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Journal articles on the topic 'Mutation frequencies'

Author: Grafiati

Published: 4 June 2025

Last updated: 1 August 2025

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1

Song, Hao, Yao Huang, and Xiaoqing Jiang. "Mutation spectrum associated with metastasis of advanced cholangiocarcinoma." Journal of International Medical Research 50, no. 6 (2022): 030006052211020. http://dx.doi.org/10.1177/03000605221102080.

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Background The mutations associated with metastasis in advanced-stage cholangiocarcinoma (CCA) have not been investigated. Objective To explore mutations in patients with advanced CCA and independent factors related to metastasis. Methods This retrospective study performed next-generation sequencing of tumor specimens from patients with advanced CCA treated between January 2017 and December 2019. Tumor mutational burden (TMB), microsatellite instability, and programmed cell death ligand (PD-L)1 positivity were determined. Factors independently associated with metastasis were explored via logis

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2

Lamb, Bernard C., Muhammad Saleem, William Scott, Nina Thapa, and Eviatar Nevo. "Inherited and Environmentally Induced Differences in Mutation Frequencies Between Wild Strains of Sordaria fimicola From “Evolution Canyon”." Genetics 149, no. 1 (1998): 87–99. http://dx.doi.org/10.1093/genetics/149.1.87.

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Abstract We have studied whether there is natural genetic variation for mutation frequencies, and whether any such variation is environment-related. Mutation frequencies differed significantly between wild strains of the fungus Sordaria fimicola isolated from a harsher or a milder microscale environment in “Evolution Canyon,” Israel. Strains from the harsher, drier, south-facing slope had higher frequencies of new spontaneous mutations and of accumulated mutations than strains from the milder, lusher, north-facing slope. Collective total mutation frequencies over many loci for ascospore pigmen

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Yang, Zhi, Priyatama Pandey, Darryl Shibata, David V. Conti, Paul Marjoram, and Kimberly D. Siegmund. "HiLDA: a statistical approach to investigate differences in mutational signatures." PeerJ 7 (August 28, 2019): e7557. http://dx.doi.org/10.7717/peerj.7557.

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We propose a hierarchical latent Dirichlet allocation model (HiLDA) for characterizing somatic mutation data in cancer. The method allows us to infer mutational patterns and their relative frequencies in a set of tumor mutational catalogs and to compare the estimated frequencies between tumor sets. We apply our method to two datasets, one containing somatic mutations in colon cancer by the time of occurrence, before or after tumor initiation, and the second containing somatic mutations in esophageal cancer by sex, age, smoking status, and tumor site. In colon cancer, the relative frequencies o

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Lawson-Michod, Katherine A., David Nix, Lindsay Collin, et al. "Abstract 3506: High-grade serous ovarian cancer somatic mutational signatures in Black and White individuals." Cancer Research 83, no. 7_Supplement (2023): 3506. http://dx.doi.org/10.1158/1538-7445.am2023-3506.

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Abstract Causes of racial disparities in ovarian cancer survival are likely multifactorial, including socio-environmental, structural, and biological factors. Mutational signatures reflect endogenous and exogenous exposures, which may differ by race and ethnicity. This study aims to characterize mutational signatures and their associated etiologies among Black high-grade serous ovarian cancer (HGSC) cases, and to compare the occurrence and distribution of signatures with White TCGA cases. Mutational profiling with whole exome sequencing in matched blood and tumor formalin-fixed paraffin-embedd

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Chen, Renxiang, Masaru Yokoyama, Hironori Sato, Cavan Reilly, and Louis M. Mansky. "Human Immunodeficiency Virus Mutagenesis during Antiviral Therapy: Impact of Drug-Resistant Reverse Transcriptase and Nucleoside and Nonnucleoside Reverse Transcriptase Inhibitors on Human Immunodeficiency Virus Type 1 Mutation Frequencies." Journal of Virology 79, no. 18 (2005): 12045–57. http://dx.doi.org/10.1128/jvi.79.18.12045-12057.2005.

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ABSTRACT The development of antiviral drug resistance is an important problem in the treatment of human immunodeficiency virus type 1 (HIV-1) infection. Potent antiretroviral therapy is currently used for treatment, and typically consists of at least two reverse transcriptase (RT) inhibitors. We have previously reported that both drugs and drug-resistant RT mutants can increase virus mutation frequencies. To further assess the contributions of nucleoside RT inhibitors (NRTIs), nonnucleoside RT inhibitors (NNRTIs), and drug-resistant RTs to HIV mutagenesis, a new high-throughput assay system wa

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Bradley, L. A., D. D. Johnson, G. E. Palomaki, J. E. Haddow, N. H. Robertson, and R. M. Ferrie. "Hereditary haemochromatosis mutation frequencies in the general population." Journal of Medical Screening 5, no. 1 (1998): 34–36. http://dx.doi.org/10.1136/jms.5.1.34.

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Objectives This study aims to expand our knowledge of the general population frequency of two mutations, C282Y and H63D, identified in the candidate gene for hereditary haemochromatosis, and to determine whether the testing can be performed using routinely obtained cheek-brush (buccal) samples. Setting Banked buccal lysate samples, randomised and coded for anonymity, from a cohort of couples who underwent prenatal cystic fibrosis screening in Maine. Methods A multiplex ARMS test was performed on buccal cell lysates to identify the two mutations. Results Genotype frequencies found among the 100

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Martinez, J. L., and F. Baquero. "Mutation Frequencies and Antibiotic Resistance." Antimicrobial Agents and Chemotherapy 44, no. 7 (2000): 1771–77. http://dx.doi.org/10.1128/aac.44.7.1771-1777.2000.

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Brazhnik, K., S. Sun, O. Alani, et al. "Single-cell analysis reveals different age-related somatic mutation profiles between stem and differentiated cells in human liver." Science Advances 6, no. 5 (2020): eaax2659. http://dx.doi.org/10.1126/sciadv.aax2659.

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Accumulating somatic mutations have been implicated in age-related cellular degeneration and death. Because of their random nature and low abundance, somatic mutations are difficult to detect except in single cells or clonal cell lineages. Here, we show that in single hepatocytes from human liver, an organ exposed to high levels of genotoxic stress, somatic mutation frequencies are high and increase substantially with age. Considerably lower mutation frequencies were observed in liver stem cells (LSCs) and organoids derived from them. Mutational spectra in hepatocytes showed signatures of oxid

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9

Korkmaz, D. T., P. G. Atak, and Ç. Çelik. "Frequencies of the Common Mefv Gene Mutations in Adiyaman, Southeast Anatolia, Turkey." Balkan Journal of Medical Genetics 17, no. 2 (2014): 67–71. http://dx.doi.org/10.2478/bjmg-2014-0076.

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Abstract Familial Mediterranean fever (FMF) is an autosomal recessive disorder characterized by fever and serosal inflammation. The reasons for the disorder are mutations in the Mediterranean fever (MEFV) gene; the most common of which are M694V, M680I, M694I and V726A. In this study, we aimed to screen these common mutations of the MEFV gene and then determine the prevalence of FMF according to these mutations in Adıyaman, Southeast Anatolia, Turkey. Seven hundred and sixty-seven healthy individuals from the region of Adıyaman participated in the study. Polymerase chain reaction-amplification

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10

Monroe, J. Grey, Thanvi Srikant, Pablo Carbonell-Bejerano, et al. "Mutation bias reflects natural selection in Arabidopsis thaliana." Nature 602, no. 7895 (2022): 101–5. http://dx.doi.org/10.1038/s41586-021-04269-6.

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AbstractSince the first half of the twentieth century, evolutionary theory has been dominated by the idea that mutations occur randomly with respect to their consequences1. Here we test this assumption with large surveys of de novo mutations in the plant Arabidopsis thaliana. In contrast to expectations, we find that mutations occur less often in functionally constrained regions of the genome—mutation frequency is reduced by half inside gene bodies and by two-thirds in essential genes. With independent genomic mutation datasets, including from the largest Arabidopsis mutation accumulation expe

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Kelly, John K. "Deleterious Mutations and the Genetic Variance of Male Fitness Components in Mimulus guttatus." Genetics 164, no. 3 (2003): 1071–85. http://dx.doi.org/10.1093/genetics/164.3.1071.

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Abstract Deleterious mutations are relevant to a broad range of questions in genetics and evolutionary biology. I present an application of the “biometric method” for estimating mutational parameters for male fitness characters of the yellow monkeyflower, Mimulus guttatus. The biometric method rests on two critical assumptions. The first is that experimental inbreeding changes genotype frequencies without changing allele frequencies; i.e., there is no genetic purging during the experiment. I satisfy this condition by employing a breeding design in which the parents are randomly extracted, full

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Hwang, Ying T., and Charles B. C. Hwang. "Exonuclease-Deficient Polymerase Mutant of Herpes Simplex Virus Type 1 Induces Altered Spectra of Mutations." Journal of Virology 77, no. 5 (2003): 2946–55. http://dx.doi.org/10.1128/jvi.77.5.2946-2955.2003.

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ABSTRACT The effect of exonuclease activity of the herpes simplex virus DNA polymerase (Pol) on DNA replication fidelity was examined by using the supF mutagenesis assay. The recombinants with exonuclease-deficient Pol, containing an integrated supF gene in the thymidine kinase locus (tk), exhibited supF mutation frequencies ranging from 0.14 to 5.6%, consistent with the tk mutation frequencies reported previously (Y. T. Hwang, B.-Y. Liu, D. M. Coen, and C. B. C. Hwang, J. Virol. 71:7791-7798, 1997). The increased mutation frequencies were 10- to 500-fold higher than those observed for wild-ty

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Dunson, David B., and Kenneth R. Tindall. "Bayesian Analysis of Mutational Spectra." Genetics 156, no. 3 (2000): 1411–18. http://dx.doi.org/10.1093/genetics/156.3.1411.

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Abstract Studies that examine both the frequency of gene mutation and the pattern or spectrum of mutational changes can be used to identify chemical mutagens and to explore the molecular mechanisms of mutagenesis. In this article, we propose a Bayesian hierarchical modeling approach for the analysis of mutational spectra. We assume that the total number of independent mutations and the numbers of mutations falling into different response categories, defined by location within a gene and/or type of alteration, follow binomial and multinomial sampling distributions, respectively. We use prior di

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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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Valdes, A. M., M. Slatkin, and N. B. Freimer. "Allele frequencies at microsatellite loci: the stepwise mutation model revisited." Genetics 133, no. 3 (1993): 737–49. http://dx.doi.org/10.1093/genetics/133.3.737.

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Abstract We summarize available data on the frequencies of alleles at microsatellite loci in human populations and compare observed distributions of allele frequencies to those generated by a simulation of the stepwise mutation model. We show that observed frequency distributions at 108 loci are consistent with the results of the model under the assumption that mutations cause an increase or decrease in repeat number by one and under the condition that the product Nu, where N is the effective population size and u is the mutation rate, is larger than one. We show that the variance of the distr

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Dimitrov, George, Vladislav Nankov, Natalia Chilingirova, Zornitsa Kamburova, and Savelina Popovska. "Molecular Landscape of Metastatic Lung Adenocarcinoma in Bulgarian Patients—A Prospective Study." International Journal of Molecular Sciences 26, no. 14 (2025): 7017. https://doi.org/10.3390/ijms26147017.

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Lung adenocarcinoma exhibits a heterogeneous molecular landscape shaped by key oncogenic drivers and tumor suppressor gene alterations. Mutation frequencies vary geographically, influenced by genetic ancestry and environmental factors. However, the molecular profile of lung adenocarcinoma in Bulgarian patients remains largely uncharacterized. We conducted a prospective study of 147 Bulgarian patients with metastatic lung adenocarcinoma, analyzing clinicopathologic features and somatic mutation frequencies using next-generation sequencing. Key mutations and their prevalence were assessed and co

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Maldonado, J. Alberto, Chin-Hsien Tai, and Christine Alewine. "Genomic characterization of somatic mutations by race and ethnicity in pancreatic cancer defined through AACR project GENIE." Journal of Clinical Oncology 41, no. 16_suppl (2023): 4138. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.4138.

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4138 Background: KRAS, TP53, SMAD4, and CDKN2A are widely recognized as the most common somatic mutations amongst patients with pancreatic ductal adenocarcinoma (PDAC); however, previous genomic studies have disproportionately included non-Hispanic White (NHW) patients with little to no inclusion of racial and ethnic minorities, particularly non-Hispanic Black (NHB) and Hispanic patients. Additionally, little is known about the distribution of KRAS point mutations in PDAC in specific racial and ethnic groups. Here, we describe somatic mutation differences in a larger and more racially and ethn

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Jennings, Tara S., Anton N. Nguyen, Weiping Chu, Dan Mercola, and Farah Rahmatpanah. "Abstract 4955: Somatic mutation frequency in prostate cancer patients of different ancestries and age of onset." Cancer Research 85, no. 8_Supplement_1 (2025): 4955. https://doi.org/10.1158/1538-7445.am2025-4955.

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Abstract Background: Prostate cancer (PCa) varies significantly in outcomes based on age of onset and genetic ancestry. Early-onset PCa (EoPCa), diagnosed in men under 55, exhibits aggressive behavior, poor differentiation, and resistance to hormonal therapies, resulting in worse outcomes compared to late-onset PCa (LoPCa). African American (AA) men face more aggressive disease and higher incidence rates than White men with European heritage (EA), even after accounting for socioeconomic factors. Investigating somatic mutations in PCa is essential to understanding disease progression, as the bi

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Yamane, Yuki, Koichi Goto, Akikazu Kawase, et al. "Ethnic difference of driver mutation frequencies and correlations between driver mutations and histologic subtypes in lung adenocarcinoma." Journal of Clinical Oncology 30, no. 15_suppl (2012): 1552. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.1552.

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1552 Background: The frequencies of known driver mutation in lung adenocarcinoma from patients in the United States have been reported by the NCI’s Lung Cancer Mutation Consortium (LCMC), indicating driver mutations were detected in 54% (280/516) of tumors. In this report, mutations found: EGFR 17%, KRAS 22%, HER2 0.6%, PIK3CA 1.2%, BRAF 2%, MET amplification 0.6%, MAP2K1 0.4%, NRAS 0.4%, AKT 0%, ALK rearrangements 7%. However little is known about ethnic difference of driver mutation frequencies and correlations between driver mutations and histological subtypes in lung adenocarcinoma. Method

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Ahsan, Muhammad Danyal, Emily M. Webster, Sarah R. Levi, et al. "Abstract 4258: Racial and ethnic differences in the mutational landscape of low-grade serous ovarian cancer." Cancer Research 83, no. 7_Supplement (2023): 4258. http://dx.doi.org/10.1158/1538-7445.am2023-4258.

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Abstract Objective To characterize the mutational landscape of low grade serous ovarian cancer (LGSOC) with racial/ethnic stratification. Methods The AACR Project GENIE database version 12.0 was queried via cBioPortal (http://genie.cbioportal.org) for low-grade serous ovarian cancer (LGSOC) samples. This is a publicly available, de-identified, multi-institutional database of next-generation sequencing genomic profiling results for tumor samples. Mutation frequencies for 9 homologous recombination deficiency (HRD) genes, 4 MAP-Kinase (MAP-K) pathway genes and 6 mismatch-repair (MMR) deficiency

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Ito-Harashima, Sayoko, Phillip E. Hartzog, Himanshu Sinha, and John H. McCusker. "The tRNA-Tyr Gene Family ofSaccharomyces cerevisiae: Agents of Phenotypic Variation and Position Effects on Mutation Frequency." Genetics 161, no. 4 (2002): 1395–410. http://dx.doi.org/10.1093/genetics/161.4.1395.

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AbstractExtensive phenotypic diversity or variation exists in clonal populations of microorganisms and is thought to play a role in adaptation to novel environments. This phenotypic variation or instability, which occurs by multiple mechanisms, may be a form of cellular differentiation and a stochastic means for modulating gene expression. This work dissects a case of phenotypic variation in a clinically derived Saccharomyces cerevisiae strain involving a cox15 ochre mutation, which acts as a reporter. The ochre mutation reverts to sense at a low frequency while tRNA-Tyr ochre suppressors (SUP

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Riner, Andrea N., Enrique I. Velazquez-Villarreal, Seeta Rajpara, et al. "Somatic Genomic Profiling of Pancreatic Ductal Adenocarcinomas From a Diverse Cohort of Patients." Pancreas 54, no. 3 (2025): e171-e178. https://doi.org/10.1097/mpa.0000000000002408.

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Objectives Black/African American (B/AA) pancreatic ductal adenocarcinoma (PDAC) patients have worse clinical outcomes than White patients and are underrepresented in genomic databases. We aimed to expand our understanding of the PDAC somatic landscape from a diverse cohort. Materials and Methods Formalin-fixed paraffin-embedded specimens from 24 surgically resected PDAC cases were collected, with self-reported race/ethnicity. Whole exome sequencing was performed on malignant and benign tissue. Bioinformatics analysis included deduction of genetic ancestry and somatic mutational analysis, with

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Bhattacharyya, Saptarshi. "Analysis of Mutational Profiles of SARS-CoV-2 Structural and Non-Structural Proteins with Emphasis on Spike Protein Variants." Trends in Sciences 19, no. 17 (2022): 5768. http://dx.doi.org/10.48048/tis.2022.5768.

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SARS-CoV-2 has very recently posed a potential threat to humanity due to its very rapid rate of mutations and repairing mechanism. The spread of this virus is considered to have occurred in Wuhan, China in December 2019. Characterized by high rates of transmission, the virus is constantly evolving towards attaining higher rates of stability and transmissibility through acquiring mutations in its genome. Therefore, this study aims to analyse the mutational profiles of SARS-CoV-2 isolates. Analysis of the mutational profiles in individual SARS-CoV-2 proteins will allow us to look into the rates

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Pfaff, Elke, Marc Remke, Dominik Sturm, et al. "TP53 Mutation Is Frequently Associated With CTNNB1 Mutation or MYCN Amplification and Is Compatible With Long-Term Survival in Medulloblastoma." Journal of Clinical Oncology 28, no. 35 (2010): 5188–96. http://dx.doi.org/10.1200/jco.2010.31.1670.

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Purpose The role of TP53 mutations in the tumorigenesis of sporadic medulloblastoma (MB) and the value of TP53 mutation status as a prognostic marker are not yet definitely elucidated. A recent report identified TP53 mutations in MB as an adverse prognostic marker. Hence, the current study was conducted to validate the prognostic role of TP53 mutation in MB and to understand its contribution to tumorigenesis. Methods A comprehensive genetic analysis of 310 MB samples was performed by screening for TP53 mutations and further relating the TP53 mutation status to p53 immunostaining, cytogenetic a

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Georghiou, S. B., M. Seifert, D. Catanzaro, et al. "Frequency and Distribution of Tuberculosis Resistance-Associated Mutations between Mumbai, Moldova, and Eastern Cape." Antimicrobial Agents and Chemotherapy 60, no. 7 (2016): 3994–4004. http://dx.doi.org/10.1128/aac.00222-16.

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ABSTRACTMolecular diagnostic assays, with their ability to rapidly detect resistance-associated mutations in bacterial genes, are promising technologies to control the spread of drug-resistant tuberculosis (DR-TB). Sequencing assays provide detailed information for specific gene regions and can help diagnostic assay developers prioritize mutations for inclusion in their assays. We performed pyrosequencing of sevenMycobacterium tuberculosisgene regions (katG,inhA,ahpC,rpoB,gyrA,rrs, andeis) for 1,128 clinical specimens from India, Moldova, and South Africa. We determined the frequencies of each

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Seong, Keon Mook, Da-Young Lee, Kyong Sup Yoon, et al. "Establishment of Quantitative Sequencing and Filter Contact Vial Bioassay for Monitoring Pyrethroid Resistance in the Common Bed Bug, Cimex lectularius." Journal of Medical Entomology 47, no. 4 (2010): 592–99. http://dx.doi.org/10.1093/jmedent/47.4.592.

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Abstract Two point mutations (V419L and L925I) in the voltage-sensitive sodium channel α-subunit gene have been identified in deltamethrin-resistant bed bugs. A quantitative sequencing (QS) protocol was developed to establish a population-based genotyping method as a molecular resistance-monitoring tool based on the frequency of the two mutations. The nucleotide signal ratio at each mutation site was generated from sequencing chromatograms and plotted against the corresponding resistance allele frequency. Frequency prediction equations were generated from the plots by linear regression, and th

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Shikhbabaeva, Dzhariyat, Vasily Shuvaev, Sergey Kapustin, et al. "The Influence of Hemostasis Genetic Features on Thrombosis Rates in Patients with Polycythemia Vera." Blood 126, no. 23 (2015): 5180. http://dx.doi.org/10.1182/blood.v126.23.5180.5180.

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Abstract Background. Thrombotic complications are the main cause of disability and mortality in Polycythemia Vera (PV) patients. Thrombosis in PV is a result of both inherited (genetic) and acquired predisposition under the external factors influence. Effective personalized prophylactic antithrombotic therapy is a key factor to save quantity and quality of life in PV patients. Objective. The objective of study was to assess the prevalence of hereditary thrombophilia genetic markers in PV patients in overall and groups with or without thrombotic complications. Materials and methods. 104 PV pati

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Vuong, Linh, and Quang Nguyen. "Oncogenic driver mutations in Vietnamese patients with lung adenocarcinoma." Journal of Advanced Biotechnology and Experimental Therapeutics 6, no. 2 (2023): 412. http://dx.doi.org/10.5455/jabet.2023.d136.

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Mutation profiles of oncogenes play essential roles in cancer therapy, but data on the prevalence of lung cancer oncogenic driver mutations in Vietnamese patients are limited. This study aims to evaluate the mutation status of EGFR, ALK, ROS1, RET and MET and analyze the association of gene mutations with clinicopathological characteristics of lung adenocarcinoma. Of the 179 lung adenocarcinoma tissues, EGFR, ALK, ROS1, RET and MET mutation frequencies were 44.6; 7.9; 3.0; 3.0 and 2.0 percent, respectively. EGFR, ALK, ROS1 and RET alterations tended to be higher in females. Moreover, rearrange

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Shah, Jasmine M., Aparna C., and Pallavi S. Nair. "Plant Growth Promoting Rhizobacteria (PGPRs) Alter Plant Host Somatic Mutation Frequencies." INTERNATIONAL JOURNAL OF PLANT AND ENVIRONMENT 5, no. 03 (2019): 149–54. http://dx.doi.org/10.18811/ijpen.v5i03.2.

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Plant growth promoting rhizobacteria (PGPRs) are a group of soil bacteria which can induce positive growth in plants by different mechanisms. This work intends to find the effect of PGPRs on two classes of somatic mutations in the host, frame shift mutation (FSM) and somatic homologous recombination (SHR) and, compare the same with that of a pathogen. Somatic mutations in plants are important as they are an adaptation strategy to overcome stressful conditions and also get passed on to the next generations. The mutation detector Arabidopsis thaliana lines carrying a non-functional β-glucuronida

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Phung, Quy H., David B. Winter, Rudaina Alrefai, and Patricia J. Gearhart. "Cutting Edge: Hypermutation in Ig V Genes from Mice Deficient in the MLH1 Mismatch Repair Protein." Journal of Immunology 162, no. 6 (1999): 3121–24. http://dx.doi.org/10.4049/jimmunol.162.6.3121.

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Abstract During somatic hypermutation of Ig V genes, mismatched nucleotide substitutions become candidates for removal by the DNA mismatch repair pathway. Previous studies have shown that V genes from mice deficient for the MSH2 and PMS2 mismatch repair proteins have frequencies of mutation that are comparable with those from wild-type (wt) mice; however, the pattern of mutation is altered. Because the absence of MSH2 and PMS2 produced different mutational spectra, we examined the role of another protein involved in mismatch repair, MLH1, on the frequency and pattern of hypermutation. MLH1-def

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Nishino, Hiroshi, Daniel J. Schaid, Victoria L. Buettner, Jan Haavik, and Steve S. Sommer. "Mutational specificity: Mutation frequencies butnot mutant frequencies in Big Blue® mice fit a Poisson distribution." Environmental and Molecular Mutagenesis 28, no. 4 (1996): 414–17. http://dx.doi.org/10.1002/(sici)1098-2280(1996)28:4<414::aid-em16>3.0.co;2-i.

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Wood, Anthony C., Yonghong Zhang, Qianxing Mo, et al. "Evaluation of Tumor DNA Sequencing Results in Patients with Gastric and Gastroesophageal Junction Adenocarcinoma Stratified by TP53 Mutation Status." Oncologist 27, no. 4 (2022): 307–13. http://dx.doi.org/10.1093/oncolo/oyac018.

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Abstract Background Gastric cancer (GC) and gastroesophageal junction adenocarcinomas (GEJ) are molecularly diverse. TP53 is the most frequently altered gene with approximately 50% of patients harboring mutations. This qualitative study describes the distinct genomic alterations in GCs and GEJs stratified by TP53 mutation status. Patients and Methods Tumor DNA sequencing results of 324 genes from 3741 patients with GC and GEJ were obtained from Foundation Medicine. Association between gene mutation frequency and TP53 mutation status was examined using Fisher’s exact test. Functional gene group

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Mao, Guanxian, Peng Xuxing, Wu Hao, et al. "Mutational landscape of early-stage non-small cell lung cancer patients using a 451 gene panel." Journal of Clinical Oncology 37, no. 15_suppl (2019): e20048-e20048. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.e20048.

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e20048 Background: Many studies have reported mutation landscapes of non-small cell lung cancer (NSCLC), but most of the data were from advanced-stage patients. This study reports the mutation landscape of early-stage NSCLC patients. Methods: Many studies have reported mutation landscapes of non-small cell lung cancer (NSCLC), but most of the data were from advanced-stage patients. This study reports the mutation landscape of early-stage NSCLC patients. Results: In all, 74 tDNA and ctDNA samples were analyzed. A total of 285 mutations were identified, including 174 in tDNA and 111 in plasma ct

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DuBridge, R. B., P. Tang, H. C. Hsia, P. M. Leong, J. H. Miller, and M. P. Calos. "Analysis of mutation in human cells by using an Epstein-Barr virus shuttle system." Molecular and Cellular Biology 7, no. 1 (1987): 379–87. http://dx.doi.org/10.1128/mcb.7.1.379-387.1987.

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We developed highly sensitive shuttle vector systems for detection of mutations formed in human cells using autonomously replicating derivatives of Epstein-Barr virus (EBV). EBV vectors carrying the bacterial lacI gene as the target for mutation were established in human cells and later returned to Escherichia coli for rapid detection and analysis of lacI mutations. The majority of the clonal cell lines created by establishment of the lacI-EBV vector show spontaneous LacI- frequencies of less than 10(-5) and are suitable for studies of induced mutation. The ability to isolate clonal lines repr

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DuBridge, R. B., P. Tang, H. C. Hsia, P. M. Leong, J. H. Miller, and M. P. Calos. "Analysis of mutation in human cells by using an Epstein-Barr virus shuttle system." Molecular and Cellular Biology 7, no. 1 (1987): 379–87. http://dx.doi.org/10.1128/mcb.7.1.379.

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We developed highly sensitive shuttle vector systems for detection of mutations formed in human cells using autonomously replicating derivatives of Epstein-Barr virus (EBV). EBV vectors carrying the bacterial lacI gene as the target for mutation were established in human cells and later returned to Escherichia coli for rapid detection and analysis of lacI mutations. The majority of the clonal cell lines created by establishment of the lacI-EBV vector show spontaneous LacI- frequencies of less than 10(-5) and are suitable for studies of induced mutation. The ability to isolate clonal lines repr

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Machielsen, Ronnie, Ingrid J. van Alen-Boerrigter, Lucy A. Koole, Roger S. Bongers, Michiel Kleerebezem, and Johan E. T. Van Hylckama Vlieg. "Indigenous and Environmental Modulation of Frequencies of Mutation in Lactobacillus plantarum." Applied and Environmental Microbiology 76, no. 5 (2009): 1587–95. http://dx.doi.org/10.1128/aem.02595-09.

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ABSTRACT Reliability of microbial (starter) strains in terms of quality, functional properties, growth performance, and robustness is essential for industrial applications. In an industrial fermentation process, the bacterium should be able to successfully withstand various adverse conditions during processing, such as acid, osmotic, temperature, and oxidative stresses. Besides the evolved defense mechanisms, stress-induced mutations participate in adaptive evolution for survival under stress conditions. However, this may lead to accumulation of mutant strains, which may be accompanied by loss

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Knoepfel, Stefanie Andrea, Nadine Christina Salisch, Peter Michael Huelsmann, Pia Rauch, Hauke Walter, and Karin Jutta Metzner. "Comparison of G-to-A Mutation Frequencies Induced by APOBEC3 Proteins in H9 Cells and Peripheral Blood Mononuclear Cells in the Context of Impaired Processivities of Drug-Resistant Human Immunodeficiency Virus Type 1 Reverse Transcriptase Variants." Journal of Virology 82, no. 13 (2008): 6536–45. http://dx.doi.org/10.1128/jvi.00554-08.

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ABSTRACT APOBEC3 proteins can inhibit human immunodeficiency virus type 1 (HIV-1) replication by inducing G-to-A mutations in newly synthesized viral DNA. However, HIV-1 is able to overcome the antiretroviral activity of some of those enzymes by the viral protein Vif. We investigated the impact of different processivities of HIV-1 reverse transcriptases (RT) on the frequencies of G-to-A mutations introduced by APOBEC3 proteins. Wild-type RT or the M184V, M184I, and K65R+M184V RT variants, which are increasingly impaired in their processivities, were used in the context of a vif-deficient molec

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Arigbede, Olumide M., David Gbogbo, and Sarah Buxbaum. "Mutational burden among patients with metastatic prostate cancer differs by race in 3 key genes: An analysis of genomic and clinical data from the AACR Project GENIE biopharma collaborative in cBioPortal." Journal of Clinical Oncology 42, no. 16_suppl (2024): 5106. http://dx.doi.org/10.1200/jco.2024.42.16_suppl.5106.

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5106 Background: Prostate cancer exhibits a range of aggressive oncological traits due to its genomic heterogeneity. The extent to which clinical and demographic variables affect cancer behaviors and increase disparities is a complex and open question. Objective: We aim to comprehensively explore the genomic and epigenetic characteristics of metastatic prostate cancer (PCa) across different racial groups to elucidate potential molecular and immune mechanisms underlying disparities in disease progression and treatment response. Methods: Data from the Association for Cancer Research Project Geno

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Abdelsamia, Mahmoud, Daniel Joseph Chavarin, Jonathan Coy, et al. "Somatic genomic landscape of prostate adenocarcinoma at a comprehensive cancer center in New Mexico: A retrospective study (2015-2022)." Journal of Clinical Oncology 43, no. 5_suppl (2025): 200. https://doi.org/10.1200/jco.2025.43.5_suppl.200.

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200 Background: Prostate cancer is the second leading cause of cancer-related deaths in men. In New Mexico, it is the leading cause of cancer death among specific populations, particularly American Indians and African Americans. This study investigates the frequency and diversity of somatic mutations in patients with prostate adenocarcinoma treated at the University of New Mexico Comprehensive Cancer Center (UNMCCC). Methods: We conducted a retrospective analysis of patients with prostate adenocarcinoma treated at UNMCCC from 2015 to 2022 who underwent screening for somatic mutations via next-

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Ghilardi, Sara, Giulietta Minozzi, Maria Grazia De Iorio, et al. "Genotypic and Allelic Frequencies of Degenerative Myelopathy in an Italian Canine Population." Animals 14, no. 18 (2024): 2712. http://dx.doi.org/10.3390/ani14182712.

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Canine degenerative myelopathy is a fatal neurodegenerative disorder that affects the spinal cord. It is a late-onset disease, with symptoms becoming evident later in life at approximately 8 years of age. The principal aim of this study was to retrospectively evaluate allelic and genotypic frequencies of the c.118G > A and c.52A > T mutations located on the SOD1 gene in an Italian canine population to provide detailed information on the prevalence of the mutations in the country. The genetic data of different breeds were collected through DNA tests over a nine-year period in the Italian

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Demetri, George D., Michael Jeffers, Peter Reichardt, et al. "Mutational analysis of plasma DNA from patients (pts) in the phase III GRID study of regorafenib (REG) versus placebo (PL) in tyrosine kinase inhibitor (TKI)-refractory GIST: Correlating genotype with clinical outcomes." Journal of Clinical Oncology 31, no. 15_suppl (2013): 10503. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.10503.

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10503 Background: The phase III GRID study showed that REG provides a significant improvement in progression-free survival (PFS) compared with PL in pts with advanced gastrointestinal stromal tumors (GIST) following failure of at least imatinib (IM) and sunitinib (SU; HR 0.27, p<0.0001). Determining GIST genotype in TKI-refractory disease has proven challenging due to inter-tumoral heterogeneity and pt preference to avoid serial biopsies. To overcome this, we analysed circulating DNA in plasma as a source of tumor DNA and studied the correlation between mutational status and clinical outcom

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Nagy, Ákos, Bence Bátai, Alexandra Balogh, et al. "Quantitative Analysis and Monitoring of EZH2 Mutations Using Liquid Biopsy in Follicular Lymphoma." Genes 11, no. 7 (2020): 785. http://dx.doi.org/10.3390/genes11070785.

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Recent advances in molecular technologies enable sensitive and quantitative assessment of circulating tumor DNA, offering a noninvasive disease monitoring tool for patients with malignant disorders. Here, we demonstrated on four follicular lymphoma cases that circulating tumor DNA based EZH2 mutation analysis performed by a highly sensitive droplet digital PCR method may be a valuable treatment monitoring approach in EZH2 mutant follicular lymphoma. EZH2 variant allele frequencies changed in parallel with the volume of metabolically active tumor sites observed on 18F-fluorodeoxyglucose positro

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Guillemaud, T., A. Brun, N. Anthony, et al. "Incidence of insecticide resistance alleles in sexually-reproducing populations of the peach–potato aphid Myzus persicae (Hemiptera: Aphididae) from southern France." Bulletin of Entomological Research 93, no. 4 (2003): 289–97. http://dx.doi.org/10.1079/ber2003241.

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AbstractIntensive chemical treatments have led to the development of a number of insecticide resistance mechanisms in the peach–potato aphid Myzus persicae (Sulzer). Some of these mechanisms are known to be associated with negative pleiotropic effects (resistance costs). Molecular and biochemical methods were used to determine the genotypes or phenotypes associated with four insecticide resistance mechanisms in single aphids from sexually-reproducing populations in southern France. The mechanisms considered were E4 and FE4 carboxylesterase overproduction, modified acetycholinesterase, and kdr

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Ranathunge, Tharaka, Lahiru Udayanga, Sumudu Sarasija, et al. "Voltage-Gated Sodium Channel (Vgsc) Mutation-Based Pyrethroid Resistance in Aedes aegypti Populations of Three Endemic Dengue Risk Areas of Sri Lanka." BioMed Research International 2021 (May 22, 2021): 1–10. http://dx.doi.org/10.1155/2021/8874092.

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Background. Pyrethroid insecticides are widely used in many countries for chemical-based control of Ae. aegypti. Regardless of their efficacy, the constant use of insecticides has induced insecticide resistance mechanisms, such as knockdown resistance (kdr) in mosquitoes. Sri Lankan Vector Controlling Entities (VCE) have been using a variety of pyrethroid insecticides as the primary approach for dengue control. However, development of any resistance among the Aedes mosquitoes has been limitedly studied in the country. Therefore, the current study was conducted to evaluate the prevalence of F15

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Vasilyeva, Tatyana A., Andrey V. Marakhonov, Sergey I. Kutsev, and Rena A. Zinchenko. "Relative Frequencies of PAX6 Mutational Events in a Russian Cohort of Aniridia Patients in Comparison with the World’s Population and the Human Genome." International Journal of Molecular Sciences 23, no. 12 (2022): 6690. http://dx.doi.org/10.3390/ijms23126690.

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Genome-wide sequencing metadata allows researchers to infer bias in the relative frequencies of mutational events and to predict putative mutagenic models. In addition, much less data could be useful in the evaluation of the mutational frequency spectrum and the prevalent local mutagenic process. Here we analyzed the PAX6 gene locus for mutational spectra obtained in our own and previous studies and compared them with data on other genes as well as the whole human genome. MLPA and Sanger sequencing were used for mutation searching in a cohort of 199 index patients from Russia with aniridia and

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Gong, Jun, Marvin Sy, and Marwan Fakih. "Tumor mutational burden of microsatellite stable metastatic colorectal tumors by patient factors and KRAS, BRAF, and PIK3CA mutation status." Journal of Clinical Oncology 35, no. 4_suppl (2017): 627. http://dx.doi.org/10.1200/jco.2017.35.4_suppl.627.

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627 Background: Microsatellite instability (MSI) can predict response to pembrolizumab in metastatic colorectal cancer (mCRC). Benefit to PD-1 blockade is limited in microsatellite stable (MSS) mCRC yet MSS tumors represent >95% of all mCRC cases. Evidence suggests that high mutational load remains an important predictor of benefit to checkpoint inhibition across several tumors. We aimed to explore associations between tumor mutational burden (TMB) and various patient factors and mutations of interest to identify features of patients (pts) with MSS mCRC of potential significance to prognosi

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Jung, Sungwon, Jong Lyul Lee, Tae Won Kim, et al. "Molecular characterization of dysplasia-initiated colorectal cancer with assessing matched tumor and dysplasia samples." Annals of Coloproctology 38, no. 1 (2022): 72–81. http://dx.doi.org/10.3393/ac.2021.00290.0041.

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Purpose: Ulcerative colitis (UC) is known to have an association with the increased risk of colorectal cancer (CRC), and UC-associated CRC does not follow the typical progress pattern of adenoma-carcinoma. The aim of this study is to investigate molecular characteristics of UC-associated CRC and further our understanding of the association between UC and CRC.Methods: From 5 patients with UC-associated CRC, matched normal, dysplasia, and tumor specimens were obtained from formalin-fixed paraffin-embedded (FFPE) samples for analysis. Genomic DNA was extracted and whole exome sequencing was condu

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Hlavac, Viktor, Beatrice Mohelnikova-Duchonova, Martin Lovecek, et al. "Targeted Sequencing of Pancreatic Adenocarcinomas from Patients with Metachronous Pulmonary Metastases." Genes 11, no. 12 (2020): 1391. http://dx.doi.org/10.3390/genes11121391.

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Mutation spectra of 250 cancer driver, druggable, and actionable genes were analyzed in surgically resected pancreatic ductal adenocarcinoma (PDAC) patients who developed metachronous pulmonary metastases. Targeted sequencing was performed in DNA from blood and archival samples of 15 primary tumors and three paired metastases. Results were complemented with the determination of G12V mutation in KRAS by droplet digital PCR. The median number of protein-changing mutations was 52 per patient. KRAS and TP53 were significantly enriched in fractions of mutations in hotspots. Individual gene mutation

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Ayten, Ömer, Tayfun Çalışkan, Kadir Canoğlu, Neslihan Kaya Terzi, Levent Emirzeoğlu, and Oğuzhan Okutan. "Oncogenic Mutation Frequencies in Lung Cancer Patients." Hamidiye Medical Journal 1, no. 1 (2020): 17–21. http://dx.doi.org/10.4274/hamidiyemedj.galenos.2020.74429.

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Zhang, X. B., C. Urlando, K. S. Tao, and J. A. Heddle. "Factors affecting somatic mutation frequencies in vivo." Mutation Research/DNAging 338, no. 1-6 (1995): 189–201. http://dx.doi.org/10.1016/0921-8734(95)00024-z.

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