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Journal articles on the topic 'Cluster mutation'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

Conroy, Jeffrey M., Sarabjot Pabla, Marc S. Ernstoff, et al. "Comprehensive immune and mutational profile of melanoma." Journal of Clinical Oncology 36, no. 5_suppl (2018): 182. http://dx.doi.org/10.1200/jco.2018.36.5_suppl.182.

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182 Background: The association between tumor mutational profiles and immune signatures has not been well-characterized. Methods: 306 melanoma samples were tested by NGS using a comprehensive cancer panel for mutational status and an immune response panel which interrogates the expression profile of 54 validated immune-related genes. The ranking of gene expression, mutational burden and 7 immune phenotypes was compared to a reference population. 38% cases were positive for activating BRAF mutations, 12% for RAS, and 6% for NF1. The remaining 44% were considered triple wild type. Principal comp

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Montalban-Bravo, Guillermo, David Swanson, Rashmi Kanagal-Shamanna, et al. "Influence of Co-Mutational Patterns in Disease Phenotype and Clinical Outcomes of Chronic Myelomonocytic Leukemia." Blood 142, Supplement 1 (2023): 4601. http://dx.doi.org/10.1182/blood-2023-178061.

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Introduction: Chronic myelomonocytic leukemia (CMML) is characterized by recurrent somatic mutations in a conserved number of genes and functional pathways. Although specific genomic events are associated with disease phenotype and prognosis, identification of genomically-defined disease subgroups based on common recurrent cooperative genomic patterns is needed to refine disease classification and identify disease subsets with unique clinical behavior. Methods: To evaluate if CMML is defined by recurrent co-mutational profiles defining unique clinicopathologic subgroups we evaluated a cohort o

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Mandilaras, Victoria, Swati Garg, Michael Cabanero, et al. "TP53 mutations in high grade serous ovarian cancer and impact on clinical outcomes: a comparison of next generation sequencing and bioinformatics analyses." International Journal of Gynecologic Cancer 29, no. 2 (2019): 346–52. http://dx.doi.org/10.1136/ijgc-2018-000087.

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ObjectiveMutations in TP53 are found in the majority of high grade serous ovarian cancers, leading to gain of function or loss of function of its protein product, p53, involved in oncogenesis. There have been conflicting reports as to the impact of the type of these on prognosis. We aim to further elucidate this relationship in our cohort of patients.Methods229 patients with high grade serous ovarian cancer underwent tumor profiling through an institutional molecular screening program with targeted next generation sequencing. TP53 mutations were classified using methods previously described in

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Yu, Zhenhua, and Fang Du. "AMC: accurate mutation clustering from single-cell DNA sequencing data." Bioinformatics 38, no. 6 (2021): 1732–34. http://dx.doi.org/10.1093/bioinformatics/btab857.

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Abstract Summary Single-cell DNA sequencing (scDNA-seq) now enables high-resolution profiles of intra-tumor heterogeneity. Existing methods for phylogenetic inference from scDNA-seq data perform acceptably well on small datasets but suffer from low computational efficiency and/or degraded accuracy on large datasets. Motivated by the fact that mutations sharing common states over single cells can be grouped together, we introduce a new software called AMC (accurate mutation clustering) to accurately cluster mutations, thus improve the efficiency of phylogenetic inference. AMC first employs prin

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Huang, He, Zhimin Wang, Hao Chen, et al. "Co-mutation-based subtyping of Chinese patients with gastric cancer." Journal of Clinical Oncology 41, no. 16_suppl (2023): e16070-e16070. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.e16070.

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e16070 Background: The incidence of gastric cancer is decreasing globally, in contrast, that of Chinese patients has been increased from 35.9% to 48.3%. In-depth investigation of the characteristic of Chinese gastric cancer patients could help to understand the disease mechanism and improve the treatment of gastric cancer. Methods: Tumor tissues were obtained from 96 Chinese gastric cancer patients and tested by high-coverage ( > 1000x) panel sequencing containing 624 cancer-related genes. Genomic mutations including substitutions, insertions, deletions, rearrangements, fusions, and copy nu

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Papanicolau-Sengos, Antonios, Sarabjot Pabla, Grace K. Dy, et al. "Correlation of lung cancer mutational profile with immune profile." Journal of Clinical Oncology 36, no. 5_suppl (2018): 146. http://dx.doi.org/10.1200/jco.2018.36.5_suppl.146.

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146 Background: The association between neoplasm mutational and immune profiles has not been well-characterized. Methods: We collected 26 lung cancer formalin-fixed paraffin embedded (FFPE) samples which had been tested with a comprehensive mutation profile to detect clinically actionable mutations, and a comprehensive immune gene expression profile, which interrogates PD-L1 immunohistochemistry (IHC), PD-L1/2 copy number, CD3/CD8 IHC, microsatellite instability status, mutational burden, and the expression profile of 54 immune-related genes. The ranking of gene expression and 7 immune phenoty

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Lanino, Luca, Somedeb Ball, Jan Philipp Bewersdorf, et al. "Data-Driven Harmonization of 2022 Who and ICC Classifications of Myelodysplastic Syndromes/Neoplasms (MDS): A Study By the International Consortium for MDS (icMDS)." Blood 142, Supplement 1 (2023): 998. http://dx.doi.org/10.1182/blood-2023-186580.

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Background. The inclusion of gene mutations and chromosomal abnormalities in the 2022 WHO and ICC Classifications of MDS has enhanced diagnostic precision and is expected to improve clinical decision-making process. Although these two systems share similarities, clinically relevant discrepancies still exist and potentially cause inconsistency in their adoption in a clinical setting. In this study on behalf of the International Consortium for MDS (icMDS), we adopted a data-driven approach to provide a harmonization roadmap between the 2022 WHO and ICC classification for MDS. A modified Delphi P

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Xu, Qi, and Jeanne Kowalski-Muegge. "Mutation-site localized non-B DNA burden and survival heterogeneity in early-stage pancreatic cancer." Journal of Clinical Oncology 41, no. 16_suppl (2023): 4166. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.4166.

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4166 Background: Pancreatic cancer is a highly aggressive disease with a poor prognosis, and one in which most measure of genomic instability (e.g., tumor mutation burden (TMB), fraction of genome altered (FGA)) have thus far, not proven informative in differentiating survival. Non-B DNA are alternative DNA forms that deviate from the canonical B-DNA structure with potential to increase susceptibility to mutations, leading to the development of cancer. The role of non-B in pancreatic cancer has not been fully explored. Herein, we investigate the relationship between gene mutation sites co-loca

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Meier, Patricia Stutzmann, Silvia Utz, Suzanne Aebi, and Kathrin Mühlemann. "Low-Level Resistance to Rifampin in Streptococcus pneumoniae." Antimicrobial Agents and Chemotherapy 47, no. 3 (2003): 863–68. http://dx.doi.org/10.1128/aac.47.3.863-868.2003.

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ABSTRACT Rifampin is recommended for combination therapy of meningitis due to β-lactam-resistant Streptococcus pneumoniae. High-level rifampin resistance (MIC, ≥4 mg/liter) has been mapped to point mutations in clusters I and III of rpoB of the pneumococcus. The molecular basis of low-level resistance (MICs, ≥0.5 and <4 mg/liter) was analyzed. Spontaneous mutants of clinical pneumococcal isolates were selected on Columbia sheep blood agar plates containing rifampin at 0.5, 4, 10, or 50 mg/liter. Low-level resistance could be assigned to mutations in cluster II (I545N, I545L). Sensitive (MIC

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Svicher, Valentina, Tobias Sing, Maria Mercedes Santoro, et al. "Involvement of Novel Human Immunodeficiency Virus Type 1 Reverse Transcriptase Mutations in the Regulation of Resistance to Nucleoside Inhibitors." Journal of Virology 80, no. 14 (2006): 7186–98. http://dx.doi.org/10.1128/jvi.02084-05.

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ABSTRACT We characterized 16 additional mutations in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) whose role in drug resistance is still unknown by analyzing 1,906 plasma-derived HIV-1 subtype B pol sequences from 551 drug-naïve patients and 1,355 nucleoside RT inhibitor (NRTI)-treated patients. Twelve mutations positively associated with NRTI treatment strongly correlated both in pairs and in clusters with known NRTI resistance mutations on divergent evolutionary pathways. In particular, T39A, K43E/Q, K122E, E203K, and H208Y clustered with the nucleoside analogue mu

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Malcovati, Luca, Simon Crouch, Aniek O. De Graaf, et al. "Mutation Profiles Identify Distinct Clusters of Lower Risk Myelodysplastic Syndromes with Unique Clinical and Biological Features and Clinical Endpoints." Blood 136, Supplement 1 (2020): 29. http://dx.doi.org/10.1182/blood-2020-138549.

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Background. The severity of hematopoietic impairment and the kinetics of disease progression in lower risk myelodysplastic syndromes (LR-MDS) are extremely variable. Genomic profiling has the potential to inform the clinical management of these disorders, including improved classification, risk assessment and therapeutic choice. In the present study, based on a comprehensive mutation analysis in a large and clinically well-characterized cohort of LR-MDS patients, either recruited into the European MDS Registry or referred to European excellence centers involved in the MDS-RIGHT project, we ado

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O’Brien, Elizabeth, Lauren E. Salay, Esther A. Epum, Katherine L. Friedman, Walter J. Chazin, and Jacqueline K. Barton. "Yeast require redox switching in DNA primase." Proceedings of the National Academy of Sciences 115, no. 52 (2018): 13186–91. http://dx.doi.org/10.1073/pnas.1810715115.

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Eukaryotic DNA primases contain a [4Fe4S] cluster in the C-terminal domain of the p58 subunit (p58C) that affects substrate affinity but is not required for catalysis. We show that, in yeast primase, the cluster serves as a DNA-mediated redox switch governing DNA binding, just as in human primase. Despite a different structural arrangement of tyrosines to facilitate electron transfer between the DNA substrate and [4Fe4S] cluster, in yeast, mutation of tyrosines Y395 and Y397 alters the same electron transfer chemistry and redox switch. Mutation of conserved tyrosine 395 diminishes the extent o

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Jones, Adam G., Gunilla Rosenqvist, Anders Berglund, and John C. Avise. "Clustered Microsatellite Mutations in the Pipefish Syngnathus typhle." Genetics 152, no. 3 (1999): 1057–63. http://dx.doi.org/10.1093/genetics/152.3.1057.

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Abstract Clustered mutations are copies of a mutant allele that enter a population's gene pool together due to replication from a premeiotic germline mutation and distribution to multiple successful gametes of an individual. Although the phenomenon has been studied in Drosophila and noted in a few other species, the topic has received scant attention despite claims of being of major importance to population genetics theory. Here we capitalize upon the reproductive biology of male-pregnant pipefishes to document the occurrence of clustered microsatellite mutations and to estimate their rates an

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Zhang, Yuehui, Jia Song, Qili Shi, et al. "The prognostic signature of the somatic mutations in Ewing sarcoma: from a network view." Japanese Journal of Clinical Oncology 49, no. 7 (2019): 604–13. http://dx.doi.org/10.1093/jjco/hyz037.

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AbstractBackgroundEwing sarcoma is a malignant bone tumor mainly affecting teenagers and young adults. Its main driver mutation, the EWS-FLI1 fusion gene, has been identified more than 20 years ago, whereas its other somatic mutations have been just recently reported.MethodsIn this study, we organized the somatic mutations from 216 Ewing sarcoma cases into 216 individual protein–protein interaction networks by using interactome information. These mutation networks were then classified into five different clusters based on their structural similarities. The prognostic effect of mutation genes w

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Chen, Shanyu, Xiaoyu He, Ruilin Li, Xiaohong Duan, and Beifang Niu. "HotSpot3D web server: an integrated resource for mutation analysis in protein 3D structures." Bioinformatics 36, no. 12 (2020): 3944–46. http://dx.doi.org/10.1093/bioinformatics/btaa258.

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Abstract Motivation HotSpot3D is a widely used software for identifying mutation hotspots on the 3D structures of proteins. To further assist users, we developed a new HotSpot3D web server to make this software more versatile, convenient and interactive. Results The HotSpot3D web server performs data pre-processing, clustering, visualization and log-viewing on one stop. Users can interactively explore each cluster and easily re-visualize the mutational clusters within browsers. We also provide a database that allows users to search and visualize proximal mutations from 33 cancers in the Cancer

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Ploquin, Anne, Michael Genin, Mohamed Hebbar, et al. "Spatial heterogeneity of KRAS mutations in colorectal cancers: A population-based study in northern France." Journal of Clinical Oncology 37, no. 15_suppl (2019): e15101-e15101. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.e15101.

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e15101 Background: Somatic mutations in the KRAS gene are present in about 40% of tumors from colorectal cancer (CRC) patients and are associated with a resistance to anti-EGFR therapies. However, no clinical features have been linked to KRAS mutations in CRC. In this study, we attempted to identify the potential geographical population clusters of KRAS mutations in CRC patients in northern France. Methods: All patients with CRC who were identified to have KRAS mutations performed by pyrosequencing between 2008 and 2014 at the Regional Molecular Biology Platform at Lille University Hospital we

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Moss, Tyler J., Yuan Qi, Liu Xi, et al. "Comprehensive genomic characterization of upper tract urothelial carcinoma (UTUC)." Journal of Clinical Oncology 35, no. 6_suppl (2017): 375. http://dx.doi.org/10.1200/jco.2017.35.6_suppl.375.

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375 Background: Integrated analysis of UTUC was performed to characterize the genomic landscape of UTUC and provide insights into biology. Methods: 31 untreated samples underwent WES, RNAseq, and RPPA. Consensus mutation calls from independent pipelines of 2 centers identified gene expression clusters using unsupervised consensus hierarchical clustering (UCHC). Results: Clinical data are shown in the Table. WES identified mutations in FGFR3 (74.1%; 92% low grade, 60% high grade), KMT2D (44.4%), PIK3CA (25.9%), TP53 (22.2%). APOBEC and CpG signatures were identified. Expressed marker genes from

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Tsukada, Keita, Shin-ya Nishio, Mitsuru Hattori, and Shin-ichi Usami. "Ethnic-Specific Spectrum ofGJB2andSLC26A4Mutations." Annals of Otology, Rhinology & Laryngology 124, no. 1_suppl (2015): 61S—76S. http://dx.doi.org/10.1177/0003489415575060.

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Objective:The mutation spectrum of the GJB2 and SLC26A4 genes, the 2 most common genes causing deafness, are known to be ethnic specific. In this study, the spectrum of the reported GJB2 and SLC26A4 mutations in different populations are reviewed and considered from a human migration perspective.Methods:Fifty-two and 17 articles on GJB2 and SLC26A4 mutations, respectively, were reviewed through the PubMed database from April 1996 to September 2014. The 4 most prevalent mutations were selected and compared. A cluster analysis was subsequently performed for these selected mutations.Results:The p

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Matsutani, Taro, Yuki Ueno, Tsukasa Fukunaga, and Michiaki Hamada. "Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference." Bioinformatics 35, no. 22 (2019): 4543–52. http://dx.doi.org/10.1093/bioinformatics/btz266.

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Abstract Motivation A cancer genome includes many mutations derived from various mutagens and mutational processes, leading to specific mutation patterns. It is known that each mutational process leads to characteristic mutations, and when a mutational process has preferences for mutations, this situation is called a ‘mutation signature.’ Identification of mutation signatures is an important task for elucidation of carcinogenic mechanisms. In previous studies, analyses with statistical approaches (e.g. non-negative matrix factorization and latent Dirichlet allocation) revealed a number of muta

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Gallì, Anna, Gabriele Todisco, Eulalia Catamo, et al. "Relationship between clone metrics and clinical outcome in clonal cytopenia." Blood 138, no. 11 (2021): 965–76. http://dx.doi.org/10.1182/blood.2021011323.

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Abstract Clonal cytopenia of undetermined significance (CCUS) is associated with an increased risk of developing a myeloid neoplasm with myelodysplasia (MN). To identify the features of the mutant clone(s) that is associated with clinical phenotype and progression, we studied the following cohorts of individuals: 311 patients with idiopathic cytopenia of undetermined significance (ICUS), 532 community-dwelling individuals without hematologic phenotype (n = 355) or with unexplained anemia (n = 177), and 592 patients with overt MN. Ninety-two of 311 (30%) patients with ICUS carried a somatic gen

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Liu, Siyang, and Fang Li. "Periodicities in Cluster Algebras and Cluster Automorphism Groups." Algebra Colloquium 28, no. 04 (2021): 601–24. http://dx.doi.org/10.1142/s100538672100047x.

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We study the relations between two groups related to cluster automorphism groups which are defined by Assem, Schiffler and Shamchenko. We establish the relationships among (strict) direct cluster automorphism groups and those groups consisting of periodicities of labeled seeds and exchange matrices, respectively, in the language of short exact sequences. As an application, we characterize automorphism-finite cluster algebras in the cases of bipartite seeds or finite mutation type. Finally, we study the relation between the group [Formula: see text] for a cluster algebra [Formula: see text] and

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Shu, Ran, Li Bian, Ying Yang, et al. "Abstract 3964: HLA typing and its association with TMB in a pan-cancer Chinese cohort study." Cancer Research 85, no. 8_Supplement_1 (2025): 3964. https://doi.org/10.1158/1538-7445.am2025-3964.

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Background: Previous studies have linked HLA-I heterozygosity to immunotherapy efficacy. Given that tumor mutational burden (TMB) is a well-established biomarker for immunotherapy, this study explores the relationships among HLA-I heterozygosity, HLA-I subtypes, and TMB. Methods: Whole exome sequencing (WES) was performed on all samples. HLA-I typing was identified using HLAscan and clustered with HLAClustRView. Mutation analysis was performed with Maftools. Results: We analyzed 810 patients, covering over 20 tumor types, with 163 in the any-homozygous group and 647 in the all-heterozygous gro

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Saudino, Giovanni, Dafne Suraci, Veronica Nasta, Simone Ciofi-Baffoni, and Lucia Banci. "Molecular Basis of Multiple Mitochondrial Dysfunctions Syndrome 2 Caused by CYS59TYR BOLA3 Mutation." International Journal of Molecular Sciences 22, no. 9 (2021): 4848. http://dx.doi.org/10.3390/ijms22094848.

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Multiple mitochondrial dysfunctions syndrome (MMDS) is a rare neurodegenerative disorder associated with mutations in genes with a vital role in the biogenesis of mitochondrial [4Fe–4S] proteins. Mutations in one of these genes encoding for BOLA3 protein lead to MMDS type 2 (MMDS2). Recently, a novel phenotype for MMDS2 with complete clinical recovery was observed in a patient containing a novel variant (c.176G > A, p.Cys59Tyr) in compound heterozygosity. In this work, we aimed to rationalize this unique phenotype observed in MMDS2. To do so, we first investigated the structural impact of t

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Akhmetova, Ainur, Venera Bismilda, Lyailya Chingissova, Maxim Filipenko, Ainur Akilzhanova, and Ulan Kozhamkulov. "Prevalence of Beijing Central Asian/Russian Cluster 94-32 among Multidrug-Resistant M. tuberculosis in Kazakhstan." Antibiotics 13, no. 1 (2023): 9. http://dx.doi.org/10.3390/antibiotics13010009.

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The Beijing genotype is the most distributed M. tuberculosis family in Kazakhstan. In this study, we identified dominant Beijing clusters in Kazakhstan and assessed their drug susceptibility profiles and association with the most widely spread mutation Ser531Leu of the rpoB gene and the mutation Ser315Thr of the katG gene associated with resistance to rifampicin and isoniazid, respectively. M. tuberculosis isolates (n = 540) from new TB cases were included in the study. MIRU-VNTR genotyping was performed for 540 clinical isolates to determine M. tuberculosis families using 24 loci. RD analysis

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Pare-Brunet, Laia, Rebeca Sanz-Pamplona, Adriana Lopez-Doriga, et al. "Expression and methylation profiles associated with recurrent mutations in stage II colorectal cancer." Journal of Clinical Oncology 31, no. 15_suppl (2013): e14613-e14613. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.e14613.

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e14613 Background: Aberration of normal genetic and epigenetic patterns occurs at early stages of colorectal cancer (CRC) and accumulates throughout cancer progression. To characterize pre-metastatic tumors, a series of stage II, microsatellite stable, colon tumors and their paired mucosa were profiled on RNA expression and DNA methylation microarrays ( www.colonomics.org ). Our aim is to define molecular subtypes based on recurrent gene mutations, methylation and expression profiles, and explore if these molecular subtypes are associated to patients’ prognosis. Methods: We have sequenced exom

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Hamidi, Habib, Zoe June Assaf, Solange Peters, et al. "Abstract CT095: Mutation-based subtypes identified in the 1L NSCLC study BFAST using unsupervised machine learning clustering based on consensus non-negative matrix factorization." Cancer Research 85, no. 8_Supplement_2 (2025): CT095. https://doi.org/10.1158/1538-7445.am2025-ct095.

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Abstract Background: Patients with the same disease stage and other clinical parameters often have markedly different prognoses and display variable responses to standard treatments, even within oncogenic subsets. This clinical variability may be driven by molecular heterogeneity and mutational complexity that may be captured by mutational signatures with the potential for impact on patient management. Methods: BFAST (NCT03178552) is a Phase II/III global, multicenter, open-label, multi-cohort screening and interventional umbrella trial designed to evaluate the safety and efficacy of targeted

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Wouters, Bas J., Claudia A. Erpelinck, Peter J. Valk, Roel G. Verhaak, Bob Löwenberg, and Ruud Delwel. "Unique Gene Expression Profiles of AML Patients with CEBPA Mutations." Blood 106, no. 11 (2005): 745. http://dx.doi.org/10.1182/blood.v106.11.745.745.

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Abstract The transcription factor CCAAT/enhancer binding protein alpha (C/EBPalpha) is critical for granulopoiesis. 5–10% of patients with acute myeloid leukemia (AML) carry mutations in the coding region of the CEBPA gene. In a gene expression profiling study of 285 de novo AML patients we previously identified sixteen distinct clusters of AML (Valk et al, N Engl J Med 2004). Eighteen patients (6.3%) carried mutations in CEBPA, and 17 of them were found in two clusters (clusters #4 and #15), indicating that patients with CEBPA mutations exhibit unique gene expression profiles. In cluster #15,

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Chen, Chien-Yuan, Liang-In Lin, Wen-Chien Chou, et al. "Hierarchical Cluster Analysis of Immunophenotype in AML Patients with NPM1 Gene Mutation Reveals Two Distinct Groups with Different Prognosis." Blood 112, no. 11 (2008): 1495. http://dx.doi.org/10.1182/blood.v112.11.1495.1495.

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Abstract Acute myeloid leukemia (AML) is a group of heterogeneous diseases characterized by increasing immature progenitors in the bone marrow and peripheral blood. Prior reports suggested a relationship between surface antigens expression and prognosis of AML. However, there were some debates in subsequent studies. In this study, we performed cluster analysis of the immunophenotype expression profile in AML patients with NPM1 gene mutation, and correlated the result with clinical characteristics, other gene mutations and prognosis. Patients and Methods A total of 534 patients diagnosed as hav

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Reading, Nathan. "Scattering Fans." International Mathematics Research Notices 2020, no. 23 (2018): 9640–73. http://dx.doi.org/10.1093/imrn/rny260.

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Abstract Scattering diagrams arose in the context of mirror symmetry, Donaldson–Thomas theory, and integrable systems. We show that a consistent scattering diagram with minimal support cuts the ambient space into a complete fan. A special class of scattering diagrams, the cluster scattering diagrams, is closely related to cluster algebras. We show that the cluster scattering fan associated to an exchange matrix $B$ refines the mutation fan for $B$ (a complete fan that encodes the geometry of mutations of $B$). We conjecture that, when $B$ is $n\times n$ for $n&gt;2$, these two fans coincid

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Figueroa, Maria E., Sanne Lugthart, Yushan Li, et al. "Epigenetic Signatures Identify New Clinically Relevant Subtypes and Define Gene Regulatory Patterns in Patients with Acute Myeloid Leukemia (AML)." Blood 112, no. 11 (2008): 756. http://dx.doi.org/10.1182/blood.v112.11.756.756.

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Abstract AML is heterogeneous group of diseases with variable clinical outcomes. While cytogenetics, molecular markers and gene expression profiling can help to classify these patients, they still cannot fully explain the biology and clinical outcomes of the disease. Epigenetic gene deregulation is a hallmark of cancer and our preliminary data suggest that epigenetic signatures are critical determinants of cellular phenotype in AML. Therefore, we hypothesized that aberrant epigenetic regulation of genes would provide critical insight into the biological complexity of AML and identify new and c

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Pioszak, Augen A., and Alexander J. Ninfa. "Genetic and Biochemical Analysis of Phosphatase Activity of Escherichia coli NRII (NtrB) and Its Regulation by the PII Signal Transduction Protein." Journal of Bacteriology 185, no. 4 (2003): 1299–315. http://dx.doi.org/10.1128/jb.185.4.1299-1315.2003.

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ABSTRACT Mutant forms of Escherichia coli NRII (NtrB) were isolated that retained wild-type NRII kinase activity but were defective in the PII-activated phosphatase activity of NRII. Mutant strains were selected as mimicking the phenotype of a strain (strain BK) that lacks both of the related PII and GlnK signal transduction proteins and thus has no mechanism for activation of the NRII phosphatase activity. The selection and screening procedure resulted in the isolation of numerous mutants that phenotypically resembled strain BK to various extents. Mutations mapped to the glnL (ntrB) gene enco

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KING, ALASTAIR, and MATTHEW PRESSLAND. "Labelled seeds and the mutation group." Mathematical Proceedings of the Cambridge Philosophical Society 163, no. 2 (2016): 193–217. http://dx.doi.org/10.1017/s0305004116000918.

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AbstractWe study the set${\mathcal{S}}$of labelled seeds of a cluster algebra of rankninside a field${\mathcal{F}}$as a homogeneous space for the groupMnof (globally defined) mutations and relabellings. Regular equivalence relations on${\mathcal{S}}$are associated to subgroupsWof AutMn(${\mathcal{S}}$), and we thus obtain groupoidsW\${\mathcal{S}}$. We show that for two natural choices of equivalence relation, the corresponding groupsWcandW+act on${\mathcal{F}}$, and the groupoidsWc\${\mathcal{S}}$andW+\${\mathcal{S}}$act on the model field${\mathcal{K}}$=ℚ(x1,. . .,xn). The groupoidW+\${\math

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O'Sullivan, Jennifer, Aaron T. Gerds, Claire N. Harrison та ін. "Evidence of NF-ΚB Pathway Activation in Patients with Advanced, High Molecular Risk Myelofibrosis". Blood 138, Supplement 1 (2021): 3584. http://dx.doi.org/10.1182/blood-2021-149666.

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Abstract Introduction: Patients with myelofibrosis who discontinue treatment with the JAK1/2 inhibitor ruxolitinib have a poor prognosis that is often associated with advanced phases of disease and severe cytopenias. While these patients are more likely to have high molecular risk genomic markers, biological drivers of disease in this advanced population are not well characterized. PAC203, a Phase 2 dose-finding study in patients with symptomatic myelofibrosis who were intolerant of or resistant to ruxolitinib, represents an opportune cohort for analyzing the association between high molecular

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Martyn, Gabriella E., Beeke Wienert, Ryo Kurita, Yukio Nakamura, Kate G. R. Quinlan, and Merlin Crossley. "A natural regulatory mutation in the proximal promoter elevates fetal globin expression by creating a de novo GATA1 site." Blood 133, no. 8 (2019): 852–56. http://dx.doi.org/10.1182/blood-2018-07-863951.

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Abstract β-hemoglobinopathies, such as sickle cell disease and β-thalassemia, result from mutations in the adult β-globin gene. Reactivating the developmentally silenced fetal γ-globin gene elevates fetal hemoglobin levels and ameliorates symptoms of β-hemoglobinopathies. The continued expression of fetal γ-globin into adulthood occurs naturally in a genetic condition termed hereditary persistence of fetal hemoglobin (HPFH). Point mutations in the fetal γ-globin proximal promoter can cause HPFH. The −113A&gt;G HPFH mutation falls within the −115 cluster of HPFH mutations, a binding site fo

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Poonthong, Tanapon, and Jeerayut Wetweerapong. "Non-centroid-based discrete differential evolution for data clustering." Bulletin of Electrical Engineering and Informatics 14, no. 1 (2025): 596–605. http://dx.doi.org/10.11591/eei.v14i1.8811.

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Data clustering can find similarities and hidden patterns within data. Given a predefined number of groups, most partitional clustering algorithms use representative centers to determine their corresponding clusters. These algorithms, such as K-means and optimization-based algorithms, create and update centroids to give (hyper) spherical shape clusters. This research proposes a non-centroid-based discrete differential evolution (NCDDE) algorithm to solve clustering problems and provide non-spherical shape clusters. The algorithm directs the population of discrete vectors to search for data gro

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Bloehdorn, Johannes, Martin Sill, Andreas Bühler, et al. "Microrna Expression in Fludarabine-Refractory CLL Implicates Independent Mechanisms of Resistance and Is Associated with Response and Progression Free Survival After Alemtuzumab Treatment: Results From the CLL2H Trial." Blood 120, no. 21 (2012): 2874. http://dx.doi.org/10.1182/blood.v120.21.2874.2874.

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Abstract Abstract 2874 Although novel treatment options have improved response rates and survival in CLL, the portion of cases with refractory disease remains considerably high and management is challenging. The humanized anti-CD52 monoclonal antibody alemtuzumab is standard treatment in refractory CLL and shows efficacy irrespective of the underlying genomic aberrations or mutation status of TP53. However, only about half of all refractory cases can be explained by TP53 mutation/deletion and treatment remains unsatisfactory. To elucidate pathogenic and prognostic factors, we performed microRN

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Antić, Željko, Stefan H. Lelieveld, Cédric G. van der Ham, Edwin Sonneveld, Peter M. Hoogerbrugge, and Roland P. Kuiper. "Unravelling the Sequential Interplay of Mutational Mechanisms during Clonal Evolution in Relapsed Pediatric Acute Lymphoblastic Leukemia." Genes 12, no. 2 (2021): 214. http://dx.doi.org/10.3390/genes12020214.

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Pediatric acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy and is characterized by clonal heterogeneity. Genomic mutations can increase proliferative potential of leukemic cells and cause treatment resistance. However, mechanisms driving mutagenesis and clonal diversification in ALL are not fully understood. In this proof of principle study, we performed whole genome sequencing of two cases with multiple relapses in order to investigate whether groups of mutations separated in time show distinct mutational signatures. Based on mutation allele frequencies at diagnosis

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Szatko, Alicja, Dorota Leszczyńska, Beata Woźniak, and Piotr Glinicki. "The relation between clinical course of pheochromocytoma-paraganglioma (PPGL) and complex genetic etiology." Wiedza Medyczna 5, no. 2 (2023): 21–29. http://dx.doi.org/10.36553/wm.150.

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Recent years brought a remarkable progress on understanding the pathophysiology of rare, neuroendocrine tumours– pheochormocytomas and paragangliomas (PPGLs). Approximately 70% PPGLs are associated with germline or somatic mutation in one of more than 25 identified susceptibility genes, which were grouped into three clusters.Cluster 1 includes genes encoding proteins involved in Krebs cycle and hypoxia pathway – cluster 1 related PPGL are usually located extra-adrenally (often manifest as head and neck paragangliomas), they are also characterized by noradrenergic/dopaminergic biochemical pheno

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Stegat, Lotte, Christian Thomas, Leonille Schweizer, et al. "HGG-45. Characterization of spinal diffuse midline gliomas, H3 K28M-mutant." Neuro-Oncology 24, Supplement_1 (2022): i71. http://dx.doi.org/10.1093/neuonc/noac079.260.

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Abstract Diffuse midline gliomas (DMGs) are malignant gliomas that arise in the midline structures of the central nervous system. Due to their aggressive and diffuse growth and a two-year survival rate of less than 10%, DMGs are assigned to CNS WHO grade 4. Depending on the localization, median age of patients is about 11‒20 years. Genetically, most tumors are defined by a K28M-mutation in one of the highly homologous genes encoding histone protein H3. Since DMGs most frequently occur in pons and thalamus, comparatively little is known about spinal DMGs. Therefore, we histologically, molecular

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Xu, Fei, Qingkang Meng, Feng Wu, et al. "Identification of Warning Transition Points from Hepatitis B to Hepatocellular Carcinoma Based on Mutation Accumulation for the Early Diagnosis and Potential Drug Treatment of HBV-HCC." Oxidative Medicine and Cellular Longevity 2022 (September 5, 2022): 1–29. http://dx.doi.org/10.1155/2022/3472179.

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The accumulation of multiple genetic mutations is essential during the occurrence and development of hepatocellular carcinoma induced by hepatitis B (HBV-HCC), but understanding their cooperative effects and identifying the warning transition point from hepatitis B to HCC are challenges. In the genomic analysis of somatic mutations of the patient with HBV-HCC in a patient-specific protein-protein interaction (ps-PPI) network, we find mutation influence can propagate along the ps-PPI network. Therefore, in the article, we got the mutation cluster as a new research unit using the Random Walks wi

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Samaraweera, Saumya E., Francine E. Garrett-Bakelman, Yaseswini Neelamraju, et al. "Hypermethylation of GADD45A Defines a Methylation Profile Distinct to Mutant IDH1/2, and Correlates with More Aggressive AML." Blood 128, no. 22 (2016): 2877. http://dx.doi.org/10.1182/blood.v128.22.2877.2877.

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Abstract We have previously reported that hypermethylationof the GADD45A promoter (GADD45AmeHI) occurs frequently in AML at a specific CpG residue (CpG1) and associates with poor overall survival for patients on standard chemotherapy (Perugini et al, Leukemia 2013). Sequenom multiplex analysis of 195 AML patients revealed a co-occurrence of GADD45AmeHI with recurrent mutations at conserved residues in IDH1 and IDH2 (p<0.0001, Fisher's exact test). These mutations in IDH1 and IDH2 result in enzyme isoforms that produce high levels of the onco-metabolite 2-hydroxyglutarate with a wide-range o

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Georgin-Lavialle, S., B. Terrier, K. Olivier, and A. Mekinian. "OP0049 FURTHER CHARACTERIZATION OF CLINICAL AND LABORATORY FEATURES OCCURRING IN VEXAS SYNDROME IN A LARGE-SCALE ANALYSIS OF MULTICENTER CASE-SERIES OF 116 FRENCH PATIENTS." Annals of the Rheumatic Diseases 81, Suppl 1 (2022): 33.3–33. http://dx.doi.org/10.1136/annrheumdis-2022-eular.992.

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BackgroundA new autoinflammatory syndrome related to somatic mutations of UBA1 was recently described and called VEXAS syndrome.ObjectivesTo describe clinical characteristics, laboratory findings and outcomes of VEXAS syndrome.MethodsCase-series. Patients referred to a French multicenter registry between November 2020 and May 2021.116 patients with VEXAS syndrome. Frequency and median of parameters and vital status, from diagnosis to the end of the follow-up.ResultsMain clinical features were skin lesions (83.5%), non-infectious fever (63.6%), weight loss (62%), lung involvement (49.6%), ocula

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Chin, Doris B., Rosa Arroyo-Garcia, Oswaldo E. Ochoa, Rick V. Kesseli, Dean O. Lavelle, and Richard W. Michelmore. "Recombination and Spontaneous Mutation at the Major Cluster of Resistance Genes in Lettuce (Lactuca sativa)." Genetics 157, no. 2 (2001): 831–49. http://dx.doi.org/10.1093/genetics/157.2.831.

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Abstract Two sets of overlapping experiments were conducted to examine recombination and spontaneous mutation events within clusters of resistance genes in lettuce. Multiple generations were screened for recombinants using PCR-based markers flanking Dm3. The Dm3 region is not highly recombinagenic, exhibiting a recombination frequency 18-fold lower than the genome average. Recombinants were identified only rarely within the cluster of Dm3 homologs and no crossovers within genes were detected. Three populations were screened for spontaneous mutations in downy mildew resistance. Sixteen Dm mutan

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Fatehi, Farzad, Soroor Advani, Ali Asghar Okhovat, Bentolhoda Ziaadini, Hosein Shamshiri, and Shahriar Nafissi. "Thigh and Leg Muscle MRI Findings in GNE Myopathy." Journal of Neuromuscular Diseases 8, no. 4 (2021): 735–42. http://dx.doi.org/10.3233/jnd-210629.

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Background: Muscle MRI protocols have been developed to assess muscle involvement in a wide variety of muscular dystrophies. Different muscular dystrophies can involve muscle groups in characteristic patterns. These patterns can be identified in muscle MRI in the form of fatty infiltration. Objective: This study was conducted to add the existing knowledge of muscle MRI in GNE myopathy and evaluate the correlation of muscular involvement with different gene mutations. Methods: The MRI scans of the 18 GNE patients were analyzed retrospectively. Cluster analysis was done for grouping the muscles

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Nölting, Ullrich, Pietzsch, et al. "Current Management of Pheochromocytoma/Paraganglioma: A Guide for the Practicing Clinician in the Era of Precision Medicine." Cancers 11, no. 10 (2019): 1505. http://dx.doi.org/10.3390/cancers11101505.

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Pheochromocytomas and paragangliomas (PCC/PGLs) are rare, mostly catecholamine-producing neuroendocrine tumors of the adrenal gland (PCCs) or the extra-adrenal paraganglia (PGL). They can be separated into three different molecular clusters depending on their underlying gene mutations in any of the at least 20 known susceptibility genes: The pseudohypoxia-associated cluster 1, the kinase signaling-associated cluster 2, and the Wnt signaling-associated cluster 3. In addition to tumor size, location (adrenal vs. extra-adrenal), multiplicity, age of first diagnosis, and presence of metastatic dis

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Bonacci, Paolo Giuseppe, Dalida Angela Bivona, Dafne Bongiorno, et al. "Low Represented Mutation Clustering in SARS-CoV-2 B.1.1.7 Sublineage Group with Synonymous Mutations in the E Gene." Diagnostics 11, no. 12 (2021): 2286. http://dx.doi.org/10.3390/diagnostics11122286.

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Starting in 2019, the COVID-19 pandemic is a global threat that is difficult to monitor. SARS-CoV-2 is known to undergo frequent mutations, including SNPs and deletions, which seem to be transmitted together, forming clusters that define specific lineages. Reverse-Transcription quantitative PCR (RT-qPCR) has been used for SARS-CoV-2 diagnosis and is still considered the gold standard method. Our Eukaryotic Host Pathogens Interaction (EHPI) laboratory received six SARS-CoV-2-positive samples from a Sicilian private analysis laboratory, four of which showed a dropout of the E gene. Our sequencin

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Morimoto, Suguru, Hideki Makishima, Yasunobu Nagata, et al. "DNA Methylation and Genetic Profiles in 320 Patients with Myelodysplastic Syndromes." Blood 132, Supplement 1 (2018): 1799. http://dx.doi.org/10.1182/blood-2018-99-116489.

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Abstract MDS is a heterogeneous group of myeloid neoplasms caused by genetic and epigenetic alterations. During the past decade, the major driver mutations in MDS have been fully investigated. However, the role of epigenetic alterations, particularly those of DNA methylation, has less intensively been studied, even though abnormal DNA methylation has long been implicated in the pathogenesis of MDS. In this study, we analyzed DNA methylation status of bone marrow mononuclear cells from 320 cases with MDS-SLD (n = 7), MDS-RS (n = 63), MDS-MLD (n = 51), MDS-EB (n = 186), MDS-U (n = 1), and MDS wi

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Schroeder, Michael P., Martin Neumann, Cornelia Eckert, et al. "Multi-Genomics of Relapsed B-Cell Precursor Acute Lymphoblastic Leukemia Reveals Three Distinct Genetic Clusters Characterized By Different Alterations." Blood 128, no. 22 (2016): 453. http://dx.doi.org/10.1182/blood.v128.22.453.453.

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Abstract Introduction: Despite the recent identification of the Ph-like subgroup of B-cell precursor Acute Lymphoblastic Leukemia (BCP-ALL), a large number of BCP-ALL patients lack cytogenetic and molecular defined lesions. To get a higher resolution and a broader molecular view of relapsed BCP-ALL, we designed a multi-omics study to reveal age-overriding relapse-driving alterations that may unravel novel molecular targets. Methods: We studied 150 paired samples (initial diagnosis: ID; relapse: REL; complete remission: CR) from 50 patients without known translocations. The cohort consisted of

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Striedner, Yasmin, Barbara Arbeithuber, Sofia Moura, et al. "Exploring the Micro-Mosaic Landscape of FGFR3 Mutations in the Ageing Male Germline and Their Potential Implications in Meiotic Differentiation." Genes 15, no. 2 (2024): 191. http://dx.doi.org/10.3390/genes15020191.

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Advanced paternal age increases the risk of transmitting de novo germline mutations, particularly missense mutations activating the receptor tyrosine kinase (RTK) signalling pathway, as exemplified by the FGFR3 mutation, which is linked to achondroplasia (ACH). This risk is attributed to the expansion of spermatogonial stem cells carrying the mutation, forming sub-clonal clusters in the ageing testis, thereby increasing the frequency of mutant sperm and the number of affected offspring from older fathers. While prior studies proposed a correlation between sub-clonal cluster expansion in the te

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Sultana, Sharmin, Miha Kitajima, Hironori Kobayashi, et al. "A Natural Variation of Fumonisin Gene Cluster Associated with Fumonisin Production Difference in Fusarium fujikuroi." Toxins 11, no. 4 (2019): 200. http://dx.doi.org/10.3390/toxins11040200.

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Fusarium fujikuroi, a member of the Fusarium fujikuroi species complex, stands out as a rice bakanae disease pathogen with a high production of gibberellic acid. Not all, but some F. fujikuroi strains are known to produce a carcinogenic mycotoxin fumonisin. Fumonisin biosynthesis is dependent on the FUM cluster composed of 16 FUM genes. The FUM cluster was detected not only from a fumonisin producing strain, but also from a fumonisin nonproducing strain that does not produce a detectable level of fumonisin. Genetic mapping indicated the causative mutation(s) of fumonisin nonproduction is prese

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