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Journal articles on the topic 'MUTANT SCORE'

Author: Grafiati

Published: 11 September 2023

Last updated: 31 July 2025

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1

Rupinder, Kaur* Sanjay Tyagi. "A NOVEL APPROACH TO DETECT EQUIVALENT MUTANTS USING CONTROL FLOW GRAPH." INTERNATIONAL JOURNAL OF ENGINEERING SCIENCES & RESEARCH TECHNOLOGY 5, no. 7 (2016): 1070–77. https://doi.org/10.5281/zenodo.57991.

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Software testing verifies and validates software systems. Mutation testing is a testing procedure where mutants are created by seeding fault to the code. Test cases are exercised on these mutants to measure the adequacy given by mutation score. If the mutants are not killed, then either the test data is not sufficient or there is the presence of equivalent mutant, which is an undecidable problem. Equivalent mutant problem makes testing process more difficult and tedious. A technique has been proposed in this paper to detect equivalent mutants by observing RIP model and control flow graph of or

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Sugave, Shounak Rushikesh, Yogesh R. Kulkarni, and Balaso. "Multi-Objective Optimization Model and Hierarchical Attention Networks for Mutation Testing." International Journal of Swarm Intelligence Research 14, no. 1 (2023): 1–23. http://dx.doi.org/10.4018/ijsir.319714.

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Mutation testing is devised for measuring test suite adequacy by identifying the artificially induced faults in software. This paper presents a novel approach by considering multiobjectives-based optimization. Here, the optimal test suite generation is performed using the proposed water cycle water wave optimization (WCWWO). The best test suites are generated by satisfying the multi-objective factors, such as time of execution, test suite size, mutant score, and mutant reduction rate. The WCWWO is devised by a combination of the water cycle algorithm (WCA) and water wave optimization (WWO). Th

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Almahasheer, Arwa Ali, Amal Mahmoud, Hesham El-Komy, et al. "Novel Feather Degrading Keratinases from Bacillus cereus Group: Biochemical, Genetic and Bioinformatics Analysis." Microorganisms 10, no. 1 (2022): 93. http://dx.doi.org/10.3390/microorganisms10010093.

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In this study, five keratinolytic bacteria were isolated from poultry farm waste of Eastern Province, Saudi Arabia. The highest keratinase activity was obtained at 40–45 °C, pH 8–9, feather concentration 0.5–1%, and using white chicken feather as keratin substrate for 72 h. Enhancement of keratinase activity through physical mutagen UV radiation and/or chemical mutagen ethyl methanesulfonate (EMS) resulted in five mutants with 1.51–3.73-fold increased activity over the wild type. When compared with the wild type, scanning electron microscopy validated the mutants’ effectiveness in feather degr

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Xie, Yuancai, Yingmei Li, Linfeng Dong, Shifu Chen, and Jixian Liu. "A differential analysis of TCR repertoire between patients with EGFR-mutant and KRAS-mutant non–small-cell lung cancer." Journal of Clinical Oncology 41, no. 16_suppl (2023): e21012-e21012. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.e21012.

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e21012 Background: T-cell receptor (TCR) repertoire could partially represent tumor micro-environment. EGFR and KRAS are common driver genes mutated and often mutually exclusive in non-small cell lung cancer (NSCLC). There’s a hypothesis that the immune system responds differently according to different mutations. Here we investigated the TCR features, including diversity, clonality, evenness and sequence similarity in EGFR and KRAS mutated NSCLC patients, to better understand the immune response in carcinogenesis. Methods: A total of 71 EGFR-mutant and 31 KRAS-mutant NSCLC tissue samples unde

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Yu, Guangyang, Ying Pang, Mythili Merchant, et al. "Tumor Mutation Burden, Expressed Neoantigens and the Immune Microenvironment in Diffuse Gliomas." Cancers 13, no. 23 (2021): 6092. http://dx.doi.org/10.3390/cancers13236092.

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Background: A consistent correlation between tumor mutation burden (TMB) and tumor immune microenvironment has not been observed in gliomas as in other cancers. Methods: Driver germline and somatic mutations, TMB, neoantigen, and immune cell signatures were analyzed using whole exome sequencing (WES) and transcriptome sequencing of tumor and WES of matched germline DNA in a cohort of 66 glioma samples (44 IDH-mutant and 22 IDH-wildtype). Results: Fourteen samples revealed a hypermutator phenotype (HMP). Eight pathogenic (P) or likely pathogenic (LP) germline variants were detected in 9 (19%) p

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Karsy, Michael, Jian Guan, and L. Eric Huang. "Prognostic role of mitochondrial pyruvate carrier in isocitrate dehydrogenase–mutant glioma." Journal of Neurosurgery 130, no. 1 (2018): 56–66. http://dx.doi.org/10.3171/2017.9.jns172036.

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OBJECTIVEGliomas are one of the most common types of primary brain tumors. Recent studies have supported the importance of key genetic alterations, including isocitrate dehydrogenase (IDH) mutations and 1p19q codeletion, in glioma prognosis. Mutant IDH produces 2-hydroxyglutarate from α-ketoglutarate, a key metabolite of the Krebs cycle. The mitochondrial pyruvate carrier (MPC) is composed of MPC1 and MPC2 subunits and is functionally essential for the Krebs cycle. The authors sought to explore the impact of MPC1 and MPC2 expression on patient prognosis.METHODSGenomic and clinical data in pati

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Guimarães-Souza, Nadia Karina, Liliya Marsovna Yamaleyeva, Baisong Lu, Ana Claudia Mallet de Souza Ramos, Colin Edward Bishop, and Karl Erik Andersson. "Superoxide overproduction and kidney fibrosis: a new animal model." Einstein (São Paulo) 13, no. 1 (2015): 79–88. http://dx.doi.org/10.1590/s1679-45082015ao3179.

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Objective To establish whether the mutation in the Immp2L gene induces renal fibrosis and whether aging exacerbates renal morphology in mice. Methods Female mutant mice with mutation in the inner mitochondrial membrane peptidase 2-like protein at 3 and 18 months of age were used. Renal fibrosis was analyzed using classic fibrosis score, Masson’s trichrome staining, and analysis of profibrotic markers using real time polymerase chain reaction (superoxide dismutase 1, metalloproteinase-9, erythropoietin, transforming growth factor beta), and immunostaining (fibroblasts and Type IV collagen). Oxi

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Senecal, Justin Bruni, Yasmine Madan, Rabia Tahir, et al. "External Validation of the JAKPOT Score for Diagnosing JAK2-Positive Erythrocytosis: A Retrospective Cohort Study." Journal of Clinical Medicine 14, no. 15 (2025): 5173. https://doi.org/10.3390/jcm14155173.

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Background/Objectives: Erythrocytosis is a common laboratory abnormality affecting approximately 4% of males and 0.4% of females. The JAKPOT score was recently developed to differentiate primary from secondary erythrocytosis without molecular testing. JAKPOT+ patients meet any of the following criteria: erythrocytes > 6.45 × 1012/L, platelets > 350 × 109/L, or neutrophils > 6.2 × 109/L. We aimed to validate this score and identify predictors of JAK2-positive erythrocytosis in a retrospective cohort. Methods: We identified 213 patients (50 female, mean age 57 years) with undifferentiat

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He, Qiong, Yamin Li, Xihong Zhou, et al. "The combination of fibrinogen concentrations and the platelet-to-lymphocyte ratio predicts survival in patients with advanced lung adenocarcinoma treated with EGFR-TKIs." Journal of International Medical Research 49, no. 4 (2021): 030006052110040. http://dx.doi.org/10.1177/03000605211004021.

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ObjectiveThis study aimed to identify a predictive marker of response to epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) in patients with EGFR-mutant advanced lung adenocarcinoma.MethodsA cohort of 190 patients with EGFR-mutant advanced lung adenocarcinoma was analyzed. Receiver operating characteristic curve analysis was used to evaluate the optimal cutoffs for fibrinogen levels, the neutrophil-to-lymphocyte ratio (NLR), and the platelet-to-lymphocyte ratio (PLR) for predicting progression-free survival (PFS). Univariate and multivariate survival analyses were performe

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Boucai, Laura, Venkatraman Seshan, Michelle Williams, et al. "Characterization of Subtypes of BRAF-Mutant Papillary Thyroid Cancer Defined by Their Thyroid Differentiation Score." Journal of Clinical Endocrinology & Metabolism 107, no. 4 (2021): 1030–39. http://dx.doi.org/10.1210/clinem/dgab851.

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Abstract Context The BRAFV600E mutation has been associated with more advanced clinical stage in papillary thyroid cancer (PTC) and decreased responsiveness to radioiodine (RAI). However, some BRAF mutant PTCs respond to RAI and have an indolent clinical behavior suggesting the presence of different subtypes of BRAF mutant tumors with distinct prognosis. Objective To characterize the molecular and clinical features of 2 subtypes of BRAF-mutant PTCs defined by their degree of expression of iodine metabolism genes. Design 227 BRAF-mutant PTCs from the Cancer Genome Atlas Thyroid Cancer study wer

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Delorenzi, Mauro, Sarah Gerster, Josep Tabernero, et al. "Microarray gene expression study of the RESPECT trial for the identification of prognostic and predictive markers." Journal of Clinical Oncology 31, no. 15_suppl (2013): e14561-e14561. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.e14561.

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e14561 Background: The RESPECT trial (n = 198) tested the addition of Sorafenib to standard mFOLFOX6 treatment in first line metastatic colorectal cancer (mCRC) patients but resulted in no statistical significant improvement in progression free survival, and no evidence for overall benefit. Sorafenib inhibits several Raf kinases (including B-Raf). Samples with high BRAF-mutant-like score were previously shown to identify a subset of colon tumors with a similar biology and outcome to BRAF mutant patients (Popovici et al. J. Clin. Oncol., 30(12):1288–95, 2012). Methods: A subset of 125 patients

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Saw, Stephanie, Gillianne Lai, Aaron C. Tan, et al. "PD-L1 score as a prognostic biomarker in Asian patients with early-stage, EGFR-mutated lung cancer." Journal of Clinical Oncology 40, no. 16_suppl (2022): 8527. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.8527.

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8527 Background: Adjuvant Atezolizumab was recently approved in stage II-IIIA non-small cell lung cancer (NSCLC) with PD-L1 ≥1%. However, disease-free survival (DFS) benefit was mainly driven by PD-L1 ≥50% and among EGFR-mutated subgroup, atezolizumab did not demonstrate DFS benefit when PD-L1 0% patients were included. We sought to determine the prognostic value of PD-L1 score in early-stage EGFR-mutated NSCLC. Methods: Consecutive patients with Stage IA-IIIA NSCLC diagnosed 1/1/2010 – 31/12/2019 who underwent curative surgery at National Cancer Centre Singapore with evaluable EGFR and PD-L1

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Poon, CC, P. Gordon, K. Liu, et al. "GP.06 Differential microglia and macrophage profiles in human IDH-mutant and -wildtype glioblastoma reveal therapeutic vulnerabilities." Canadian Journal of Neurological Sciences / Journal Canadien des Sciences Neurologiques 46, s1 (2019): S7. http://dx.doi.org/10.1017/cjn.2019.82.

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Background: Microglia and macrophages (MMs) are the largest component of the inflammatory infiltrate in glioblastoma (GBM). However, whether there are immunophenotypic differences in isocitrate dehydrogenase (IDH)-mutated and -wildtype GBMs is unknown. Studies on specimens of untreated IDH-mutant GBMs are rare given they comprise 10% of all GBMs and often receive treatment at lower grades that can drastically alter MM phenotypes. Methods: We obtained large samples of untreated IDH-mutant and -wildtype GBMs. Using immunofluorescence techniques with single-cell automated segmentation, and compar

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Miyawaki, Eriko, Haruyasu Murakami, Keita Mori, et al. "PD-L1 expression and response to pembrolizumab in patients with EGFR-mutant non-small cell lung cancer." Japanese Journal of Clinical Oncology 50, no. 5 (2020): 617–22. http://dx.doi.org/10.1093/jjco/hyaa033.

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Abstract Epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer is less likely to express programmed death-ligand 1 (PD-L1) than tumors with wild-type EGFR and is associated with poor response to pembrolizumab. To understand the relationship between EGFR mutation and PD-L1 expression in pembrolizumab response, we retrospectively evaluated the factors contributing to the high tumor proportion score in 155 EGFR-mutant non-small cell lung cancer cases and their associated response to pembrolizumab. Uncommon EGFR mutations were significantly associated with a PD-L1 tumor proport

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Masoodi, Tariq Ahmad, Sulaiman A. Al Shammari, May N. Al-Muammar, and Adel A. Alhamdan. "Screening and Evaluation of Deleterious SNPs in APOE Gene of Alzheimer’s Disease." Neurology Research International 2012 (2012): 1–8. http://dx.doi.org/10.1155/2012/480609.

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Introduction. Apolipoprotein E (APOE) is an important risk factor for Alzheimer’s disease (AD) and is present in 30–50% of patients who develop late-onset AD. Several single-nucleotide polymorphisms (SNPs) are present in APOE gene which act as the biomarkers for exploring the genetic basis of this disease. The objective of this study is to identify deleterious nsSNPs associated with APOE gene.Methods. The SNPs were retrieved from dbSNP. Using I-Mutant, protein stability change was calculated. The potentially functional nonsynonymous (ns) SNPs and their effect on protein was predicted by PolyPh

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Kakar, Kifayatullah, Tran Dang Xuan, Nguyen Van Quan, et al. "Efficacy of N-methyl-N-nitrosourea (MNU) Mutation on Enhancing the Yield and Quality of Rice." Agriculture 9, no. 10 (2019): 212. http://dx.doi.org/10.3390/agriculture9100212.

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Mutation technology has been applied more in recent decades to achieve novel products that are not commonly found in nature. An experiment was conducted to examine the effects of an N-methyl-N-nitrosourea (MNU) mutation on the growth, yield, and physicochemical properties of rice. Seeds of two rice cultivars (K1: DT84, and K3: Q5), along with their mutant lines (K2: mutated DT84, and K4: mutated Q5), were sown, and the established seedlings were transplanted to an open field. Ten hills per plot were randomly selected to evaluate growth parameters, yield, and components. Physicochemical attribu

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Hide, Takuichiro, Jun Hatakeyama, Chiharu Kimura-Yoshida, et al. "Genetic modifiers of otocephalic phenotypes inOtx2heterozygous mutant mice." Development 129, no. 18 (2002): 4347–57. http://dx.doi.org/10.1242/dev.129.18.4347.

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Mice heterozygous for the Otx2 mutation display a craniofacial malformation, known as otocephaly or agnathia-holoprosencephaly complex. The severity of the phenotype is dependent on the genetic background of a C57BL/6 (B6) strain; most of the offspring of Otx2 knock-out chimeras, which are equivalent to the F1 of CBA and B6 strains, backcrossed with B6 females display reduction or loss of mandible, whereas those backcrossed with CBA females do not show noticeable phenotype at birth. The availability of phenotypically disparate strains renders identification of Otx2 modifier loci possible. In t

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Grewal, Eric P., Leland G. K. Richardson, Jing Sun, et al. "Suppression of antitumor immune signatures and upregulation of VEGFA as IDH-mutant gliomas progress to higher grade." Neurosurgical Focus 56, no. 2 (2024): E2. http://dx.doi.org/10.3171/2023.11.focus23694.

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OBJECTIVE Several studies have compared the immune microenvironment of isocitrate dehydrogenase (IDH)–wildtype glioma versus IDH-mutant glioma. The authors sought to determine whether histological tumor progression in a subset of IDH-mutant glioma was associated with concomitant alterations in the intratumoral immune microenvironment. METHODS The authors performed bulk RNA sequencing on paired and unpaired samples from patients with IDH-mutant glioma who underwent surgery for tumor progression across multiple timepoints. They compared patterns of differential gene expression, overall inflammat

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Jacobsen, Ilse, Isabel Hennig-Pauka, Nina Baltes, Matthias Trost, and Gerald-F. Gerlach. "Enzymes Involved in Anaerobic Respiration Appear To Play a Role in Actinobacillus pleuropneumoniae Virulence." Infection and Immunity 73, no. 1 (2005): 226–34. http://dx.doi.org/10.1128/iai.73.1.226-234.2005.

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ABSTRACT Actinobacillus pleuropneumoniae, the etiological agent of porcine pleuropneumonia, is able to survive on respiratory epithelia, in tonsils, and in the anaerobic environment of encapsulated sequesters. It was previously demonstrated that a deletion of the anaerobic dimethyl sulfoxide reductase gene (dmsA) results in attenuation in acute disease (N. Baltes, S. Kyaw, I. Hennig-Pauka, and G. F. Gerlach, Infect. Immun. 71:6784-6792, 2003). In the present study, using two-dimensional polyacrylamide gel electrophoresis and quadrupole time-of-flight mass spectrometry, we identified an asparta

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Grewal, Eric, Leland G. Richardson, Jing Sun, et al. "1349 Suppression of Antitumor Immune Signatures and Upregulation of VEGFA as IDH-Mutant Gliomas Progress to Higher Grade." Neurosurgery 71, Supplement_1 (2025): 228. https://doi.org/10.1227/neu.0000000000003360_1349.

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INTRODUCTION: Several studies have compared the immune microenvironment of isocitrate dehydrogenase (IDH)–wildtype glioma versus IDH-mutant glioma. However, how this microenvironment shifts with progression events and changes as tumors increase in grade has been underexplored to date. METHODS: We performed bulk RNA sequencing on paired and unpaired samples from patients with IDH-mutant glioma who underwent surgery for tumor progression across multiple timepoints. We compared patterns of differential gene expression, overall inflammatory signatures, and transcriptomic measures of relative immun

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Yeatman, Timothy Joseph, Mingli Yang, Michael J. Schell, et al. "Identification of mutation biomarkers underpinning colon cancer sidedness and cetuximab sensitivity." Journal of Clinical Oncology 36, no. 4_suppl (2018): 629. http://dx.doi.org/10.1200/jco.2018.36.4_suppl.629.

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629 Background: Currently, extended RAS testing ( KRAS/ NRAS) in colorectal cancer (CRC) patients identifies only non-responders to EGFR inhibitor (EGFRi) therapies, and accurate prediction of drug-sensitive subpopulations remains problematic in patients, even with wild-type RAS. Moreover, the molecular basis for the laterality of anti-EGFR sensitivity is poorly understood. Methods: 468 CRCs were analyzed by global gene expression analysis, DNA sequencing (1321 cancer related genes) and MSI analysis. Tumors were stratified by a validated gene expression cetuximab sensitivity (CTX-S) score, and

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Adderley, Helen M., Mihaela Aldea, Jaqueline Aredo, et al. "Abstract 2975: RAS precision medicine transatlantic partnership: Exploration of RAS and NF1 co-mutations in NSCLC." Cancer Research 82, no. 12_Supplement (2022): 2975. http://dx.doi.org/10.1158/1538-7445.am2022-2975.

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Abstract Background: RAS is the most commonly mutated oncogene in cancer, with KRAS mutated in ~30% of non-small cell lung cancer (NSCLC). RAS is a small GTPase cycling between GTP-bound ‘ON’ state and GDP-bound ‘OFF’ state. KRAS oncoproteins cycle between these states via hydrolysis and nucleotide exchange with the aid of GAPs, including NF1, and GEFs. Given the ’inactive state’ inhibition of recently developed KRAS G12C inhibitors on the GDP-bound state, this has highlighted the continued reliance of KRAS-mutants upon cycling, and the potential for mutants to retain dependence upon upstream

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Nakatogawa, Hirokazu, Junya Fukai, Hiroshi Kawaji, et al. "10184- MPC-17 CHARACTERISTICS AND OUTCOMES OF DIFFUSE NON-MIDLINE GLIOMAS WITH H3F3A GENE MUTATION IN THE KANSAI MOLECULAR DIAGNOSIS NETWORK FOR CNS TUMORS (KANSAI NETWORK)." Neuro-Oncology Advances 6, Supplement_4 (2024): iv15. http://dx.doi.org/10.1093/noajnl/vdae173.057.

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Abstract PURPOSE Diffuse gliomas with H3F3A gene mutation such as H3.3 K27M and G34R/V in cerebral hemisphere can be found in diffuse gliomas rarely. These tumors may be called histone H3 K27M-mutant diffuse non-midline gliomas (NDMG) and H3 G34-mutant diffuse hemispheric gliomas (DHG), respectively. This study investigates clinical, radiological and molecular characteristics as well as treatment outcomes of patients with H3 K27-mutant NDMG compared with H3 G34-mutant DHG. METHODS We collected histone H3-mutant diffuse glioma cases at non-midline location and enrolled in Kansai Molecular Diagn

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Liu, Yating, Jie Yang, Xinyu Li, et al. "Pan-cancer analysis reveals the characteristics and roles of tooth agenesis mutant genes." Medicine 102, no. 50 (2023): e36001. http://dx.doi.org/10.1097/md.0000000000036001.

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Tooth development is regulated by numerous genes and signaling pathways. Some studies suggest that mutations in these genes may be associated with several cancer types. However, the tooth agenesis mutated genes role in the prognosis and their clinical therapeutic potentials in pan-cancer have not been elaborately explored. Moreover, the intrinsic correlation between tooth agenesis and cancers also needs to be further verified. We preliminarily analyzed expression levels and prognostic values of causative genes of tooth agenesis, and explored the correlation between the expression of tooth agen

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Yan, Dong, Lixin Sun, Jiandong Yang, et al. "Prognostic values of immune landscape in Ras-mutant colorectal cancer peritoneal metastases." Journal of Clinical Oncology 40, no. 16_suppl (2022): e15583-e15583. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.e15583.

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e15583 Background: The peritoneal metastasis (PM) in patients with colorectal cancer (CRC) is associated with poor survival, especially in those with Ras mutations. However, knowledge on the mechanism of molecular biology in CRC peritoneal metastasis (CRCPM) is limited, and the impact of tumor immune microenvironment (TME) on PM pathogenesis and the prognosis of CRCPM remain unclear. Therefore, we characterized the TME of CRCPM and evaluated its potential diagnostic and prognostic values. Methods: This study involved 21 patients with metastatic CRC (mCRC), of whom 11 with CRCPM were classified

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Yan, Dong, Lixin Sun, Jiandong Yang, et al. "Prognostic values of immune landscape in Ras-mutant colorectal cancer peritoneal metastases." Journal of Clinical Oncology 40, no. 16_suppl (2022): e15583-e15583. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.e15583.

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e15583 Background: The peritoneal metastasis (PM) in patients with colorectal cancer (CRC) is associated with poor survival, especially in those with Ras mutations. However, knowledge on the mechanism of molecular biology in CRC peritoneal metastasis (CRCPM) is limited, and the impact of tumor immune microenvironment (TME) on PM pathogenesis and the prognosis of CRCPM remain unclear. Therefore, we characterized the TME of CRCPM and evaluated its potential diagnostic and prognostic values. Methods: This study involved 21 patients with metastatic CRC (mCRC), of whom 11 with CRCPM were classified

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Dao Trong, Philip, Saskia Rösch, Heimo Mairbäurl, et al. "Identification of a Prognostic Hypoxia-Associated Gene Set in IDH-Mutant Glioma." International Journal of Molecular Sciences 19, no. 10 (2018): 2903. http://dx.doi.org/10.3390/ijms19102903.

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Glioma growth is often accompanied by a hypoxic microenvironment favorable for the induction and maintenance of the glioma stem cell (GSC) phenotype. Due to the paucity of cell models of Isocitrate Dehydrogenase 1 mutant (IDH1mut) GSCs, biology under hypoxic conditions has not been sufficiently studied as compared to IDH1 wildtype (IDH1wt) GSCs. We therefore grew well-characterized IDH1mut (n = 4) and IDH1wt (n = 4) GSC lines under normoxic (20%) and hypoxic (1.5%) culture conditions and harvested mRNA after 72 h. Transcriptome analyses were performed and hypoxia regulated genes were further a

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Berzero, Giulia, Luisa Bellu, Capucine Baldini, et al. "Sustained Tumor Control With MAPK Inhibition in BRAF V600–Mutant Adult Glial and Glioneuronal Tumors." Neurology 97, no. 7 (2021): e673-e683. http://dx.doi.org/10.1212/wnl.0000000000012330.

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ObjectiveTo assess whether RAF and MEK inhibitors (RAFi/MEKi) can provide long-term clinical benefit in adult patients with BRAF V600–mutant glial and glioneuronal tumors (GGNTs), we analyzed tumor response and long-term outcome in a retrospective cohort.MethodsWe performed a retrospective search in the institutional databases of 6 neuro-oncology departments for adult patients with recurrent or disseminated BRAF V600–mutant GGNTs treated with RAFi/MEKi.ResultsTwenty-eight adults with recurrent or disseminated BRAF V600–mutant gangliogliomas (n = 9), pleomorphic xanthoastrocytomas (n = 9), and

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Moorman, Nathaniel J., Chie Yu Lin, and Samuel H. Speck. "Identification of Candidate Gammaherpesvirus 68 Genes Required for Virus Replication by Signature-Tagged Transposon Mutagenesis." Journal of Virology 78, no. 19 (2004): 10282–90. http://dx.doi.org/10.1128/jvi.78.19.10282-10290.2004.

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ABSTRACT Current methods for determining the role of a given gene product in the gammaherpesvirus 68 (γHV68) life cycle require generation of a specific mutation by either homologous recombination in mammalian cells or bacterial artificial chromosome-mediated mutagenesis in Escherichia coli. The mutant virus is then compared to wild-type virus, and the role of the gene in the viral life cycle is deduced from its phenotype. This process is both time-consuming and labor intensive. Here we present the use of random, transposon-mediated signature-tagged mutagenesis for the identification of candid

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Martinez Lago, Nieves, Marta Covela Rúa, Elena Brozos, et al. "The role of Systemic Inflammation Score (SIS) in BRAF(V600) mutant metastatic colorectal cancer (mCRC)." Journal of Clinical Oncology 38, no. 15_suppl (2020): e16051-e16051. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e16051.

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e16051 Background: Multiple studies have reported prognostic association of neutrophil to lymphocyte ratio (NLR), platelet to lymphocyte ratio (PLT) and albumin levels in patients (pts) with colorectal cancer. However, it is unknown the prognostic impact in patients with BRAF(V600) mutant metastatic colorectal cancer (mCRC). Methods: Observational, retrospective, multicentric study pts with BRAF V600mt mCRC treated at 9 university Spanish hospitals in NW Spain, belonging to GITuD Group. Demographic, clinic, pathological characteristics, overall survival (OS) and progression free survival (PFS)

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Keshtvarz, Maryam, Mahdieh Mahboobi, Marek Kieliszek, et al. "Engineering of Cytolethal Distending Toxin B by Its Reducing Immunogenicity and Maintaining Stability as a New Drug Candidate for Tumor Therapy; an In Silico Study." Toxins 13, no. 11 (2021): 785. http://dx.doi.org/10.3390/toxins13110785.

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The cytolethal distending toxin (CDT), Haemophilus ducreyi, is one of the bacterial toxins that have recently been considered for targeted therapies, especially in cancer therapies. CDT is an A-B2 exotoxin. Its catalytic subunit (CdtB) is capable of inducing DNA double strand breaks, cell cycle arrest and apoptosis in host eukaryotic cells. The sequence alignment indicates that the CdtB is structurally homologyr to phosphatases and deoxyribonucleases I (DNase I). Recently, it has been found that CdtB toxicity is mainly related to its nuclease activity. The immunogenicity of CDT can reduce its

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Goetz, Andrew, Frances Shanahan, Logan Brooks, et al. "Computational Modeling of Drug Response Identifies Mutant-Specific Constraints for Dosing panRAF and MEK Inhibitors in Melanoma." Cancers 16, no. 16 (2024): 2914. http://dx.doi.org/10.3390/cancers16162914.

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Purpose: This study explores the potential of pre-clinical in vitro cell line response data and computational modeling in identifying the optimal dosage requirements of pan-RAF (Belvarafenib) and MEK (Cobimetinib) inhibitors in melanoma treatment. Our research is motivated by the critical role of drug combinations in enhancing anti-cancer responses and the need to close the knowledge gap around selecting effective dosing strategies to maximize their potential. Results: In a drug combination screen of 43 melanoma cell lines, we identified specific dosage landscapes of panRAF and MEK inhibitors

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Chandler, David, Sash Lopaticki, Dexing Huang, et al. "The stretcher spontaneous neurodegenerative mutation models Charcot-Marie-Tooth disease type 4D." F1000Research 2 (February 13, 2013): 46. http://dx.doi.org/10.12688/f1000research.2-46.v1.

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Mice affected by a spontaneous mutation which arose within our colony exhibited a neuromuscular phenotype involving tremor and characteristic stretching of the rear limbs. The mutant, named stretcher, was used to breed a backcross cohort for genetic mapping studies. The gene responsible for the mutant phenotype was mapped to a small region on mouse chromosome 15, with a LOD score above 20. Candidate genes within the region included the Ndrg1 gene. Examination of this gene in the mutant mouse strain revealed that exons 10 to 14 had been deleted. Mutations in the human orthologue are known to re

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Schneider, Friederike, Annika Dufour, Tobias Benthaus, et al. "A New Molecular and Clinical Prognostic Score for Risk Stratification in CN-AML." Blood 114, no. 22 (2009): 2635. http://dx.doi.org/10.1182/blood.v114.22.2635.2635.

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Abstract Abstract 2635 Poster Board II-611 Background: Cytogenetically normal acute myeloid leukemia (CN-AML) is associated with an intermediate outcome. A number of clinical and molecular risk factors have been characterized pointing to the heterogeneity of this group. The purpose of the study was to define a prognostic model based on pre-treatment patient characteristics to facilitate choice of therapy by definition of patient groups with different prognoses. Patients and methods: We evaluated four molecular markers (mutations of NPM1, CEBPA, MLL-PTD; FLT3-ITD mutant level; interaction term

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El Baiomy, Mohamed Ali, Salah Aref, and Mohamed El-Ghonemy. "Influence of CYP3A5 and SLCO1 on Imatinib Response Among Egyptian Patients with Chronic Myeloid Leukemia in Chronic Phase." Blood 128, no. 22 (2016): 5135. http://dx.doi.org/10.1182/blood.v128.22.5135.5135.

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Abstract Background Imatinib (IM) was approved as a molecular target tyrosine kinase inhibitor (TKI) drug that selectively inhibits BCR/ABL1 tyrosine kinase which causes Philadelphia-positive chronic myeloid leukemia (CML) and so far has been one of the first-choice treatment option in CML with excellent results. However, only a proportion of patients achieve major molecular response. Hence, the need to find whether there are some factors that affect the response to treatment is essential. Although IM pharmacokinetics is influenced by several enzymes and transporters, little is known about the

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Ramadhan, Dwi Syah Fitra, and Daryono H. Tjahjono. "Prediksi dan Identifikasi Struktur Protein EGFR Kanker Paru dengan Mutasi Titik L718Q/T790M Secara Pemodelan Homologi In Silico." Jurnal Sains dan Kesehatan 2, no. 4 (2020): 491–96. http://dx.doi.org/10.25026/jsk.v2i4.257.

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EGFR receptors play an important role in the growth of cancer cells, and these receptors have undergone various types of mutations. At this time, the effect of the L718Q / T790M point mutation on the EGFR receptor is not known, therefore the aim of this study is to predict the EGFR structure with the L718Q / T790M point mutation using in silico homology modeling. The mutant protein was successfully modeled using SWISS-Model expasy webserver and showed good evaluation results after the protein was minimized as indicated by the results of the Ramachandran outlier score of 0%, clashscore 0.98, an

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Rothermel, Luke Daniel, Mehrdad Zarei, Alexander W. Loftus, et al. "A powerful drug combination strategy targeting BRAF-mutant melanoma." Journal of Clinical Oncology 41, no. 16_suppl (2023): 3152. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.3152.

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3152 Background: BRAF inhibitors, such as vemurafenib and dabrafenib, are effective in treating patients with melanoma harboring (V600E) BRAF mutations. These drugs block the activity of the mutated BRAF protein, which impacts the development and progression of melanoma. Despite initial efficacy, drug resistance reliably occurs leading to disease relapse. Here we show how BRAF inhibitors cause metabolic reprogramming in melanoma cells to achieve drug resistance and promote cell survival. Previously we demonstrated that wild-type isocitrate dehydrogenase 1 (wtIDH1) supports mitochondrial functi

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Montégut, Coline, Jean-Sébastien Guillamo, François Ducray, et al. "NCOG-09. PREDICTIVE GERIATRIC FACTORS IN ELDERLY PATIENTS TREATED FOR IDH-MUTANT HIGH-GRADE GLIOMAS: A FRENCH POLA NETWORK STUDY." Neuro-Oncology 23, Supplement_6 (2021): vi153. http://dx.doi.org/10.1093/neuonc/noab196.600.

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Abstract We aimed to describe the characteristics, patterns of care and predictive geriatric factors of elderly patients with IDH-mutant (IDHm) high-grade gliomas (HGG) included in the French POLA network, dedicated to HGG (including 68% of IDHm HGG). For IDHm HGG patients over the age of 70 years, geriatric features were collected: G8 score items (appetite, weight loss, mobility, neuropsychological disorders, body mass index, medications, self-rated health, age), Activities and Instrumental Activities of Daily Living (ADL, IADL) scores, Charlson’s comorbidity Index (CCI) and biological marker

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Dorta Suarez, M., B. Jimenez Munarriz, A. Del Barrio, et al. "12P Molecular features of KRAS mutant NSCLC: Weaving a future score for immune-checkpoint inhibitors (ICI)." Annals of Oncology 32 (October 2021): S1349. http://dx.doi.org/10.1016/j.annonc.2021.08.2008.

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Gómez-Almería, Marta, Sonia Burgaz, Carlos Costas-Insua, et al. "BiP Heterozigosity Aggravates Pathological Deterioration in Experimental Amyotrophic Lateral Sclerosis." International Journal of Molecular Sciences 22, no. 22 (2021): 12533. http://dx.doi.org/10.3390/ijms222212533.

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In the present study, we investigated the involvement of the chaperone protein BiP (also known as GRP78 or Hspa5), a master regulator of intracellular proteostasis, in two mouse models of neurodegenerative diseases: amyotrophic lateral sclerosis (ALS) and Parkinson’s disease (PD). To this end, we used mice bearing partial genetic deletion of the BiP gene (BiP+/− mice), which, for the ALS model, were crossed with mutant SOD1 (mSOD1) transgenic mice to generate mSOD1/BiP+/− double mutant mice. Our data revealed a more intense neurological decline in the double mutants, reflected in a greater det

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Oklejewicz, Małgorzata, Serge Daan, Eddy Van Der Zee, and Menno Gerkema. "MEMORY RETENTION IN WILD-TYPE AND TAU MUTANT SYRIAN HAMSTERS." Behaviour 138, no. 6 (2001): 789–96. http://dx.doi.org/10.1163/156853901752233415.

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AbstractRats are known to display a temporary deficit in memory function 6 h after training on a learning task, a phenomenon known as the 'Kamin effect'. Later studies showed that maximal retrieval recurs in 24 h intervals after a single training and implied the role of the circadian clock in the suppression of memory retrieval at non-24 h intervals. This study aimed to investigate this further by analysing retention deficits following passive avoidance training in the Syrian hamster. The availability of hamsters carrying the tau mutation was exploited to address the role of the circadian syst

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Poojitha, T. N. S., K. V. L. Pushpanjali, D. Goutham, K. V. Yashwanth, and Srinivas Prasad. "A study on mutation testing of object oriented programs." International Journal of Engineering & Technology 7, no. 1.1 (2017): 243. http://dx.doi.org/10.14419/ijet.v7i1.1.9478.

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Mutation testing is a modern approach which gives more appropriate results. In comparison to traditional approaches, it gives high quality output. Previously it is not used mostly because of its high cost factor. This is because mutation testing deals with white box testing. White Box testing checks every module of the software in detail. If we use this it takes a lot of time and money. Recent approaches which came in mutation testing made it easy to implement for any software. Mutation take a look ating could be a fault based mostly testing technique within which mutants area unit generated w

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DeCuypere, Michael, Melissa LoPresti, Hinda Najem, et al. "Vulnerability to immune therapy in BRAF- and MYB-altered pediatric gliomas." Journal of Clinical Oncology 41, no. 16_suppl (2023): 2066. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.2066.

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2066 Background: The frequency and expression of predictive immune biomarkers in pediatric gliomas is relatively unknown. Here, we sought to define predictive signatures of immunotherapy responders by examining immune checkpoint expression, immune cell population signatures, and gene amplifications in a variety of pediatric gliomas. Methods: We profiled a cohort of pediatric, adolescent, and young adult glioma samples submitted to Caris Life Sciences (Phoenix, AZ) for analysis (N = 207). The cohort was further stratified by driver mutations: IDH mutant (N = 103), H3-3A mutant (N = 36), MYB-alt

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Tan, Lili, Yunzhan Gong, and Yawen Wang. "A Model for Predicting Statement Mutation Scores." Mathematics 7, no. 9 (2019): 778. http://dx.doi.org/10.3390/math7090778.

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A test suite plays a key role in software testing. Mutation testing is a powerful approach to measure the fault-detection ability of a test suite. The mutation testing process requires a large number of mutants to be generated and executed. Hence, mutation testing is also computationally expensive. To solve this problem, predictive mutation testing builds a classification model to predict the test result of each mutant. However, the existing predictive mutation testing methods only can be used to estimate the overall mutation scores of object-oriented programs. To overcome the shortcomings of

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Arsyad, Nur Rohmah, Risanto Siswosudarmo, and Ardhanu Kusumanto. "Hubungan antara Ekspresi P53 Mutan terhadap Operabilitas Kanker Serviks Stadium IIB Pasca Kemoterapi Neoajuvan." Jurnal Kesehatan Reproduksi 7, no. 1 (2020): 49. http://dx.doi.org/10.22146/jkr.53838.

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Background: The therapy for stage IIB cervical cancer according to FIGO is concurrent chemoradiation. The neoadjuvant chemotherapy followed by radical hysterectomy is an alternative therapy to improve the survival rate of cancer patients. Cervical cancer is mainly caused by the infection of Human Papilloma Virus (HPV), which contains protein E6 and E7 that downregulate the apoptotic function of p53. The absent of p53 wild-type and the present of p53 mutation play roles on the cervical cancer pathogenesis.Objective: To analyze the association between the expression of mutant p53 to the stage II

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Shi, Diana D., Adam C. Wang, Michael M. Levitt, et al. "DDRE-29. DE NOVO PYRIMIDINE SYNTHESIS IS A TARGETABLE VULNERABILITY IN IDH-MUTANT GLIOMA." Neuro-Oncology Advances 3, Supplement_1 (2021): i12—i13. http://dx.doi.org/10.1093/noajnl/vdab024.051.

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Abstract 70–90% of lower-grade gliomas and secondary glioblastomas harbor gain-of-function mutations in isocitrate dehydrogenase 1 (IDH1), causing overproduction of the oncometabolite (R)-2-hydroxyglutarate [(R)-2HG]. Although inhibitors of mutant IDH enzymes are effective in other cancers, including leukemia, they have shown guarded efficacy in preclinical and clinical brain tumor studies, thus underscoring the need to identify additional therapeutic targets in IDH mutant glioma. We sought to identify tumor-specific metabolic vulnerabilities induced by IDH1 mutations that could be exploited t

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Jamshidi, Pouya, Kristyn Galbraith, Matthew Mccord, et al. "PATH-44. VARIANT ALLELIC FREQUENCY OF DRIVER MUTATIONS PREDICTS SUCCESS OF GENOMIC METHYLATION CLASSIFICATION IN CNS TUMORS." Neuro-Oncology 24, Supplement_7 (2022): vii160. http://dx.doi.org/10.1093/neuonc/noac209.617.

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Abstract Whole genome CpG DNA methylation profiling is an extremely valuable tool in the workup of central nervous system (CNS) tumors. Reliability of such profiling depends on sufficient tumor cellularity. Many neoplastic entities have well-known driver mutations that occur in virtually 100% of tumor cells, and next-generation sequencing (NGS) assays can detect those mutations and report their relative amounts in the form of Variant Allelic Frequency (VAF). Since NGS and methylation profiling are often done on the same tumor block, we sought to determine whether driver mutation VAF affects th

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DeStefanis, Rebecca A., Autumn M. Olson, Alyssa K. DeZeeuw, et al. "Abstract 1128: MTORC1/2 and HDAC1/2 inhibition promote tumor response through inhibition of MYC." Cancer Research 82, no. 12_Supplement (2022): 1128. http://dx.doi.org/10.1158/1538-7445.am2022-1128.

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Abstract Background: The identification of treatment strategies targeting PIK3CA mutant colorectal cancer (CRC) are of great clinical interest. Previous work from our lab has identified MTORC1/2 and HDAC1/2 inhibition with copanlisib (cop; PI3K/MTOR) and romidepsin (romi; HDAC1/2) as a potential therapeutic strategy. We hypothesized that changes in c-MYC protein levels and c-MYC target gene (CTG) alterations might be a potential mechanism of action for this combination. Methods: Known CTGs were identified and their expression levels were examined in PIK3CA mutant vs WT CRCs using the cBioPorta

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Hannaway, Nicola, Stefania Kassaris, Janine Marie Davies, Alannah Smrke, Anna Tinker, and Yvette Drew. "Using chemotherapy response by KELIM score to predict response to first line maintenance PARP inhibitor therapy in non-BRCA mutant/homologous recombination deficiency (HRD) unknown high grade serous ovarian cancer (HGSOC)." Journal of Clinical Oncology 41, no. 16_suppl (2023): e17547-e17547. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.e17547.

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e17547 Background: Maintenance PARP inhibitor therapy after response to first line chemotherapy is now standard of care in advanced HGSOC. Niraparib is available to all patients based on the PRIMA trial data; however, the progression free survival (PFS) benefit for patients without BRCA mutations or homologous recombination deficiency (HRD) is limited. Funded HRD testing is not accessible in many countries. Patient selection for PARPi therapy in non-BRCA mutant HGSOC is challenging. The calculated CA-125 ELIMination of Rate Constant K (KELIM) score is a mathematical model developed to evaluate

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Lefler, Daniel S., Andrew Elliott, Erik Blomain, et al. "Characterizing patterns of mTORC1 activation across sarcoma subtypes using single-sample gene set enrichment analysis (ssGSEA) and a national biomarker database." Journal of Clinical Oncology 42, no. 16_suppl (2024): 11544. http://dx.doi.org/10.1200/jco.2024.42.16_suppl.11544.

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11544 Background: The mTOR pathway is a central signaling circuit that contributes to cancer cell proliferation, angiogenesis, metabolism, and other pivotal processes. The phase III SUCCEED trial showed marginal benefit of mTOR inhibition (mTORi) in chemo-responsive sarcomas, despite promising foundational phase II data. Since these trials did not account for mTOR-related physiology, we sought to identify sarcoma subgroups that display mTORC1 activated/activation phenotypes (mTORC1-act) that might derive more benefit from mTORi. Methods: DNA (592-gene or whole exome; N=7028) and RNA (whole tra

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