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Journal articles on the topic 'Mutation spectra'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

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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2

Tu, Xinyu, Fan Wang, Gianni Liti, Michael Breitenbach, Jia-Xing Yue, and Jing Li. "Spontaneous Mutation Rates and Spectra of Respiratory-Deficient Yeast." Biomolecules 13, no. 3 (2023): 501. http://dx.doi.org/10.3390/biom13030501.

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The yeast petite mutant was first discovered in the yeast Saccharomyces cerevisiae, which shows growth stress due to defects in genes encoding the respiratory chain. In a previous study, we described that deletion of the nuclear-encoded gene MRPL25 leads to mitochondrial genome (mtDNA) loss and the petite phenotype, which can be rescued by acquiring ATP3 mutations. The mrpl25Δ strain showed an elevated SNV (single nucleotide variant) rate, suggesting genome instability occurred during the crisis of mtDNA loss. However, the genome-wide mutation landscape and mutational signatures of mitochondri

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Xiao, Ming, Fubo Ma, Jun Yu, et al. "A Computer Simulation of SARS-CoV-2 Mutation Spectra for Empirical Data Characterization and Analysis." Biomolecules 13, no. 1 (2022): 63. http://dx.doi.org/10.3390/biom13010063.

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It is very important to compute the mutation spectra, and simulate the intra-host mutation processes by sequencing data, which is not only for the understanding of SARS-CoV-2 genetic mechanism, but also for epidemic prediction, vaccine, and drug design. However, the current intra-host mutation analysis algorithms are not only inaccurate, but also the simulation methods are unable to quickly and precisely predict new SARS-CoV-2 variants generated from the accumulation of mutations. Therefore, this study proposes a novel accurate strand-specific SARS-CoV-2 intra-host mutation spectra computation

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Stuart, Gregory R., Yoshimitsu Oda, Johan G. de Boer, and Barry W. Glickman. "Mutation Frequency and Specificity With Age in Liver, Bladder and Brain of lacI Transgenic Mice." Genetics 154, no. 3 (2000): 1291–300. http://dx.doi.org/10.1093/genetics/154.3.1291.

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Abstract Mutation frequency and specificity were determined as a function of age in nuclear DNA from liver, bladder, and brain of Big Blue lacI transgenic mice aged 1.5–25 months. Mutations accumulated with age in liver and accumulated more rapidly in bladder. In the brain a small initial increase in mutation frequency was observed in young animals; however, no further increase was observed in adult mice. To investigate the origin of mutations, the mutational spectra for each tissue and age were determined. DNA sequence analysis of mutant lacI transgenes revealed no significant changes in muta

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5

Rogozin, I. B. "Computational analysis of mutation spectra." Briefings in Bioinformatics 4, no. 3 (2003): 210–27. http://dx.doi.org/10.1093/bib/4.3.210.

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6

DeMarini, David M. "Mutation spectra of complex mixtures." Mutation Research/Reviews in Mutation Research 411, no. 1 (1998): 11–18. http://dx.doi.org/10.1016/s1383-5742(98)00009-x.

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7

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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8

Rajaei, Moein, Ayush Shekhar Saxena, Lindsay M. Johnson, et al. "Mutability of mononucleotide repeats, not oxidative stress, explains the discrepancy between laboratory-accumulated mutations and the natural allele-frequency spectrum in C. elegans." Genome Research 31, no. 9 (2021): 1602–13. http://dx.doi.org/10.1101/gr.275372.121.

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Important clues about natural selection can be gleaned from discrepancies between the properties of segregating genetic variants and of mutations accumulated experimentally under minimal selection, provided the mutational process is the same in the laboratory as in nature. The base-substitution spectrum differs between C. elegans laboratory mutation accumulation (MA) experiments and the standing site-frequency spectrum, which has been argued to be in part owing to increased oxidative stress in the laboratory environment. Using genome sequence data from C. elegans MA lines carrying a mutation (

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9

Lippert, Malcolm J., Jennifer A. Freedman, Melissa A. Barber, and Sue Jinks-Robertson. "Identification of a Distinctive Mutation Spectrum Associated with High Levels of Transcription in Yeast." Molecular and Cellular Biology 24, no. 11 (2004): 4801–9. http://dx.doi.org/10.1128/mcb.24.11.4801-4809.2004.

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ABSTRACT High levels of transcription are associated with increased mutation rates in Saccharomyces cerevisiae, a phenomenon termed transcription-associated mutation (TAM). To obtain insight into the mechanism of TAM, we obtained LYS2 forward mutation spectra under low- versus high-transcription conditions in which LYS2 was expressed from either the low-level pLYS2 promoter or the strong pGAL1-10 promoter, respectively. Because of the large size of the LYS2 locus, forward mutations first were mapped to specific LYS2 subregions, and then those mutations that occurred within a defined 736-bp tar

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Katz, Sophia, Sarit Avrani, Meitar Yavneh, Sabrin Hilau, Jonathan Gross, and Ruth Hershberg. "Dynamics of Adaptation During Three Years of Evolution Under Long-Term Stationary Phase." Molecular Biology and Evolution 38, no. 7 (2021): 2778–90. http://dx.doi.org/10.1093/molbev/msab067.

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Abstract Many bacterial species that cannot sporulate, such as the model bacterium Escherichia coli, can nevertheless survive for years, following exhaustion of external resources, in a state termed long-term stationary phase (LTSP). Here we describe the dynamics of E. coli adaptation during the first three years spent under LTSP. We show that during this time, E. coli continuously adapts genetically through the accumulation of mutations. For nonmutator clones, the majority of mutations accumulated appear to be adaptive under LTSP, reflected in an extremely convergent pattern of mutation accum

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11

Wang, Gaowei, Hang Su, Helin Yu, Ruoshi Yuan, Xiaomei Zhu, and Ping Ao. "Endogenous network states predict gain or loss of functions for genetic mutations in hepatocellular carcinoma." Journal of The Royal Society Interface 13, no. 115 (2016): 20151115. http://dx.doi.org/10.1098/rsif.2015.1115.

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Cancers have been typically characterized by genetic mutations. Patterns of such mutations have traditionally been analysed by posteriori statistical association approaches. One may ponder the possibility of a priori determination of any mutation regularity. Here by exploring biological processes implied in a mechanistic theory recently developed (the endogenous molecular–cellular network theory), we found that the features of genetic mutations in cancers may be predicted without any prior knowledge of mutation propensities. With hepatocellular carcinoma (HCC) as an example, we found that the

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Bacolla, Albino, Guliang Wang, Aklank Jain, et al. "Non-B DNA-forming Sequences and WRN Deficiency Independently Increase the Frequency of Base Substitution in Human Cells." Journal of Biological Chemistry 286, no. 12 (2011): 10017–26. http://dx.doi.org/10.1074/jbc.m110.176636.

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Although alternative DNA secondary structures (non-B DNA) can induce genomic rearrangements, their associated mutational spectra remain largely unknown. The helicase activity of WRN, which is absent in the human progeroid Werner syndrome, is thought to counteract this genomic instability. We determined non-B DNA-induced mutation frequencies and spectra in human U2OS osteosarcoma cells and assessed the role of WRN in isogenic knockdown (WRN-KD) cells using a supF gene mutation reporter system flanked by triplex- or Z-DNA-forming sequences. Although both non-B DNA and WRN-KD served to increase t

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Malyarchuk, B. A. "Comparative Analysis of Mitochondrial Genome Mutation Spectra in Human Populations." Молекулярная биология 57, no. 5 (2023): 792–96. http://dx.doi.org/10.31857/s0026898423050117.

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Nucleotide sequence variability of whole mitochondrial genomes (mtDNA) was analyzed and mutation spectra were reconstructed (by L-chain of mtDNA) in four regional groups of indigenous populations representing Northeastern and Southern Siberia, Western Asia, and the Americas. The pyrimidine transitions were found to be predominant in all groups, and of these, the substitutions T→C were most frequent. The second most common in all regional groups (except Northeastern Siberia) are substitutions A→G. Of the transversions, in all the populations studied the substitutions C→A prevail. Between-region

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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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15

Bebenek, Anna, Geraldine T. Carver, Holly Kloos Dressman, et al. "Dissecting the Fidelity of Bacteriophage RB69 DNA Polymerase: Site-Specific Modulation of Fidelity by Polymerase Accessory Proteins." Genetics 162, no. 3 (2002): 1003–18. http://dx.doi.org/10.1093/genetics/162.3.1003.

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Abstract Bacteriophage RB69 encodes a replicative B-family DNA polymerase (RB69 gp43) with an associated proofreading 3′ exonuclease. Crystal structures have been determined for this enzyme with and without DNA substrates. We previously described the mutation rates and kinds of mutations produced in vivo by the wild-type (Pol+ Exo+) enzyme, an exonuclease-deficient mutator variant (Pol+ Exo-), mutator variants with substitutions at Tyr567 in the polymerase active site (PolM Exo+), and the double mutator PolM Exo-. Comparing the mutational spectra of the Pol+ Exo- and Pol+ Exo+ enzymes revealed

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16

Rajkumari, Jinu Devi. "Efficiency and effectiveness of physical and chemical mutagens in Trigonella foenum graecum L." NBU Journal of Plant Sciences 6, no. 1 (2012): 87–88. http://dx.doi.org/10.55734/nbujps.2012.v06i01.013.

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Trigonella foemum graecum L was utilized to study the Chlorophyll mutations, mutagenic efficiency and effectiveness by physical mutagen gamma rays and chemical mutagen EMS. The frequency of chlorophyll mutation in M1 & M2 generation were more in gamma treated plants but the mutation spectra and mutagenic efficiency of EMS was higher than gamma. The most efficient mutagens were 0. 02% EMS, 0.06% EMS and 3KR gamma radiation to induce mutation in T. foenum graceum L.

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17

Cetin-Atalay, Rengul, and Mehmet Ozturk. "p53 mutations as fingerprints of environmental carcinogens." Pure and Applied Chemistry 72, no. 6 (2000): 995–99. http://dx.doi.org/10.1351/pac200072060995.

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Mutations of the p53 tumor suppressor gene occur in a great majority of human cancers. The protein product of p53 gene is involved in DNA damage response. Consequently, p53 gene may be a preferred target for environmental carcinogens, which also act as DNA-damaging agents. This is probably why p53 mutations are frequent in cancers linked to environmental carcinogens. Moreover, these carcinogens leave molecular fingerprints on the p53 gene. Thus, the study of p53 mutation spectra has been a useful approach to implicate suspected carcinogens to different human cancers. This review provides furth

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18

Chawanthayatham, Supawadee, Charles C. Valentine, Bogdan I. Fedeles, et al. "Mutational spectra of aflatoxin B1in vivo establish biomarkers of exposure for human hepatocellular carcinoma." Proceedings of the National Academy of Sciences 114, no. 15 (2017): E3101—E3109. http://dx.doi.org/10.1073/pnas.1700759114.

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Aflatoxin B1(AFB1) and/or hepatitis B and C viruses are risk factors for human hepatocellular carcinoma (HCC). Available evidence supports the interpretation that formation of AFB1-DNA adducts in hepatocytes seeds a population of mutations, mainly G:C→T:A, and viral processes synergize to accelerate tumorigenesis, perhaps via inflammation. Responding to a need for early-onset evidence predicting disease development, highly accurate duplex sequencing was used to monitor acquisition of high-resolution mutational spectra (HRMS) during the process of hepatocarcinogenesis. Four-day-old male mice we

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Karolak, Aleksandra, Jurica Levatić, and Fran Supek. "A framework for mutational signature analysis based on DNA shape parameters." PLOS ONE 17, no. 1 (2022): e0262495. http://dx.doi.org/10.1371/journal.pone.0262495.

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The mutation risk of a DNA locus depends on its oligonucleotide context. In turn, mutability of oligonucleotides varies across individuals, due to exposure to mutagenic agents or due to variable efficiency and/or accuracy of DNA repair. Such variability is captured by mutational signatures, a mathematical construct obtained by a deconvolution of mutation frequency spectra across individuals. There is a need to enhance methods for inferring mutational signatures to make better use of sparse mutation data (e.g., resulting from exome sequencing of cancers), to facilitate insight into underlying b

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20

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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21

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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22

Rogozin, Igor B., Fyodor A. Kondrashov, and Galina V. Glazko. "Use of mutation spectra analysis software." Human Mutation 17, no. 2 (2001): 83–102. http://dx.doi.org/10.1002/1098-1004(200102)17:2<83::aid-humu1>3.0.co;2-e.

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23

Avizienyte, Egle, Richard A. Ward, and Andrew P. Garner. "Comparison of the EGFR resistance mutation profiles generated by EGFR-targeted tyrosine kinase inhibitors and the impact of drug combinations." Biochemical Journal 415, no. 2 (2008): 197–206. http://dx.doi.org/10.1042/bj20080728.

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Recent clinical data indicates that the emergence of mutant drug-resistant kinase alleles may be particularly relevant for targeted kinase inhibitors. In order to explore how different classes of targeted therapies impact upon resistance mutations, we performed EGFR (epidermal-growth-factor receptor) resistance mutation screens with erlotinib, lapatinib and CI-1033. Distinct mutation spectra were generated with each inhibitor and were reflective of their respective mechanisms of action. Lapatinib yielded the widest variety of mutations, whereas mutational variability was lower in the erlotinib

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Nagashima, Haruki, Yuki Hayashi, Yuki Sakamoto, Kenshi Komatsu, and Hiroshi Tauchi. "Induction of somatic mutations by low concentrations of tritiated water (HTO): evidence for the possible existence of a dose-rate threshold." Journal of Radiation Research 62, no. 4 (2021): 582–89. http://dx.doi.org/10.1093/jrr/rrab022.

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Abstract Tritium is a low energy beta emitter and is discharged into the aquatic environment primarily in the form of tritiated water (HTO) from nuclear power plants or from nuclear fuel reprocessing plants. Although the biological effects of HTO exposures at significant doses or dose rates have been extensively studied, there are few reports concerning the biological effects of HTO exposures at very low dose rates. In the present study using a hyper-sensitive assay system, we investigated the dose rate effect of HTO on the induction of mutations. Confluent cell populations were exposed to HTO

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Ahn, Eun Hyun, and Seung Hyuk Lee. "Detection of Low-Frequency Mutations and Identification of Heat-Induced Artifactual Mutations Using Duplex Sequencing." International Journal of Molecular Sciences 20, no. 1 (2019): 199. http://dx.doi.org/10.3390/ijms20010199.

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We present a genome-wide comparative and comprehensive analysis of three different sequencing methods (conventional next generation sequencing (NGS), tag-based single strand sequencing (e.g., SSCS), and Duplex Sequencing for investigating mitochondrial mutations in human breast epithelial cells. Duplex Sequencing produces a single strand consensus sequence (SSCS) and a duplex consensus sequence (DCS) analysis, respectively. Our study validates that although high-frequency mutations are detectable by all the three sequencing methods with the similar accuracy and reproducibility, rare (low-frequ

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Foster, Patricia L., Heewook Lee, Ellen Popodi, Jesse P. Townes, and Haixu Tang. "Determinants of spontaneous mutation in the bacteriumEscherichia colias revealed by whole-genome sequencing." Proceedings of the National Academy of Sciences 112, no. 44 (2015): E5990—E5999. http://dx.doi.org/10.1073/pnas.1512136112.

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A complete understanding of evolutionary processes requires that factors determining spontaneous mutation rates and spectra be identified and characterized. Using mutation accumulation followed by whole-genome sequencing, we found that the mutation rates of three widely diverged commensalEscherichia colistrains differ only by about 50%, suggesting that a rate of 1–2 × 10−3mutations per generation per genome is common for this bacterium. Four major forces are postulated to contribute to spontaneous mutations: intrinsic DNA polymerase errors, endogenously induced DNA damage, DNA damage caused by

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DeWitt, William S., Luke Zhu, Mitchell R. Vollger, et al. "mutyper: assigning and summarizing mutation types for analyzing germline mutation spectra." Journal of Open Source Software 8, no. 85 (2023): 5227. http://dx.doi.org/10.21105/joss.05227.

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Nguyen, Duong T., Baojun Wu, Hongan Long, et al. "Variable Spontaneous Mutation and Loss of Heterozygosity among Heterozygous Genomes in Yeast." Molecular Biology and Evolution 37, no. 11 (2020): 3118–30. http://dx.doi.org/10.1093/molbev/msaa150.

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Abstract Mutation and recombination are the primary sources of genetic variation. To better understand the evolution of genetic variation, it is crucial to comprehensively investigate the processes involving mutation accumulation and recombination. In this study, we performed mutation accumulation experiments on four heterozygous diploid yeast species in the Saccharomycodaceae family to determine spontaneous mutation rates, mutation spectra, and losses of heterozygosity (LOH). We observed substantial variation in mutation rates and mutation spectra. We also observed high LOH rates (1.65–11.07×

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Raffelberg, Sarah, Alexander Gutt, Wolfgang Gärtner, et al. "The amino acids surrounding the flavin 7a-methyl group determine the UVA spectral features of a LOV protein." Biological Chemistry 394, no. 11 (2013): 1517–28. http://dx.doi.org/10.1515/hsz-2013-0163.

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Abstract Flavin-binding light, oxygen, and voltage (LOV) domains are UVA/blue-light-sensing protein units that form a reversible flavin mononucleotide-cysteine adduct upon light induction. In their dark-adapted state, LOV domains exhibit the typical spectral features of fully oxidized riboflavin derivatives. A survey on the absorption spectra of various LOV domains revealed that the UVA spectral range is the most variable region (whereas the absorption band at 450 nm is virtually unchanged), showing essentially two distinct patterns found in plant phototropin LOV1 and LOV2 domains, respectivel

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Qi, Rui, Ke Bian, Fangyi Chen, Qi Tang, Xianhao Zhou, and Deyu Li. "Sequence Dependent Repair of 1,N6-Ethenoadenine by DNA Repair Enzymes ALKBH2, ALKBH3, and AlkB." Molecules 26, no. 17 (2021): 5285. http://dx.doi.org/10.3390/molecules26175285.

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Mutation patterns of DNA adducts, such as mutational spectra and signatures, are useful tools for diagnostic and prognostic purposes. Mutational spectra of carcinogens derive from three sources: adduct formation, replication bypass, and repair. Here, we consider the repair aspect of 1,N6-ethenoadenine (εA) by the 2-oxoglutarate/Fe(II)-dependent AlkB family enzymes. Specifically, we investigated εA repair across 16 possible sequence contexts (5′/3′ flanking base to εA varied as G/A/T/C). The results revealed that repair efficiency is altered according to sequence, enzyme, and strand context (ss

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Lewis, P. D., and J. M. Parry. "An exploratory analysis of multiple mutation spectra." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 518, no. 2 (2002): 163–80. http://dx.doi.org/10.1016/s1383-5718(02)00103-1.

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Chen, Chia-Hsiang, Ailing Huang, Yu-Shu Huang, and Ting-Hsuan Fang. "Identification of a Rare Novel KMT2C Mutation That Presents with Schizophrenia in a Multiplex Family." Journal of Personalized Medicine 11, no. 12 (2021): 1254. http://dx.doi.org/10.3390/jpm11121254.

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Schizophrenia is a complex genetic disorder involving many common variants with modest effects and rare mutations with high penetrance. Rare mutations associated with schizophrenia are highly heterogeneous and private for affected individuals and families. Identifying such mutations can help establish the molecular diagnosis, elucidate the pathogenesis, and provide helpful genetic counseling for affected patients and families. We performed a whole-exome sequencing analysis to search for rare pathogenic mutations co-segregating with schizophrenia transmitted in a dominant inheritance in a two-g

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Maxwell, Kara Noelle, Daniel De Sloover, Lyndsey Emery, et al. "The mutational spectrum of breast and ovarian tumors from BRCA1 and BRCA2 mutation carriers." Journal of Clinical Oncology 31, no. 15_suppl (2013): 1510. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.1510.

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1510 Background: Individuals who carry one mutated copy of the BRCA1 or BRCA2 genes have elevated lifetime risks of breast and ovarian cancer. A number of studies have investigated the somatic mutational spectra of breast and ovarian tumors; however, BRCA1/2mutated tumors are underrepresented. Methods: Sixty-eight formalin-fixed paraffin embedded samples from BRCA1/2patients have been identified. Massively parallel sequencing using 48 gene capture is in process, whole exome sequencing of tumor and matched germline DNA is planned. Data are analyzed using a custom bioinformatics pipeline. Result

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Valentine, Charles C., Robert R. Young, Mark R. Fielden, et al. "Direct quantification of in vivo mutagenesis and carcinogenesis using duplex sequencing." Proceedings of the National Academy of Sciences 117, no. 52 (2020): 33414–25. http://dx.doi.org/10.1073/pnas.2013724117.

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The ability to accurately measure mutations is critical for basic research and identifying potential drug and chemical carcinogens. Current methods for in vivo quantification of mutagenesis are limited because they rely on transgenic rodent systems that are low-throughput, expensive, prolonged, and do not fully represent other species such as humans. Next-generation sequencing (NGS) is a conceptually attractive alternative for detecting mutations in the DNA of any organism; however, the limit of resolution for standard NGS is poor. Technical error rates (∼1 × 10−3) of NGS obscure the true abun

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Bachar, Amit, Elad Itzhaki, Shmuel Gleizer, Melina Shamshoom, Ron Milo, and Niv Antonovsky. "Point mutations in topoisomerase I alter the mutation spectrum in E. coli and impact the emergence of drug resistance genotypes." Nucleic Acids Research 48, no. 2 (2019): 761–69. http://dx.doi.org/10.1093/nar/gkz1100.

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Abstract Identifying the molecular mechanisms that give rise to genetic variation is essential for the understanding of evolutionary processes. Previously, we have used adaptive laboratory evolution to enable biomass synthesis from CO2 in Escherichia coli. Genetic analysis of adapted clones from two independently evolving populations revealed distinct enrichment for insertion and deletion mutational events. Here, we follow these observations to show that mutations in the gene encoding for DNA topoisomerase I (topA) give rise to mutator phenotypes with characteristic mutational spectra. Using g

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Mas-Ponte, David, Marcel McCullough, and Fran Supek. "Spectrum of DNA mismatch repair failures viewed through the lens of cancer genomics and implications for therapy." Clinical Science 136, no. 5 (2022): 383–404. http://dx.doi.org/10.1042/cs20210682.

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Abstract Genome sequencing can be used to detect DNA repair failures in tumors and learn about underlying mechanisms. Here, we synthesize findings from genomic studies that examined deficiencies of the DNA mismatch repair (MMR) pathway. The impairment of MMR results in genome-wide hypermutation and in the ‘microsatellite instability’ (MSI) phenotype—occurrence of indel mutations at short tandem repeat (microsatellite) loci. The MSI status of tumors was traditionally assessed by molecular testing of a selected set of MS loci or by measuring MMR protein expression levels. Today, genomic data can

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Morgan, Claire, and Paul D. Lewis. "iMARS—Mutation analysis reporting software: An analysis of spontaneous cII mutation spectra." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 603, no. 1 (2006): 15–26. http://dx.doi.org/10.1016/j.mrgentox.2005.09.010.

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Zhou, Nan, Yuan Yuan, Xin Long, Chuanfang Wu, and Jinku Bao. "Mutational signatures efficiently identify different mutational processes underlying cancers with similar somatic mutation spectra." Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 806 (December 2017): 27–30. http://dx.doi.org/10.1016/j.mrfmmm.2017.07.004.

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Saumaa, Signe, Andres Tover, Lagle Kasak, and Maia Kivisaar. "Different Spectra of Stationary-Phase Mutations in Early-Arising versus Late-Arising Mutants of Pseudomonas putida: Involvement of the DNA Repair Enzyme MutY and the Stationary-Phase Sigma Factor RpoS." Journal of Bacteriology 184, no. 24 (2002): 6957–65. http://dx.doi.org/10.1128/jb.184.24.6957-6965.2002.

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ABSTRACT Stationary-phase mutations occur in populations of stressed, nongrowing, and slowly growing cells and allow mutant bacteria to overcome growth barriers. Mutational processes in starving cells are different from those occurring in growing bacteria. Here, we present evidence that changes in mutational processes also take place during starvation of bacteria. Our test system for selection of mutants based on creation of functional promoters for the transcriptional activation of the phenol degradation genes pheBA in starving Pseudomonas putida enables us to study base substitutions (C-to-A

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Levine, J. G., and R. M. Schaaper. "Complex Frameshift Mutations Medicated by Plasmid pKM101: Mutational Mechanisms Deduced from 4-aminobiphenyl-induced Mutation Spectra in Salmonella." Genetics 137, no. 1 (1994): 337. http://dx.doi.org/10.1093/genetics/137.1.337.

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Levine, J. G., R. M. Schaaper, and D. M. DeMarini. "Complex frameshift mutations mediated by plasmid pKM101: mutational mechanisms deduced from 4-aminobiphenyl-induced mutation spectra in Salmonella." Genetics 136, no. 3 (1994): 731–46. http://dx.doi.org/10.1093/genetics/136.3.731.

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Abstract We used colony probe hybridization and polymerase chain reaction/DNA sequence analysis to determine the mutations in approximately 2,400 4-aminobiphenyl (4-AB) +S9-induced revertants of the -1 frameshift allele hisD3052 and of the base-substitution allele hisG46 of Salmonella typhimurium. Most of the mutations occurred at sites containing guanine, which is the primary base at which 4-AB forms DNA adducts. A hotspot mutation involving the deletion of a CG or GC within the sequence CGCGCGCG accounted for 100 and 99.9%, respectively, of the reversion events at the hisD3052 allele in the

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Szikriszt, Bernadett, Ádám Póti, Orsolya Pipek, et al. "A comprehensive survey of the mutagenic impact of common cancer cytotoxics." Genome Biology 17, no. 1 (2016): 99. https://doi.org/10.1186/s13059-016-0963-7.

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<strong>Background: </strong>Genomic mutations caused by cytotoxic agents used in cancer chemotherapy may cause secondary malignancies as well as contribute to the evolution of treatment-resistant tumour cells. The stable diploid genome of the chicken DT40 lymphoblast cell line, an established DNA repair model system, is well suited to accurately assay genomic mutations.<strong>Results: </strong>We use whole genome sequencing of multiple DT40 clones to determine the mutagenic effect of eight common cytotoxics used for the treatment of millions of patients worldwide. We determine the spontaneou

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Auerbach, Scott S., Miaofei Xu, B. Alex Merrick, et al. "Exome Sequencing of Fresh-frozen or Formalin-fixed Paraffin-embedded B6C3F1/N Mouse Hepatocellular Carcinomas Arising Either Spontaneously or due to Chronic Chemical Exposure." Toxicologic Pathology 46, no. 6 (2018): 706–18. http://dx.doi.org/10.1177/0192623318789398.

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Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide; however, the mutational properties of HCC-associated carcinogens remain largely uncharacterized. We hypothesized that mechanisms underlying chemical-induced HCC can be characterized by evaluating the mutational spectra of these tumors. To test this hypothesis, we performed exome sequencing of B6C3F1/N HCCs that arose either spontaneously in vehicle controls ( n = 3) or due to chronic exposure to gingko biloba extract (GBE; n = 4) or methyleugenol (MEG; n = 3). Most archived tumor samples are available

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Saini, Natalie, Camille K. Giacobone, Leszek J. Klimczak, et al. "UV-exposure, endogenous DNA damage, and DNA replication errors shape the spectra of genome changes in human skin." PLOS Genetics 17, no. 1 (2021): e1009302. http://dx.doi.org/10.1371/journal.pgen.1009302.

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Human skin is continuously exposed to environmental DNA damage leading to the accumulation of somatic mutations over the lifetime of an individual. Mutagenesis in human skin cells can be also caused by endogenous DNA damage and by DNA replication errors. The contributions of these processes to the somatic mutation load in the skin of healthy humans has so far not been accurately assessed because the low numbers of mutations from current sequencing methodologies preclude the distinction between sequencing errors and true somatic genome changes. In this work, we sequenced genomes of single cell-

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Hu, Haili, Qingqing Ma, Weidong Li, Yan Wang, Wangsheng Song, and Yong Huang. "Prevalence and Mutation Analysis of Short-Chain acyl-CoA Dehydrogenase Deficiency Detected by Newborn Screening in Hefei, China." International Journal of Neonatal Screening 10, no. 4 (2024): 68. http://dx.doi.org/10.3390/ijns10040068.

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Short-chain acyl-CoA dehydrogenase deficiency (SCADD) is an autosomal recessive inborn error of mitochondrial fatty acid oxidation with highly variable biochemical and genetic characteristics. The present study aimed to estimate the prevalence and genetic characteristics of SCADD in newborns identified through screening. A total of 782,930 newborns were screened for SCADD in Hefei Neonatal Screening Center from January 2016 to December 2023. The blood samples from newborns were measured by tandem mass spectrometry (MS/MS). The suspected SCADD neonates were rechecked using next-generation gene

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Li, Jing, Simon Stenberg, Jia-Xing Yue, et al. "Genome instability footprint under rapamycin and hydroxyurea treatments." PLOS Genetics 19, no. 11 (2023): e1011012. http://dx.doi.org/10.1371/journal.pgen.1011012.

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The mutational processes dictating the accumulation of mutations in genomes are shaped by genetic background, environment and their interactions. Accurate quantification of mutation rates and spectra under drugs has important implications in disease treatment. Here, we used whole-genome sequencing and time-resolved growth phenotyping of yeast mutation accumulation lines to give a detailed view of the mutagenic effects of rapamycin and hydroxyurea on the genome and cell growth. Mutation rates depended on the genetic backgrounds but were only marginally affected by rapamycin. As a remarkable exc

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Shen, Jiang-Cheng, Ashwini S. Kamath-Loeb, Brendan F. Kohrn, Keith R. Loeb, Bradley D. Preston, and Lawrence A. Loeb. "A high-resolution landscape of mutations in the BCL6 super-enhancer in normal human B cells." Proceedings of the National Academy of Sciences 116, no. 49 (2019): 24779–85. http://dx.doi.org/10.1073/pnas.1914163116.

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The super-enhancers (SEs) of lineage-specific genes in B cells are off-target sites of somatic hypermutation. However, the inability to detect sufficient numbers of mutations in normal human B cells has precluded the generation of a high-resolution mutational landscape of SEs. Here we captured and sequenced 12 B cell SEs at single-nucleotide resolution from 10 healthy individuals across diverse ethnicities. We detected a total of approximately 9,000 subclonal mutations (allele frequencies <0.1%); of these, approximately 8,000 are present in the BCL6 SE alone. Within the BCL6 SE, we identifi

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Levy, Dan D., Bhavana Sharma, and Thomas A. Cebula. "Single-Nucleotide Polymorphism Mutation Spectra and Resistance to Quinolones in Salmonella enterica Serovar Enteritidis with a Mutator Phenotype." Antimicrobial Agents and Chemotherapy 48, no. 7 (2004): 2355–63. http://dx.doi.org/10.1128/aac.48.7.2355-2363.2004.

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ABSTRACT Resistance to quinolone antibiotics has been associated with single-nucleotide polymorphisms (SNPs) in the quinolone resistance-determining region (QRDR) of gyrA. Mutations in the gyrA gene were compared by using mutant populations derived from wild-type Salmonella enterica serovar Enteritidis and its isogenic mutS::Tn10 mutator counterpart. Spontaneous mutants arising during nonselective growth were isolated by selection with either nalidixic acid, enrofloxacin, or ciprofloxacin. QRDR SNPs were identified in approximately 70% (512 of 695) of the isolates via colony hybridization with

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Zhang, Lei, Xiao Dong, Moonsook Lee, Alexander Y. Maslov, Tao Wang, and Jan Vijg. "Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan." Proceedings of the National Academy of Sciences 116, no. 18 (2019): 9014–19. http://dx.doi.org/10.1073/pnas.1902510116.

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Accumulation of mutations in somatic cells has been implicated as a cause of aging since the 1950s. However, attempts to establish a causal relationship between somatic mutations and aging have been constrained by the lack of methods to directly identify mutational events in primary human tissues. Here we provide genome-wide mutation frequencies and spectra of human B lymphocytes from healthy individuals across the entire human lifespan using a highly accurate single-cell whole-genome sequencing method. We found that the number of somatic mutations increases from <500 per cell in newborns t

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Ramadža, Danijela Petković, Vladimir Sarnavka, Jurica Vuković, et al. "Molecular basis and clinical presentation of classic galactosemia in a Croatian population." Journal of Pediatric Endocrinology and Metabolism 31, no. 1 (2018): 71–75. http://dx.doi.org/10.1515/jpem-2017-0302.

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AbstractBackground:Classic galactosemia is an autosomal recessive disorder of galactose metabolism caused by severely decreased activity of galactose-1-phosphate uridylyltransferase (GALT) due to pathogenic mutations in theGALTgene. To date more than 330 mutations have been described, with p.Q188R and p.K285N being the most common in Caucasian populations. Although acute manifestations can be fully avoided by a galactose-restricted diet, chronic complications, such as neurological ones, cannot be prevented in a significant number of patients despite compliance with the dietary treatment.Method

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