Genomes and Genes
Summary: The number of mutations that occur in a specific sequence, GENE, or GENOME over a specified period of time such as years, CELL DIVISIONS, or generations.
- Xue Y, Wang M, Yang Z, Yu D, Han Y, Huang D, et al. Clinical features and viral quasispecies characteristics associated with infection by the hepatitis B virus G145R immune escape mutant. Emerg Microbes Infect. 2017;6:e15 pubmed publisher..These findings extend understanding of the evolution of HBV under host immune pressure and of the clinical outcomes of affected patients. ..
- Allen A, Cossette P, Delanty N, Eichler E, Goldstein D, Han Y, et al. De novo mutations in epileptic encephalopathies. Nature. 2013;501:217-21 pubmed publisher..Finally, we show that the de novo mutations observed are enriched in specific gene sets including genes regulated by the fragile X protein (P?<?10(-8)), as has been reported previously for autism spectrum disorders. ..
- Shi Y, Pan Z, Cui W, Ma Z, Pang X, Zhang W, et al. [Clinicopathologic characteristics of epidermal growth factor receptor mutations in non-small cell lung cancer in Xinjiang region]. Zhonghua Bing Li Xue Za Zhi. 2017;46:309-313 pubmed publisher..173 cases with EGFR gene mutation in 582 cases of paraffin-embedded tissue in patients with NSCLC, and the mutation rate was 29.7%(173/582). There were statistical difference in female patients (50...
- Jain M, Tripathi A. ICUS/CCUS/CHIP: basics & beyond. Expert Rev Hematol. 2017;10:915-920 pubmed publisher..Longitudinal follow up study on ICUS, CCUS, CHIP may eventually identify the pathological significance of the clonal mutations. An absence of mutation however may still be useful as good predictor of not having MDS. ..
- Folkvardsen D, Norman A, Andersen A, Michael Rasmussen E, Jelsbak L, Lillebaek T. Genomic Epidemiology of a Major Mycobacterium tuberculosis Outbreak: Retrospective Cohort Study in a Low-Incidence Setting Using Sparse Time-Series Sampling. J Infect Dis. 2017;216:366-374 pubmed publisher..from only 12% of the collected isolates, we have been able to extract important key information, such as mutation rate and conserved single-nucleotide polymorphisms to identify discrete transmission chains, as well as the ..
- Chernick A, van der Meer F. Evolution of Bovine viral diarrhea virus in Canada from 1997 to 2013. Virology. 2017;509:232-238 pubmed publisher..Distinct clustering within all sub-genotypes, particularly BVDV2a, is apparent and could lead to new levels of genotypic classification. Continuous monitoring of emerging variants is therefore necessary. ..
- Lin B, Sun X, Su S, Lv C, Zhang X, Lin L, et al. HIV drug resistance in HIV positive individuals under antiretroviral treatment in Shandong Province, China. PLoS ONE. 2017;12:e0181997 pubmed publisher..However, patients on second line ART regimens and those with low educational level need continuous monitoring. Active drug resistance testing can effectively prevent the development of drug resistance. ..
- Vijg J, Dong X, Zhang L. A high-fidelity method for genomic sequencing of single somatic cells reveals a very high mutational burden. Exp Biol Med (Maywood). 2017;242:1318-1324 pubmed publisher..Here, we review a new, whole genome amplification system that allows accurate quantification and characterization of single-cell mutational landscapes in human cells and tissues in relation to disease...
- Song J, Hussaini M, Zhang H, Shao H, Qin D, Zhang X, et al. Comparison of the Mutational Profiles of Primary Myelofibrosis, Polycythemia Vera, and Essential Thrombocytosis. Am J Clin Pathol. 2017;147:444-452 pubmed publisher..Due to the relatively small number of cases and variable testing over time, larger controlled studies are necessary to confirm the findings. ..
- Choudhury M, Uddin A, Chakraborty S. Gene expression, nucleotide composition and codon usage bias of genes associated with human Y chromosome. Genetica. 2017;145:295-305 pubmed publisher..In addition, Y-linked genes have significant difference in GC contents at the second and third codon positions, expression level, and codon usage pattern of some codons like the SPANX genes in X chromosome. ..
- Tenaillon O, Barrick J, Ribeck N, Deatherage D, Blanchard J, Dasgupta A, et al. Tempo and mode of genome evolution in a 50,000-generation experiment. Nature. 2016;536:165-70 pubmed..The populations that retained the ancestral mutation rate support a model in which most fixed mutations are beneficial, the fraction of beneficial mutations declines as ..
- Sundaresan V, Lin V, Liang F, Kaye F, Kawabata Iwakawa R, Shiraishi K, et al. Significantly mutated genes and regulatory pathways in SCLC-a meta-analysis. Cancer Genet. 2017;216-217:20-28 pubmed publisher..In addition, we observed that the mutation rate was significantly higher in samples with RB1 gene mutated when compared to samples with wild type RB1, ..
- Karami Zarandi M, Douraghi M, Vaziri B, Adibhesami H, Rahbar M, Yaseri M. Variable spontaneous mutation rate in clinical strains of multidrug-resistant Acinetobacter baumannii and differentially expressed proteins in a hypermutator strain. Mutat Res. 2017;800-802:37-45 pubmed publisher..The spontaneous mutation rate of multi-drug resistant A. baumannii strains varied broadly from 0 to 2...
- Landoulsi Z, Benromdhan S, Ben Djebara M, Damak M, Dallali H, Kefi R, et al. Using KASP technique to screen LRRK2 G2019S mutation in a large Tunisian cohort. BMC Med Genet. 2017;18:70 pubmed publisher..Comparing to Taqman assay and Sanger sequencing, KASP was shown to be a reliable, time and cost effective genotyping assay for routine G2019S screening in genetic testing laboratories. ..
- Amit M, Tam S, Abdelmeguid A, Roberts D, Takahashi Y, Raza S, et al. Mutation status among patients with sinonasal mucosal melanoma and its impact on survival. Br J Cancer. 2017;116:1564-1571 pubmed publisher..In SNNM, mutation status does not affect survival outcomes, but NRAS mutations are relatively frequent and could be targeted in this disease by MEK inhibitors. ..
- Sloan D. Using plants to elucidate the mechanisms of cytonuclear co-evolution. New Phytol. 2015;205:1040-6 pubmed
- Ilmjärv T, Naanuri E, Kivisaar M. Contribution of increased mutagenesis to the evolution of pollutants-degrading indigenous bacteria. PLoS ONE. 2017;12:e0182484 pubmed publisher..These results also implied that mutagenicity might be affected by a factor of how long bacteria have evolved to use a particular pollutant as a carbon source. ..
- Gymrek M, Willems T, Reich D, Erlich Y. Interpreting short tandem repeat variations in humans using mutational constraint. Nat Genet. 2017;49:1495-1501 pubmed publisher..Constraint scores identified known pathogenic variants with early-onset effects. Our metric will provide a valuable tool for prioritizing pathogenic STRs in medical genetics studies. ..
- Balanovsky O. Toward a consensus on SNP and STR mutation rates on the human Y-chromosome. Hum Genet. 2017;136:575-590 pubmed publisherThe mutation rate on the Y-chromosome matters for estimating the time-to-the-most-recent-common-ancestor (TMRCA, i.e. haplogroup age) in population genetics, as well as for forensic, medical, and genealogical studies...
- Budczies J, Bockmayr M, Klauschen F, Endris V, Fröhling S, Schirmacher P, et al. Mutation patterns in genes encoding interferon signaling and antigen presentation: A pan-cancer survey with implications for the use of immune checkpoint inhibitors. Genes Chromosomes Cancer. 2017;56:651-659 pubmed publisher..Since these mutations are prevalent in treatment-naïve tumors, genetic screening prior to therapy might complement current approaches at predicting response to immune checkpoint blockade. ..
- Song Y, Lim J, Min H, Kim M, Choi H, Cho S, et al. Changes in the clinicopathological characteristics and genetic alterations of follicular thyroid cancer. Eur J Endocrinol. 2017;177:465-473 pubmed publisher..Moreover, the prevalence of RAS mutations decreased. RAS and TERT promoter mutations may be associated with poor clinical outcomes in FTC, especially when the two mutations coexist. ..
- Duarte A, Ribeiro D, Oliveira P, Amaral O. Mutation Frequency of Three Neurodegenerative Lysosomal Storage Diseases: From Screening to Treatment?. Arch Med Res. 2017;48:263-269 pubmed publisher..Carrier screening in target populations may provide the foundations for more effective approaches to precision medicine. ..
- Roshan A, Jones P, Greenman C. Exact, time-independent estimation of clone size distributions in normal and mutated cells. J R Soc Interface. 2014;11: pubmed publisher..Second, we model mutation frequency distributions that deep sequencing of subclonal samples produce. ..
- Fredriksson N, Elliott K, Filges S, Van den Eynden J, Ståhlberg A, Larsson E. Recurrent promoter mutations in melanoma are defined by an extended context-specific mutational signature. PLoS Genet. 2017;13:e1006773 pubmed publisher..Our findings have implications for the interpretation of somatic mutations in regulatory regions, and underscore the importance of genomic context and extended sequence patterns to accurately describe mutational signatures in cancer. ..
- Wang S, Bo Y, Zhou X, Chen J, Li W, Liang J, et al. Significance of Heavy-Ion Beam Irradiation-Induced Avermectin B1a Production by Engineered Streptomyces avermitilis. Biomed Res Int. 2017;2017:5373262 pubmed publisher..Heavy-ion irradiation improves the mutation rate, broadens the mutation spectrum, and shortens the breeding cycle...
- Yu X, Yang M, Zhou B, Wang G, Huang Y, Wu L, et al. Characterization of Somatic Mutations in Air Pollution-Related Lung Cancer. EBioMedicine. 2015;2:583-90 pubmed publisher..This study uncovers the mutation spectrum of air pollution-related lung cancers, and provides evidence for pollution exposure-genomic mutation relationship at a large scale. ..
- Abadía Cardoso A, Freimer N, Deiner K, Garza J. Molecular Population Genetics of the Northern Elephant Seal Mirounga angustirostris. J Hered. 2017;108:618-627 pubmed publisher..We then employ a classical method for bacteria to estimate the microsatellite mutation rate in the species, deriving an estimate that is extremely similar to that estimated for a similar set of loci in ..
- Villahermosa D, Christensen O, Knapp K, Fleck O. Schizosaccharomyces pombe MutS? and MutL? Maintain Stability of Tetra-Nucleotide Repeats and Msh3 of Hepta-Nucleotide Repeats. G3 (Bethesda). 2017;7:1463-1473 pubmed publisher..We conclude that Msh3 has no obvious function in MMR in S. pombe, but contributes to DNA repeat stability in MMR-independent processes. ..
- Cekin N, Akyurek M, Pinarbasi E, Ozen F. MEFV mutations and their relation to major clinical symptoms of Familial Mediterranean Fever. Gene. 2017;626:9-13 pubmed publisher..The most common polymorphism was R202Q (13%). In addition, a novel heterozygous polymorphism at 564th nucleotide (C>T) of exon2 were found in 2 patients. ..
- Rawson J, Gohl D, Landman S, Roth M, Meissner M, Peterson T, et al. Single-Strand Consensus Sequencing Reveals that HIV Type but not Subtype Significantly Impacts Viral Mutation Frequencies and Spectra. J Mol Biol. 2017;429:2290-2307 pubmed publisher..of human immunodeficiency virus (HIV) genetic variation and evolution has been whether differences exist in mutation rate and/or mutation spectra among HIV types (i.e., HIV-1 versus HIV-2) and among HIV groups (i.e...
- Xiong Z, Shi J, Fu Z, Wan H, Tu L. Phenotypic classification of gastric signet ring cell carcinoma and its relationship with K-ras mutation. Genet Mol Res. 2017;16: pubmed publisher..The different K-ras mutation frequencies observed imply distinct genetic mechanisms in the carcinogenesis of I- and G-phenotype gastric SRC carcinomas. ..
- Moreno F, Indakoetxea B, Barandiaran M, Caballero M, Gorostidi A, Calafell F, et al. The unexpected co-occurrence of GRN and MAPT p.A152T in Basque families: Clinical and pathological characteristics. PLoS ONE. 2017;12:e0178093 pubmed publisher..A152T MAPT variant does not appear to show a discernible influence on the clinical phenotype of GRN carriers. Whether p.A152T confers a greater than expected propensity for tau pathology in these GRN carriers remains an open question. ..
- Aggarwala V, Ganguly A, Voight B. De novo mutational profile in RB1 clarified using a mutation rate modeling algorithm. BMC Genomics. 2017;18:155 pubmed publisher..of de novo mutational burden within a gene ascertained from affected probands, based on our model for mutation rate informed by local sequence context...
- Drews Piasecka E, Seremak Mrozikiewicz A, Barlik M, Kurzawinska G, Wolski H, Woyciechowska A, et al. The significance of TNF-alpha gene polymorphisms in preterm delivery. Ginekol Pol. 2014;85:428-34 pubmed
- Maharjan R, Ferenci T. A shifting mutational landscape in 6 nutritional states: Stress-induced mutagenesis as a series of distinct stress input-mutation output relationships. PLoS Biol. 2017;15:e2001477 pubmed publisher..Altogether, our conclusion is that environments influence genetic variation as well as selection. ..
- Abanda N, Djieugoué J, Lim E, Pefura Yone E, Mbacham W, Vernet G, et al. Diagnostic accuracy and usefulness of the Genotype MTBDRplus assay in diagnosing multidrug-resistant tuberculosis in Cameroon? a cross-sectional study. BMC Infect Dis. 2017;17:379 pubmed publisher..For routine MDR-TB diagnosis, this assay could be used for Mycobacterium tuberculosis cultures containing contaminants, to complement culture-based drug susceptibility testing or to determine drug resistant mutations. ..
- Psinakis F, Katseli A, Koutsandrea C, Frangia K, Florentin L, Apostolopoulou D, et al. Uveal Melanoma: GNAQ and GNA11 Mutations in a Greek Population. Anticancer Res. 2017;37:5719-5726 pubmed..Understanding their prognostic significance can allow tailored management and facilitate their use in the on-going quest of targeted uveal melanoma therapies...
- . Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012;487:330-7 pubmed publisher..Integrative analyses suggest new markers for aggressive colorectal carcinoma and an important role for MYC-directed transcriptional activation and repression. ..
- Chasovnikova O, Mitrofanov D, Anisimenko M, Voevoda M, Kovalenko S, Liakhovich V. [Prevalence of mutations BRCA1 5382insC, and CHEK2 1100delC in the population of Siberian region]. Genetika. 2012;48:768-72 pubmed..25% for BRCA1 5382insC, and 1.78 versus 0.40% for CHEK2 1100delC) were observed, pointing to their association with susceptibility to breast cancer (OR = = 7.86, 95% CI 3.51-17.30 and OR =4.46, 95% C1 2.04-9.49, respectively). ..
- Ming R, Vanburen R, Liu Y, Yang M, Han Y, Li L, et al. Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biol. 2013;14:R41 pubmed publisher..The genome has evidence of slow evolution, with a 30% slower nucleotide mutation rate than observed in grape...
- González Pérez A, Jene Sanz A, Lopez Bigas N. The mutational landscape of chromatin regulatory factors across 4,623 tumor samples. Genome Biol. 2013;14:r106 pubmed
- Bao J, Wang Q, Li L, Liu C, Zhang Z, Li J, et al. Evolutionary dynamics of recent peste des petits ruminants virus epidemic in China during 2013-2014. Virology. 2017;510:156-164 pubmed publisher..These results expanded our knowledge for PPRV evolution to achieve effective control measures. ..
- Ogundijo O, Wang X. Bayesian estimation of scaled mutation rate under the coalescent: a sequential Monte Carlo approach. BMC Bioinformatics. 2017;18:541 pubmed publisher..More importantly, population genetics parameters, for instance, the scaled population mutation rate Î˜=4N e Î¼ for diploids or Î˜=2N e Î¼ for haploids (where N e is the ..
- Krasovec R, Richards H, Gifford D, Hatcher C, Faulkner K, Belavkin R, et al. Spontaneous mutation rate is a plastic trait associated with population density across domains of life. PLoS Biol. 2017;15:e2002731 pubmed publisher..We recently identified an inverse plastic association between mutation rate and population density at 1 locus in 1 species of bacterium...
- Cobben M, Mitesser O, Kubisch A. Evolving mutation rate advances the invasion speed of a sexual species. BMC Evol Biol. 2017;17:150 pubmed publisher..The observed evolution of mutation rate is adaptive and clearly advances invasion speed both through its effect on the evolution of dispersal ..
- Panagiotopoulou H, Austin J, Zalewska K, Gonciarz M, Czarnogórska K, Gawor J, et al. Microsatellite Mutation Rate in Atlantic Sturgeon (Acipenser oxyrinchus). J Hered. 2017;108:686-692 pubmed publisher..Herein, we present an estimate of genome-wide microsatellite mutation rate in Atlantic sturgeon (Acipenser oxyrinchus) based on parent-offspring transmission patterns...
- Kang L, Zheng J, Zhu X. [Relationship between EGFR Mutations and Pathological Classification and ?Specimen of Lung Adenocarcinoma]. Zhongguo Fei Ai Za Zhi. 2017;20:382-388 pubmed publisher..05). The mutation of EGFR in female was predominant both of the two groups (P<0.05). The mutation rate of EGFR over the age of 60 was significantly lower than that below 60 in surgical specimen, while it was not ..
- Chen Z, Eggerman T, Bocharov A, Baranova I, Vishnyakova T, Kurlander R, et al. Heat shock proteins stimulate APOBEC-3-mediated cytidine deamination in the hepatitis B virus. J Biol Chem. 2017;292:13459-13479 pubmed publisher..These results indicate that heat shock proteins, in particular Hsp90, stimulate APOBEC-3-mediated DNA deamination activity, suggesting a potential physiological role in carcinogenesis and viral innate immunity. ..
- Agashe D. The road not taken: Could stress-specific mutations lead to different evolutionary paths?. PLoS Biol. 2017;15:e2002862 pubmed publisher..show a high expression of error-prone DNA repair machinery, causing a temporary increase in the genome-wide mutation rate. Although we now have a detailed map of the molecular mechanisms underlying such stress-induced mutagenesis (..
- Issa S, Bondurand N, Faubert E, Poisson S, Lecerf L, Nitschke P, et al. EDNRB mutations cause Waardenburg syndrome type II in the heterozygous state. Hum Mutat. 2017;38:581-593 pubmed publisher..Based on our results, we now estimate EDNRB mutations to be responsible for 5%-6% of WS2. ..
- Zhang J, Yan S, Liu X, Gan L, Wu Z, Gong Y, et al. Gender-related prognostic value and genomic pattern of intra-tumor heterogeneity in colorectal cancer. Carcinogenesis. 2017;38:837-846 pubmed publisher..Taking MATH into consideration in clinical trial might contribute to better therapeutic strategies in CRC with researches added on in the future. ..
- Fares M, Sabater Muñoz B, Toft C. Genome Mutational and Transcriptional Hotspots Are Traps for Duplicated Genes and Sources of Adaptations. Genome Biol Evol. 2017;9:1229-1240 pubmed publisher..Our data demonstrate that the genome traps duplicates through the accelerated regulatory and functional divergence of their gene copies providing a source of novel adaptations in yeast...