al. "A Novel Anti-Cancer Vaccine Approach for the Treatment of High-Risk Leukemia in Children." Blood 136, Supplement 1 (2020): 25. http://dx.doi.org/10.1182/blood-2020-143381.

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Introduction: There is strong experimental and clinical data to indicate the critical involvement of immune evasion in relapsed leukemia in children. A well-defined characteristic of refractory leukemia is the accumulation of genetic aberrations and mutations that may act as drivers or passengers in the process of tumor recurrence. Many of these mutations get translated into proteins that contain tumor-specific immune-stimulatory epitopes (neoantigens) that can elicit host antitumor immune responses. Although, in general, the mutation rate is lower in pediatric tumors, recent studies have show

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Sarkozy, Clementine, Stacy Hung, Katsuyoshi Takata, et al. "Mutational Landscape of Grey Zone Lymphoma." Blood 134, Supplement_1 (2019): 21. http://dx.doi.org/10.1182/blood-2019-127375.

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Introduction: Grey zone lymphoma (GZL), a B-cell lymphoma with features intermediate between large B-cell lymphoma (LBCL) and classical Hodgkin lymphoma (cHL), is a rare and poorly defined entity. To decipher its mutational landscape and discover new therapeutic targets, we performed exome sequencing of 31 GZL cases. Methods: GZL cases from the LYSA group (N=139) and BC Cancer (N=30) were centrally reviewed and classified as previously published (Sarkozy et al, Am J Surg Pathol 2019). Whole-exome sequencing was performed on 31 cases with available fresh frozen tissue, using laser micro-dissect

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Xie, Michael J., Gareth A. Cromie, Katherine Owens, et al. "Constructing and interpreting a large-scale variant effect map for an ultrarare disease gene: Comprehensive prediction of the functional impact of PSAT1 genotypes." PLOS Genetics 19, no. 10 (2023): e1010972. http://dx.doi.org/10.1371/journal.pgen.1010972.

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Reduced activity of the enzymes encoded by PHGDH, PSAT1, and PSPH causes a set of ultrarare, autosomal recessive diseases known as serine biosynthesis defects. These diseases present in a broad phenotypic spectrum: at the severe end is Neu–Laxova syndrome, in the intermediate range are infantile serine biosynthesis defects with severe neurological manifestations and growth deficiency, and at the mild end is childhood disease with intellectual disability. However, L-serine supplementation, especially if started early, can ameliorate and in some cases even prevent symptoms. Therefore, knowledge

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Anand, Shankara, Mark Bustoros, Romanos Sklavenitis-Pistofidis, et al. "Genomic Profiling of Smoldering Multiple Myeloma Classifies Molecular Groups with Distinct Pathogenic Phenotypes and Clinical Outcomes." Blood 138, Supplement 1 (2021): 723. http://dx.doi.org/10.1182/blood-2021-150767.

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Abstract Introduction: Multiple Myeloma (MM) is an incurable plasma cell malignancy commonly preceded by the asymptomatic stage smoldering multiple myeloma (SMM). MM is characterized with significant genomic heterogeneity of chromosomal gains and losses (CNVs), translocations, and point mutations (SNVs); alterations that are also observed in SMM patients. However, current SMM risk models rely solely on clinical markers and do not accurately capture progression risk. While incorporating some genomic biomarkers improves prediction, using all MM genomic features to comprehensively stratify patien

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Gerstein, Jonathon Jonah, Michelle Chan-Seng-Yue, Grainne O´Kane, et al. "Beyond Khorana score 2: Molecular correlates of venous thromboembolism in pancreatic cancer." Journal of Clinical Oncology 43, no. 4_suppl (2025): 751. https://doi.org/10.1200/jco.2025.43.4_suppl.751.

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751 Background: Pancreatic ductal adenocarcinoma (PDAC) is associated with a hypercoagulable state leading to thrombosis. Risk models such as the Khorana score automatically classify PDAC as intermediate-high risk, and recent guidelines recommend consideration of thromboprophylaxis. However, little is known about the molecular correlates of PDAC for venous thromboembolism (VTE). Methods: We examined clinical and genomic data from the prospective multi-institution COMPASS trial (NCT02750657), which enrolled patients with treatment-naïve metastatic PDAC who underwent a fresh tumor biopsy for rea

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Alfaham, Manar S., Syed Osman Ahmed, Nogayhan Seymen, et al. "Saudi Acute Myeloid Leukaemia (AML) Genome Reveals Significant Differences from That in the Western Population." Blood 144, Supplement 1 (2024): 4231. https://doi.org/10.1182/blood-2024-205025.

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Introduction AML genome in the western populations has provided pathogenetic insights, prognosticators and selection of appropriate therapies. AML genome in the Middle East may differ from that in the west, because of younger population, racial, environmental and cultural factors including high consanguinity. We report for the first time, Whole Genome Sequencing (WGS) results in AML patients treated at the King Faisal Specialist Hospital and Research Centre in Riyadh, Saudi Arabia. The study was approved by KFSHRC ethics committee. Method The clinical data of 786 adult AML patients (18-89 year

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Palomo, Laura, Blanca Xicoy, Montse Arnan, et al. "Molecular Genetic Profiling in Chronic Myelomonocytic Leukemia with Low Risk Cytogenetic Features." Blood 126, no. 23 (2015): 2883. http://dx.doi.org/10.1182/blood.v126.23.2883.2883.

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Abstract Background: Chronic myelomonocytic leukemia (CMML) is a heterogeneous disease that can vary from a myelodysplastic (MD) predominant profile to a myeloproliferative (MP) one. CMML has a variable course, with a median overall survival of 20 months and 15-30% of progression to acute myeloid leukemia (AML). Cytogenetic abnormalities are present in 20-40% of cases and recurrent gene mutations have been reported in several genes. Patients with low risk cytogenetic features (normal karyotype and isolated -Y) account for approximately 80% of CMML patients and often fall into the low risk cate

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de Wit, Renske, Soufyan Lakbir, Caterina Buranelli, Gerrit A. Meijer, Sanne Abeln, and Remond J. Fijneman. "Abstract 4344: Comprehensive analysis of LINE-1 transposable elements in colorectal cancer." Cancer Research 84, no. 6_Supplement (2024): 4344. http://dx.doi.org/10.1158/1538-7445.am2024-4344.

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Abstract Background: Colorectal cancer (CRC) is the third most frequent cancer worldwide, and approximately a third of patients die from the disease. There is therefore an urgent need to better understand CRC biology. A particular feature in (colorectal) cancer is the activation of LINE-1 (L1) retrotransposons: DNA fragments which propagate to other places in the genome through an RNA intermediate. Per genome, about 100-150 genomic L1 copies are still retrotransposition-competent, but repressed in most somatic tissues. Their role in tumor development is currently unknown. Recently, the PCAWG c

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Lee, Hui Mei, Niloofar Zandvakili, Rhea Desai, Peter J. Browett, Purvi M. Kakadia, and Stefan K. Bohlander. "Characterization of an Acute Myeloid Leukemia Murine Model Driven By MLL/AF9: Effect of Retroviral Insertion Sites and Somatic Mutations on Gene Expression." Blood 138, Supplement 1 (2021): 4329. http://dx.doi.org/10.1182/blood-2021-154012.

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Abstract The MLL/AF9 fusion is found in approximately 30% of MLL-rearranged leukemias and has an intermediate prognosis. Genomically well-characterized murine leukemia models enable us to understand leukemogenesis. We generated a retroviral transduction murine bone marrow transplantation leukemia model (MBMTLM) using the MLL/AF9 fusion gene. Fifteen of 20 mice transplanted with syngeneic bone marrow transduced with a MLL/AF9 carrying retrovirus developed leukemia after a median latency of 149 days. Half a million leukemic bone marrow (LBM) cells from two of these primary leukemias, MA03-P and

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Ding, Peikun, Xiaoxiang Huang, Quanzhou Peng, et al. "Abstract 1597: Immune suppression of the lymph node microenvironment causes oligoprogression of metastatic cancer after neoadjuvant immuno-chemotherapy." Cancer Research 85, no. 8_Supplement_1 (2025): 1597. https://doi.org/10.1158/1538-7445.am2025-1597.

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Abstract Oligometastatic disease is recognized as an intermediate state between localised and systemically metastasised disease. The diagnosis, treatment and prognosis of oligometastatic disease is currently based mainly on imaging examination. Previous clinical studies indicated that standard systemic therapy followed by radical local therapy was beneficial for survival in tumor patients with oligometastatic disease. However, different clinical outcomes (such as oligopersistant and oligoprogression) were found in synchronous and/or metachronous oligometastatic disease after the same systemic

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Polgarova, Kamila, Vojtech Kulvait, Karina Vargova, et al. "Clonal Architecture of MDS Somatic Mutations Dynamically Changes during Azacitidine Therapy and Has Very Limited Potential to Predict Patient Outcome." Blood 128, no. 22 (2016): 4294. http://dx.doi.org/10.1182/blood.v128.22.4294.4294.

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Abstract Introduction: Myelodysplastic syndromes (MDS) are clonal disorders of myeloid hematopoietic stem cells. Recent studies has shown that nearly 90% of patients with MDS carry somatic mutations in bone marrow (BM). These findings triggered a number of studies to identify potential uses of these mutations for diagnostics and prognostics purposes. We focused on a group of 38 patients with advanced stages of the disease that were selected for Azacitidine (AZA) therapy. We then utilized a set of 98 BM samples from the patient cohort that were collected in different stages before, during, and

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Macaulay, Charles W., Marcus R. Breese, and E. Alejandro Sweet-Cordero. "Abstract B011: Dynamics of predicted tumor neoepitope burden in a pan-cancer solid tumor pediatric cohort." Cancer Immunology Research 11, no. 12_Supplement (2023): B011. http://dx.doi.org/10.1158/2326-6074.tumimm23-b011.

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Abstract Human leukocyte antigen (HLA) binding of tumor neoepitopes confers clinical value in certain adult malignancies. However, the prevalence of tumors that result in HLA binding of neoepitopes in pediatric malignancies is not as well-characterized. We set out to establish the feasibility of predicting neoepitope burden and the prevalence of predicted neoepitope across a previously established cohort of pediatric oncology patients. Additionally, because this analysis requires knowledge of each patient’s HLA haplotype for predicting binding of tumor peptides, we also set out to develop a no

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Oliva, Esther Natalie, Corrado Mammi', Maria Cuzzola, et al. "NGS Evaluation of the Eqol-MDS Trial: Preliminary Analysis of Eltrombopag for Thrombocytopenia of Low-Risk MDS." Blood 138, Supplement 1 (2021): 1516. http://dx.doi.org/10.1182/blood-2021-150619.

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Abstract Background: In myelodysplastic syndromes (MDS), thrombocytopenia is an adverse risk factor. Treatments in this setting are scarce. In a randomized international phase 2 trial (EQoL-MDS, EudraCT number 2010-022890-33), we reported effecacy and safety of eltrombopag for the treatment of thrombocytopenia in the first 90 patients with lower-risk MDS with a platelet (PLT) count &lt; 30 Gi/L (Oliva et al. Lancet Hem 2017). However, there are concerns of regulatory agencies regarding the use of thrombopoetin rececptor agonists in MDS due to previous reports signalling disease progression

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Metzeler, Klaus H., Tobias Herold, Maja Rothenberg-Thurley, et al. "DNMT3A Mutations Associate with Shorter Survival and Modulate the Prognostic Impact of Mutated NPM1: an Analysis Based on Comprehensive Mutational Screening of 660 AML Patients Treated on German AML Cooperative Group (AMLCG) Trials." Blood 126, no. 23 (2015): 3815. http://dx.doi.org/10.1182/blood.v126.23.3815.3815.

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Abstract Background: Mutations in DNA methyltransferase 3A (DNMT3A) are common in acute myeloid leukemia (AML), affecting ~20% of patients (pts) and 30-40% of those with cytogenetically normal (CN-) AML. Although several groups have investigated their prognostic relevance, most studies focused on younger adults (<60 years [y]), and their results were inconsistent. Moreover, there is conflicting data regarding possible differences between mutations affecting the 'hotspot' codon R882 and other variants. We therefore performed comprehensive mutational analyses in 660 younger and older (>=60

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Swaminathan, Mahesh, Kiyomi Morita, Yan Yuanqing, et al. "Clinical Heterogeneity of AML Is Associated with Mutational Heterogeneity." Blood 132, Supplement 1 (2018): 5240. http://dx.doi.org/10.1182/blood-2018-99-117287.

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Abstract BACKGROUND: AML is a group of clinically heterogeneous diseases. We hypothesized that heterogeneous presentation of AML is a reflection of equally heterogeneous genetic process during the leukemogenesis. METHODS: 536 AML patients (pts) bone marrow samples were analyzed by targeted capture exome sequencing of 295 genes. Extensive clinical-genotype correlation was performed using well annotated clinical data. RESULTS: The median age of the cohort was 62 years (IQR: 51-72) including 297 (55%) elderly (age ≥60), and 239 (45%) young (age <60) pts. Of the 536 pts, 308 (57%) pts had de no

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Hirsch, Pierre, Ruoping Tang, Nassera Abermil, et al. "Clono-Specific Evaluation of Minimal Residual Disease in Acute Myeloid Leukemia." Blood 128, no. 22 (2016): 1208. http://dx.doi.org/10.1182/blood.v128.22.1208.1208.

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Abstract Background: The genetic landscape of adult acute myeloid leukemias (AML) has been recently unravelled. This makes achievable the determination of a comprehensive profile of driver lesions for virtually all patients at diagnosis. Recent studies using multi-target minimal residual disease (MRD) strategies with around 1% sensitivity indicate that the clearance of all molecular events after chemotherapy is associated with better survival. To improve the clono-specificity and the sensitivity of this approach, after a precise determination of AML clonal composition, we combined cytogenetic,

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Liu, Zhaoyun, Bo Yu, Mu Su, et al. "Construction of a model for evaluating the efficacy of neoadjuvant chemotherapy for breast cancer and dynamic monitoring of ctDNA response to neoadjuvant chemotherapy." Journal of Clinical Oncology 40, no. 16_suppl (2022): e12600-e12600. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.e12600.

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e12600 Background: Neoadjuvant chemotherapy (NAC) is a routine treatment of choice for patients with locally advanced breast cancer. The pathological complete response (pCR) to NAC in breast cancer is closely related to a better prognosis. In addition, there have been few studies of the role of ctDNA in the dynamic monitoring of NAC, so we explored the prediction model of NAC to predict pCR and evaluated the role of ctDNA in the dynamic monitoring of NAC. Methods: A total of 269 breast cancer patients receiving NAC were enrolled, and a total of 266 tissue samples were collected. The tissue sam

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Liu, Zhaoyun, Bo Yu, Mu Su, et al. "Construction of a model for evaluating the efficacy of neoadjuvant chemotherapy for breast cancer and dynamic monitoring of ctDNA response to neoadjuvant chemotherapy." Journal of Clinical Oncology 40, no. 16_suppl (2022): e12600-e12600. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.e12600.

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e12600 Background: Neoadjuvant chemotherapy (NAC) is a routine treatment of choice for patients with locally advanced breast cancer. The pathological complete response (pCR) to NAC in breast cancer is closely related to a better prognosis. In addition, there have been few studies of the role of ctDNA in the dynamic monitoring of NAC, so we explored the prediction model of NAC to predict pCR and evaluated the role of ctDNA in the dynamic monitoring of NAC. Methods: A total of 269 breast cancer patients receiving NAC were enrolled, and a total of 266 tissue samples were collected. The tissue sam

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Nabhani, Schafiq, Sebastian Ginzel, Hagit Miskin, et al. "Dysregulation of IL12 Signaling As a Novel Cause of an Autoimmune Lymphoproliferative like Syndrome." Blood 124, no. 21 (2014): 1420. http://dx.doi.org/10.1182/blood.v124.21.1420.1420.

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Abstract Introduction Autoimmune lymphoproliferative syndrome (ALPS) is characterized by abnormal lymphocyte homeostasis caused by defective apoptosis. Mutations in genes involved in the Fas death receptor pathway (FAS, FASLG or CASP10 genes) are the cause for the pathogenesis of ALPS. However, in 20-30% of all ALPS cases, collectively classified as ALPS-U (undetermined), the genetic defect is still unknown. The objective of this study was to employ whole-exome sequencing to search for novel gene candidates underlying ALPS-U or ALPS-like disease. Resulting candidates should be validated and th

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Foran, James M., Michael G. Heckman, Yesesri Cherukuri, et al. "Epidemiologic and Clinical Analysis of Tumor Mutational Burden (TMB) in Acute Myeloid Leukemia (AML): Exome Sequencing Study of the Mayo Clinic AML Epidemiology Cohort (MCAEC)." Blood 138, Supplement 1 (2021): 3437. http://dx.doi.org/10.1182/blood-2021-151233.

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Abstract TMB is used to guide PD-1-directed immunotherapy in solid tumor Oncology. However, it has not been systematically studied in AML, where the focus has been on cytogenetic risk and individual driver gene mutations (GM's). TMB contribution to AML epidemiology is also uncertain. We therefore studied its association with epidemiologic risk factors; driver GM's and somatic mutations (SM's) in AML risk genes which we recently demonstrated (ABCB1; CYP1A1; CYP2B6; EPHX1; ERCC1,2,& 5; MEFV; MTRR; and TERT); clinical and cytogenetic features; and outcome after therapy in the MCAEC, a highly

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Schroers-Martin, Joseph, Jurik A. Mutter, Mohammad Shahrokh Esfahani, et al. "Longitudinal Noninvasive Surveillance & Fragmentomic Characterization of Follicular Lymphoma." Blood 142, Supplement 1 (2023): 528. http://dx.doi.org/10.1182/blood-2023-187116.

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Introduction While cell-free DNA (cfDNA) plays an increasingly defined role in aggressive lymphomas, its characteristics in indolent lymphomas are less established. Many follicular lymphoma (FL) patients experience durable remissions and late relapses ( Fig A). We therefore explored circulating tumor DNA (ctDNA) kinetics during long-term blood-based surveillance in patients with FL. In addition to noninvasive detection using somatic mutations, we also evaluated gene expression inference from cfDNA utilizing a novel fragmentomic method to detect histological transformation (tFL). Methods We stu

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Sánchez-Bayona, Rodrigo, Javier de Nicolás-Hernández, Cristina Saura, et al. "Abstract P2-01-16: Pharmacogenomic variants and risk of adverse events in breast cancer patients treated with Trastuzumab-deruxtecan: results from the PROCURE project." Clinical Cancer Research 31, no. 12_Supplement (2025): P2–01–16—P2–01–16. https://doi.org/10.1158/1557-3265.sabcs24-p2-01-16.

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Abstract Background: Trastuzumab-deruxtecan (T-DXd) has shown an unprecedented clinical benefit in advanced breast cancer. Despite its meaningful anticancer outcomes, around 15-20% of patients have to discontinue T-DXd due to related toxicity (mainly pneumonitis/interstitial lung disease). To date, there is no evidence of the potential impact of pharmacogenomic variants and the risk of treatment-related adverse events (TRAE) in breast cancer patients treated with T-DXd. Methods: The PROCURE project is a translational research study comprising 26 Spanish institutions that aims to analyze pharma

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Albitar, Maher, Andrew Ip, Andre H. Goy, et al. "Reliability of Cell-Free DNA (cfDNA) Next Generation Sequencing in Predicting Chromosomal Structural Abnormalities and Cytogenetic-Risk Stratification of Patients with Myeloid Neoplasms." Blood 138, Supplement 1 (2021): 3463. http://dx.doi.org/10.1182/blood-2021-148164.

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Abstract Introduction: Cytogenetic analysis is important for stratifying patients with various myeloid neoplasms. It has been reported that whole-genome sequencing can be used as an alternative to cytogenetic analysis in acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). With the increasing use of liquid biopsy in the diagnosis and monitoring of patients with various types of neoplasms, we explored the potential of using liquid biopsy and next generation sequencing (NGS) in detecting chromosomal structural abnormalities or copy number variation (CNV) in patients with myeloid neop

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Nagata, Yasunobu, Vera Grossmann, Yusuke Okuno, et al. "Landscape Of Genetic Lesions In 944 Patients With Myelodysplastic Syndromes." Blood 122, no. 21 (2013): 521. http://dx.doi.org/10.1182/blood.v122.21.521.521.

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Abstract Background Myelodysplastic syndromes (MDS) are a heterogeneous group of myeloid neoplasms characterized by varying degrees of cytopenias and a predisposition to acute myeloid leukemia (AML). With conspicuous clinical and biological heterogeneity in MDS, an optimized choice of treatment based on accurate diagnosis and risk stratification in individual patients is central to the current therapeutic strategy. Diagnosis and prognostication in patients with myelodysplastic syndromes (MDS) may be improved by high-throughput mutation/copy number profiling. Methods A total of 944 patients wit

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Guglielmelli, Paola, Laura Calabresi, Chiara Carretta, et al. "Single Cell Mutation Analysis Delineates Clonal Architecture in Leukemic Transformation of Myeloproliferative Neoplasms." Blood 138, Supplement 1 (2021): 56. http://dx.doi.org/10.1182/blood-2021-148315.

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Abstract Introduction. Myeloproliferative neoplasms (MPN) are clonal disorders of hematopoietic stem cells that include polycythemia vera, essential thrombocythemia, and primary myelofibrosis. 10-20% of MPN pts transform to secondary acute myeloid leukemia (sAML), unresponsive to conventional therapy and associated with dismal outcome (Dunbar A, 2020). In addition to somatic driver mutations affecting JAK2, CALR or MPL, several additional variants are harbored by MPN pts inb chronic phase, and a restricted set of them were associated with risk of leukemic evolution (Vannucchi AM, Leukemia 2013

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Roberts, Kathryn G., Samuel W. Brady, Zhaohui Gu, et al. "The Genomic Landscape of Childhood Acute Lymphoblastic Leukemia." Blood 134, Supplement_1 (2019): 649. http://dx.doi.org/10.1182/blood-2019-124881.

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Introduction: Although recent studies have refined the classification of B-progenitor and T-lineage acute lymphoblastic leukemia into gene-expression based subgroups, a comprehensive integration of significantly mutated genes and pathways for each subgroup is needed to understand disease etiology. Methods: We studied 2789 children, adolescents and young adults (AYA) with newly diagnosed B-ALL (n=2,322 cases) or T-ALL (n=467) treated on Children's Oncology Group (n=1,872) and St. Jude Children's Research Hospital trials (n=917). The cohort comprised childhood NCI standard-risk (41.8%; age range

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Stasik, Sebastian, Jan Moritz Middeke, Michael Kramer, et al. "EZH2 Mutations and Impact on Clinical Outcome Analyzed in 1604 Patients with Acute Myeloid Leukemia." Blood 132, Supplement 1 (2018): 1528. http://dx.doi.org/10.1182/blood-2018-99-114421.

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Abstract Purpose: The enhancer of zeste homolog 2 (EZH2) is a histone methyltransferase and key epigenetic regulator involved in transcriptional repression and embryonic development. Loss of EZH2 activity by inactivating mutations is associated with poor prognosis in myeloid malignancies such as MDS. More recently, EZH2 inactivation was shown to induce chemoresistance in acute myeloid leukemia (AML) (Göllner et al., 2017). Data on the frequency and prognostic role of EZH2-mutations in AML are rare and mostly confined to smaller cohorts. To investigate the prevalence and prognostic impact of th

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Yang, Huixiao, Linghao Zhang, Xinmiao Kang, Yunpei Si, Ping Song, and Xin Su. "Reaction Pathway Differentiation Enabled Fingerprinting Signal for Single Nucleotide Variant Detection." Advanced Science, February 4, 2025. https://doi.org/10.1002/advs.202412680.

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AbstractAccurate identification of single‐nucleotide variants (SNVs) is paramount for disease diagnosis. Despite the facile design of DNA hybridization probes, their limited specificity poses challenges in clinical applications. Here, a differential reaction pathway probe (DRPP) based on a dynamic DNA reaction network is presented. DRPP leverages differences in reaction intermediate concentrations between SNV and WT groups, directing them into distinct reaction pathways. This generates a strong pulse‐like signal for SNV and a weak unidirectional increase signal for wild‐type (WT). Through the

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