Mutation Rates Of Loci Research Articles

Modeling the mosaic structure of bacterial genomes to infer their evolutionary history

The chronology and phylogeny of bacterial evolution are difficult to reconstruct due to a scarce fossil record. The analysis of bacterial genomes remains challenging because of large sequence divergence, the plasticity of bacterial genomes due to frequent gene loss, horizontal gene transfer, and differences in selective pressure from one locus to another. Therefore, taking advantage of the rich and rapidly accumulating genomic data requires accurate modeling of genome evolution. An important technical consideration is that loci with high effective mutation rates may diverge beyond the detection limit of the alignment algorithms used, biasing the genome-wide divergence estimates toward smaller divergences. In this article, we propose a novel method to gain insight into bacterial evolution based on statistical properties of genome comparisons. We find that the length distribution of sequence matches is shaped by the effective mutation rates of different loci, by the horizontal transfers, and by the aligner sensitivity. Based on these inputs, we build a model and show that it accounts for the empirically observed distributions, taking the Enterobacteriaceae family as an example. Our method allows to distinguish segments of vertical and horizontal origins and to estimate the time divergence and exchange rate between any pair of taxa from genome-wide alignments. Based on the estimated time divergences, we construct a time-calibrated phylogenetic tree to demonstrate the accuracy of the method.

Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola

Molecular dating methods of population splits are crucial in evolutionary biology, but they present important difficulties due to the complexity of the genealogical relationships of genes and past migrations between populations. Using the double digest restriction-site associated DNA (ddRAD) technique and an isolation-with-migration (IM) model, we studied the evolutionary history of water vole populations of the genus Arvicola, a group of complex evolution with fossorial and semi-aquatic ecotypes. To do this, we first estimated mutation rates of ddRAD loci using a phylogenetic approach. An IM model was then used to estimate split times and other relevant demographic parameters. A set of 300 ddRAD loci that included 85 calibrated loci resulted in good mixing and model convergence. The results showed that the two populations of A. scherman present in the Iberian Peninsula split 34 thousand years ago, during the last glaciation. In addition, the much greater divergence from its sister species, A. amphibius, may help to clarify the controversial taxonomy of the genus. We conclude that this approach, based on ddRAD data and an IM model, is highly useful for analyzing the origin of populations and species.

Abstract 4078: Enhanced anti-tumor activity through a combination of intravenous injectable TLR7 agonist, DSP-0509 and immune checkpoint inhibitors

Abstract Toll-like receptors (TLRs) are a family of pattern-recognition receptors (PRR) that recognize pathogen-associated molecular patterns (PAMPs). TLR7 is mainly expressed in plasmacytoid dendritic cells (pDCs) and recognizes virus derived single-stranded RNA (ssRNA). TLR7 stimulation in pDCs induces type I interferon secretion, which results in innate immune activation. In this preclinical study, the characteristic changes in the tumor microenvironment (TME) after the combination treatment of DSP-0509 with immune checkpoint inhibitors (ICIs) in DSP-0509-responsive and -resistant tumors were assessed. Mutation rates of microsatellite loci were measured by 3130 xl Genetic Analyzer. Anti-tumor activity was evaluated in syngeneic mouse models along with flow cytometric analysis of tumor infiltrating lymphocytes (TILs). Gene expression profiles in tumor tissues were measured by qPCR arrays. Mutation rates of 5 microsatellite loci and basal levels of CD8+T cell infiltration were examined in tumor tissues derived from 10 syngeneic tumor-bearing mouse models. Intravenous administration of DSP-0509 significantly suppressed tumor growth in some tumor-bearing mouse models with high mutation rates and CD8+T cell infiltration including the CT26 (P<0.05), but not in any models with low mutation rates and CD8+T cell infiltration including 4T1. Gene expression analysis revealed that the CT26 tumors highly expressed T cell inflamed genes including Ifng, Fasl and Il15 at the baseline, whereas the 4T1 tumors highly expressed immune suppressive genes including Il10 and Csf3. In contrast, the combination with anti-PD-1 antibody suppressed the tumor growth not only in the CT26 (P<0.0001) but also in the 4T1-bearing model with immune suppressive TME (P<0.05) and increased the expression of IFN-gamma signature genes including Ifng, Cxcl10 and Gzmb in both models. Similarly, the combination with anti-CTLA-4 antibody suppressed the tumor growth in both models and increased IFN-gamma signature genes. The frequency of PMN-MDSC (CD11b+Ly6g+) in 4T1 tumor was significantly decreased after the combination treatment of anti-PD-1 antibody (P<0.05). Anti-tumor activity of DSP-0509 was associated with tumor mutation rates and the presence of CD8+ T cells within the tumor. The treatment of DSP-0509 in combination with anti-PD-1 antibody showed anti-tumor activity with increased expression of IFN-gamma signature genes and decreased PMN-MDSC even in the 4T1-bearing mouse model with immune suppressive TME (i.e., “cold”). In addition, the combination treatment with anti-CTLA-4 antibody also showed the anti-tumor activity with the increased IFN-gamma signature gene expression. These results suggest that combination of ICI with DSP-0509 resulted in anti-tumor activity by changing immunogenic “cold” to “hot” TME. Citation Format: Yosuke Ota, Takeshi Otsubo, Masashi Goto, Yasushi Matsuki. Enhanced anti-tumor activity through a combination of intravenous injectable TLR7 agonist, DSP-0509 and immune checkpoint inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4078.

Influence of VEGFR single nucleotide polymorphisms on the efficacy of sunitinib therapy against renal cell carcinoma.

Single nucleotide polymorphisms (SNPs) of vascular endothelial growth factor receptor (VEGFR) may have effects on the MAPK/ERK/STAT3 signaling pathway, and the resulting phenotypes may influence the response to sunitinib-targeted therapy for renal cell carcinoma. In order to test this hypothesis patients with advanced renal cell carcinoma treated with sunitinib, were enrolled in our study. Peripheral blood samples were used to run a polymerase chain reaction-restriction fragment length polymorphism protocol to type candidate nucleotide polymorphism loci (VEGFR1, VEGFR2 and VEGFR3). The samples were also used in western blots to determine p-MAPK/ERK/STAT3 protein expression levels. The clinical responses to treatment were recorded and then a logistic regression method was applied to analyze the correlation between polymorphism of loci and effectiveness of sunitinib therapy. According to a follow-up visit (on average after 15 months of treatment) there were 16 complete responses (CR), 29 partial responses (PR) and 23 stable disease (SD) and progression of disease (PD) cases. Tests were carried out for 5 SNPs: VEGFR1 (rs664393), VEGFR2 (rsl870377 and rs7667298) and VEGFR3 (rs448012 and rs72816988). Mutation rates of rsl870377 and rs448012 loci in the CR+PR group were lower than those in the SD+PD group. No such differences were found for the other 3 loci. Relative expression levels of p-MAPk, p-ERK and p-STAT3 in the CR+PR group were significantly lower than those in the SD+PD group (P<0.05). The median progression-free survival and overall survival (OS) in the CR+PR group were higher than those in the SD+PD group (P<0.001). The median OS of the TT rsl870377 genotype was higher than that of the AA genotype, and the median OS of the GG rs448012 genotype was higher than that of the CC genotype (P<0.001). It was concluded through a logistic regression model that rsl870377 (AA) and rs448012 (GG) are independent risk factors closely associated with the effectiveness of sunitinib-targeted therapy on renal cell carcinoma. VEGFR SNPs are able to mediate the MAPK/ERK/STAT3 signaling pathway and therefore influence the effectiveness of sunitinib-targeted therapy, which makes them possible new therapeutic targets.

Eigen model of randomness in species evolution

We modify the deterministic Eigen model of species evolution into a randomized model in order to render the Eigen model more realistic for the description of species evolution. In the framework of the Eigen model, we regard the locus mutation rate of a genetic sequence as a Gaussian distributed random variable. Thus the Eigen model turns into a random model. In this randomized model, we can see that when the fluctuation strength of the mutation rate is small, the error threshold of the quasispecies changes slightly and still serves as a phase transition point. However, when the fluctuation strength becomes large, the error threshold shifts from a phase transition point into a crossover region. Since the error threshold in the real species evolution is a crossover region, we should consider the upper limit of the crossover region when dealing with practical problems.

Features of Variable Number of Tandem Repeats in Yersinia pestis and the Development of a Hierarchical Genotyping Scheme

BackgroundVariable number of tandem repeats (VNTRs) that are widely distributed in the genome of Yersinia pestis proved to be useful markers for the genotyping and source-tracing of this notorious pathogen. In this study, we probed into the features of VNTRs in the Y. pestis genome and developed a simple hierarchical genotyping system based on optimized VNTR loci.Methodology/Principal FindingsCapillary electrophoresis was used in this study for multi-locus VNTR analysis (MLVA) in 956 Y. pestis strains. The general features and genetic diversities of 88 VNTR loci in Y. pestis were analyzed with BioNumerics, and a “14+12” loci-based hierarchical genotyping system, which is compatible with single nucleotide polymorphism-based phylogenic analysis, was established.Conclusions/SignificanceAppropriate selection of target loci reduces the impact of homoplasies caused by the rapid mutation rates of VNTR loci. The optimized “14+12” loci are highly discriminative in genotyping and source-tracing Y. pestis for molecular epidemiological or microbial forensic investigations with less time and lower cost. An MLVA genotyping datasets of representative strains will improve future research on the source-tracing and microevolution of Y. pestis.

Dynamic of Mutational Events in Variable Number Tandem Repeats ofEscherichia coliO157:H7

VNTRs regions have been successfully used for bacterial subtyping; however, the hypervariability in VNTR loci is problematic when trying to predict the relationships among isolates. Since few studies have examined the mutation rate of these markers, our aim was to estimate mutation rates of VNTRs specific for verotoxigenic E. coli O157:H7. The knowledge of VNTR mutational rates and the factors affecting them would make MLVA more effective for epidemiological or microbial forensic investigations. For this purpose, we analyzed nine loci performing parallel, serial passage experiments (PSPEs) on 9 O157:H7 strains. The combined 9 PSPE population rates for the 8 mutating loci ranged from 4.4 × 10−05 to 1.8 × 10−03 mutations/generation, and the combined 8-loci mutation rate was of 2.5 × 10−03 mutations/generation. Mutations involved complete repeat units, with only one point mutation detected. A similar proportion between single and multiple repeat changes was detected. Of the 56 repeat mutations, 59% were insertions and 41% were deletions, and 72% of the mutation events corresponded to O157-10 locus. For alleles with up to 13 UR, a constant and low mutation rate was observed; meanwhile longer alleles were associated with higher and variable mutation rates. Our results are useful to interpret data from microevolution and population epidemiology studies and particularly point out that the inclusion or not of O157-10 locus or, alternatively, a differential weighting data according to the mutation rates of loci must be evaluated in relation with the objectives of the proposed study.

SnIPRE: selection inference using a Poisson random effects model.

We present an approach for identifying genes under natural selection using polymorphism and divergence data from synonymous and non-synonymous sites within genes. A generalized linear mixed model is used to model the genome-wide variability among categories of mutations and estimate its functional consequence. We demonstrate how the model's estimated fixed and random effects can be used to identify genes under selection. The parameter estimates from our generalized linear model can be transformed to yield population genetic parameter estimates for quantities including the average selection coefficient for new mutations at a locus, the synonymous and non-synynomous mutation rates, and species divergence times. Furthermore, our approach incorporates stochastic variation due to the evolutionary process and can be fit using standard statistical software. The model is fit in both the empirical Bayes and Bayesian settings using the lme4 package in R, and Markov chain Monte Carlo methods in WinBUGS. Using simulated data we compare our method to existing approaches for detecting genes under selection: the McDonald-Kreitman test, and two versions of the Poisson random field based method MKprf. Overall, we find our method universally outperforms existing methods for detecting genes subject to selection using polymorphism and divergence data.

Towards Improvements in the Estimation of the Coalescent: Implications for the Most Effective Use of Y Chromosome Short Tandem Repeat Mutation Rates

Over the past two decades, many short tandem repeat (STR) microsatellite loci on the human Y chromosome have been identified together with mutation rate estimates for the individual loci. These have been used to estimate the coalescent age, or the time to the most recent common ancestor (TMRCA) expressed in generations, in conjunction with the average square difference measure (ASD), an unbiased point estimator of TMRCA based upon the average within-locus allele variance between haplotypes. The ASD estimator, in turn, depends on accurate mutation rate estimates to be able to produce good approximations of the coalescent age of a sample. Here, a comparison is made between three published sets of per locus mutation rate estimates as they are applied to the calculation of the coalescent age for real and simulated population samples. A novel evaluation method is developed for estimating the degree of conformity of any Y chromosome STR locus of interest to the strict stepwise mutation model and specific recommendations are made regarding the suitability of thirty-two commonly used Y-STR loci for the purpose of estimating the coalescent. The use of the geometric mean for averaging ASD and across loci is shown to improve the consistency of the resulting estimates, with decreased sensitivity to outliers and to the number of STR loci compared or the particular set of mutation rates selected.

Mutation rates of spoligotypes and variable numbers of tandem repeat loci in Mycobacterium tuberculosis

Variable numbers of tandem repeat (VNTR) loci and spoligotypes are molecular markers used to study genetic diversity of bacteria such as Mycobacterium tuberculosis. Knowledge about the rate at which molecular fingerprints change, or the mutation rate, is important for interpreting molecular epidemiological data and for studying quantitative models of the evolution and epidemiology of bacteria. In this paper we estimate the mutation rates of spoligotypes and VNTR loci of M. tuberculosis using published data sets from epidemiological studies. Our method makes use of a compound parameter: twice the product of the effective population size and the mutation rate. We use a standard procedure to estimate this population genetic parameter which describes genetic diversity. The ratio of estimated diversity parameters for different markers can be used to generate new estimates for markers with unknown mutation rates. We apply this method to generate new estimates along with confidence intervals. We found mutation rates for VNTR loci to be around 7 × 10 −4 to 1.5 × 10 −2 per locus per year, and for spoligotypes to be around 0.02–0.09 per year. The spoligotype rate is similar to previous estimates while the VNTR rates are at least an order of magnitude higher than previously reported. These findings confirm the high level of discrimination observed using multilocus VNTR typing, and suggest that caution should be taken not to underestimate the extent of recent transmission when using this marker.

Effect of low-dose radiation on mutation rates of STR loci commonly used in forensic casework

The possible effect of low-dose radiation on STR markers in people exposed to radiation during their professional activities was estimated in this study. We evaluated mutation rates in 17 forensic STR loci typed by the COrDIS-18 kit (CSF1PO, D10S1248, D12S391, D13S317, D16S539, D18S51, D21S11, D2S441, D3S1358, D5S818, D7S820, D8S1179, FGA, SE33, TH01, TPOX, and vWA) in 78 families (father–mother–child) with one parent exposed to low-dose radiation before fertilization. Five mutations were observed. In two cases, the new alleles were delivered from the non-exposed parent. The calculated mutation rate for the 17 studied STR loci in families appeared to be in good concordance with data published for normal populations. No evidence for an elevated mutation rate in STR markers after low-dose radiation was found.

Mutation rates at 14 STR loci in the population from Pernambuco, Northeast Brazil

Definition about mutation rates of short tandem repeats (STRs) loci used in forensic analysis are useful for the correct interpretation of resulting genetic profiles and the definition of criterions for exclusion in paternity testing. Germline mutation of 14 STR loci was studied for 54,105 parent–child allelic transfers from 2575 paternity testing cases carried out during 2000–2007 from the Pernambuco State, Northeast Brazil. The parenthood in each of these cases was highly validated (probability > 99.99%). We identified 43 mutations at 12 loci. Locus-specific mutation rate estimates varied between 2 × 10 −4 and 2 × 10 −3, and the overall mutation rate estimate was 8 × 10 −4. Mutation events in the male germline were more frequent than in the female germline. The majority of the mutations could be explained by losses or gains of one repeat unit and there was no evidence for selection between insertion or deletion changes. Our data were compared with those of Portuguese and North-American populations for CSF1PO, D18S51, D21S11, D7S820, TH01, TPOX and demonstrated, despite the great difference in the size of the sample, that mutation rates of STR loci in a mixed population do not differ from that encountered in different populations.

New sequence data of allelic variants at the STR loci ACTBP2 (SE33), D21S11, FGA, vWA, CSF1PO, D2S1338, D16S539, D18S51 and D19S433 in Caucasoids

On the occasion of a study on mutation rates of human STR loci, numerous alleles have been sequenced. Several new sequence or length variant alleles were found.

Epistasis in polygenic traits and the evolution of genetic architecture under stabilizing selection.

We consider the effects of epistasis in a polygenic trait in the balance of mutation and stabilizing selection. The main issues are the genetic variation maintained in equilibrium and the evolution of the mutational effect distribution. The model assumes symmetric mutation and a continuum of alleles at all loci. Epistasis is modeled proportional to pairwise products of the single-locus effects. A general analytical formalism is developed. Assuming linkage equilibrium, we derive results for the equilibrium mutation load and the genetic and mutational variance in the house of cards and the Gaussian approximation. The additive genetic variation maintained in mutation-selection balance is reduced by any pattern of the epistatic interactions. The mutational variance, in contrast, is often increased. Large differences in mutational effects among loci emerge, and a negative correlation among (standard mean) locus mutation effects and mutation rates is predicted. Contrary to the common view since Waddington, we find that stabilizing selection in general does not lead to canalization of the trait. We propose that canalization as a target of selection instead occurs at the genic level. Here, primarily genes with a high mutation rate are buffered, often at the cost of decanalization of other genes. An intuitive interpretation of this view is given in the discussion.

Molecular nature of 11 spontaneous de novo mutations in Drosophila melanogaster.

To investigate the molecular nature and rate of spontaneous mutation in Drosophila melanogaster, we screened 887,000 individuals for de novo recessive loss-of-function mutations at eight loci that affect eye color. In total, 28 mutants were found in 16 independent events (13 singletons and three clusters). The molecular nature of the 13 events was analyzed. Coding exons of the locus were affected by insertions or deletions >100 nucleotides long (6 events), short frameshift insertions or deletions (4 events), and replacement nucleotide substitutions (1 event). In the case of 2 mutant alleles, coding regions were not affected. Because approximately 70% of spontaneous de novo loss-of-function mutations in Homo sapiens are due to nucleotide substitutions within coding regions, insertions and deletions appear to play a much larger role in spontaneous mutation in D. melanogaster than in H. sapiens. If so, the per nucleotide mutation rate in D. melanogaster may be lower than in H. sapiens, even if their per locus mutation rates are similar.

The evolution of gene number: are heritable and non-heritable errors equally important?

Is there a limit to the number of genes carried by an organism? Two reasons have been. First, as most mutations are deleterious, for a given per locus mutation rate there must exist an upper limit to the number of genes that is consistent with individual survival. Second, the imprecision of the mechanisms governing gene expression might also restrict genomic complexity. As gene expression errors are probably much more common than mutations, it is the latter that are more likely to impose a limit. However, these errors are not heritable and therefore cannot accumulate in populations. Which of the two sorts of effect are more likely to impose a limit? We address this issue in two ways. First, we ask about the load imposed by each sort of error. We show that the harmful effect of non-heritable failures is higher than that of heritable mutations, if (p) x (delta) > mu, where p is the rate of non-heritable failures, delta measures the harmful effect of these failures and mu is the rate of heritable mutations. Therefore, although the rate of non-heritable errors might be very high, this does not demonstrate that they are more important than mutations as their impact must be discounted by the strength of their effects. Further, we note that both theory and evidence suggest that the most common errors are of the least importance. Second, we discuss the population genetics of a new gene duplication. Previous attempts to make a connection between error rates and limits on gene number are based on group selection arguments. These fail to show a direct limitation on the spread of gene duplications. We note that empirical evidence indicates that duplication per se tends to result in expression errors that may be heritable. We therefore argue that a hybrid model, one evoking heritable expression errors, is likely to be the most realistic.

Comparison of the Power and Accuracy of Biallelic and Microsatellite Markers in Population-Based Gene-Mapping Methods

Because of their great abundance and amenability to fully automated genotyping, single-nucleotide polymorphisms (SNPs) and simple insertion/deletion are emerging as a new generation of markers for positional cloning. Although the efficiency and cost associated with the markers are important in the mapping of human disease genes, the power to detect the linkage between the marker and the disease locus, as well as the accuracy of the estimation of the map location of the disease gene, dictate the selection of the markers. Both the power and the accuracy depend not only on the type of the markers but also on other factors, such as the age of the disease mutation, the magnitude of the genetic effect, the marker-allele distribution in the population, mutation rates of marker loci, the frequency of the disease allele, the recombination fraction, and the methods for mapping the human disease genes. In this article, we develop a mathematical framework and the analytical formulas for calculation of the power and the accuracy and investigate the impact that the aforementioned factors have on the power and the accuracy, by using two population-based gene-mapping methods-likelihood-based linkage-disequilibrium mapping and the transmission/disequilibrium test, for both biallelic SNPs and microsatellites. These studies provide not only guidance in selection of the markers and in the design of the sample scheme for positional cloning but also insight into the biological bases of the mapping of human disease genes.

Mutation Rate in Human Microsatellites: Influence of the Structure and Length of the Tandem Repeat

In 10,844 parent/child allelic transfers at nine short-tandem-repeat (STR) loci, 23 isolated STR mismatches were observed. The parenthood in each of these cases was highly validated (probability >99.97%). The event was always repeat related, owing to either a single-step mutation (n=22) or a double-step mutation (n=1). The mutation rate was between 0 and 7 x 10(-3) per locus per gamete per generation. No mutations were observed in three of the nine loci. Mutation events in the male germ line were five to six times more frequent than in the female germ line. A positive exponential correlation between the geometric mean of the number of uninterrupted repeats and the mutation rate was observed. Our data demonstrate that mutation rates of different loci can differ by several orders of magnitude and that different alleles at one locus exhibit different mutation rates.

A Novel Unstable Mouse VNTR Family Expanded from SINE B1 Elements

Human hypervariable minisatellites provide highly informative loci for analyzing processes of tandem repeat turnover, but little is known about mechanisms of instability in other species. We have therefore screened the mouse genome for analogous VNTR loci. One of the probes we isolated, MMS10, detects a highly variable rodent-specific family of multiple loci derived by expansion of a common GGCAGA repeat unit from within a subset of B1 short interspersed elements. The mean germline mutation rate for loci detected by MMS10 was estimated at 1.7% per offspring band, though analysis of individual loci showed substantial variation in germinal instability apparently related to repeat array size. This MMS10 family of expanded hexanucleotide repeat loci provides a novel resource for investigating mechanisms of tandem repeat turnover in the mouse and an efficient means for monitoring germline mutations induced by external agents such as ionizing radiation.

Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci.

Using the generalized stepwise mutation model, we propose a method of estimating the relative mutation rates of microsatellite loci, grouped by the repeat motif. Applying ANOVA to the distributions of the allele sizes at microsatellite loci from a set of populations, grouped by repeat motif types, we estimated the effect of population size differences and mutation rate differences among loci. This provides an estimate of motif-type-specific mutation rates up to a multiplicative constant. Applications to four different sets of di-, tri-, and tetranucleotide loci from a number of human populations reveal that, on average, the non-disease-causing microsatellite loci have mutation rates inversely related to their motif sizes. The dinucleotides appear to have mutation rates 1.5-2 times higher than the tetranucleotides, and the non-disease-causing trinucleotides have mutation rates intermediate between the di- and tetranucleotides. In contrast, the disease-causing trinucleotides have mutation rates 3.9-6.9 times larger than the tetranucleotides. Comparison of these estimates with the direct observations of mutation rates at microsatellites indicates that the earlier suggestion of higher mutation rates of tetranucleotides in comparison with the dinucleotides may stem from a nonrandom sampling of tetranucleotide loci in direct mutation assays.