Mutations, the fuel of evolution, are first manifested as rare DNA changes within a population of cells. Although next-generation sequencing (NGS) technologies have revolutionized the study of ...genomic variation between species and individual organisms, most have limited ability to accurately detect and quantify rare variants among the different genome copies in heterogeneous mixtures of cells or molecules. We describe the technical challenges in characterizing subclonal variants using conventional NGS protocols and the recent development of error correction strategies, both computational and experimental, including consensus sequencing of single DNA molecules. We also highlight major applications for low-frequency mutation detection in science and medicine, describe emerging methodologies and provide our vision for the future of DNA sequencing.
In 2 meta-analyses, we examined the relationship between perceived discrimination and psychological well-being and tested a number of moderators of that relationship. In Meta-Analysis 1 (328 ...independent effect sizes, N = 144,246), we examined correlational data measuring both perceived discrimination and psychological well-being (e.g., self-esteem, depression, anxiety, psychological distress, life satisfaction). Using a random-effects model, the mean weighted effect size was significantly negative, indicating harm (r = −.23). Effect sizes were larger for disadvantaged groups (r = −.24) compared to advantaged groups (r = −.10), larger for children compared to adults, larger for perceptions of personal discrimination compared to group discrimination, and weaker for racism and sexism compared to other stigmas. The negative relationship was significant across different operationalizations of well-being but was somewhat weaker for positive outcomes (e.g., self-esteem, positive affect) than for negative outcomes (e.g., depression, anxiety, negative affect). Importantly, the effect size was significantly negative even in longitudinal studies that controlled for prior levels of well-being (r = −.15). In Meta-Analysis 2 (54 independent effect sizes, N = 2,640), we examined experimental data from studies manipulating perceptions of discrimination and measuring well-being. We found that the effect of discrimination on well-being was significantly negative for studies that manipulated general perceptions of discrimination (d = −.25), but effects did not differ from 0 when attributions to discrimination for a specific negative event were compared to personal attributions (d = .06). Overall, results support the idea that the pervasiveness of perceived discrimination is fundamental to its harmful effects on psychological well-being.
The consecutive reactions of acid involved siloxane formation are firstly measured in bulk and analysed by Raman spectroscopy. Influencing factors, which can be identified as the chemical properties ...of the silanes, the silylium cations, and miscibility are pointed out by using a special technique. The procedure is based on a modified Raman sample cell, which allows a single-phase system with controlled water content to be systematically quantitatively monitored. Additional to the novel opportunity to analyse the acid "catalysed" condensation during the formation of polysiloxanes, this publication contains an alternated theoretical mechanism for sol-gel synthesis considering a restricted water content. A major aspect of this introducing study is a detailed analysis and identification of the relevant Raman vibrational bands and their origin on the hand of ten different organyltrialkoxysilanes (methoxy and ethoxy). The ability to determine the kinetics of the acid catalysed formation is demonstrated on homologous series of alkyltrimethoxysilanes.
Characterized by a certain focus on the heavily discussed topic of image fusion in its beginnings, sensor data fusion has played a significant role in the remote sensing research community for a long ...time. With this article, we aim to provide a short overview of established definitions, targeting a generalized understanding of the topic. In addition, a review of the state of the art of remote sensing data fusion research is given. By bringing together the conventional view expressed in the classical data fusion community and a review of current activities in the field of Earth observation, this article provides a holistic view of generic data fusion concepts and their applicability to the remote sensing domain.
Mitochondrial DNA (mtDNA) is believed to be highly vulnerable to age-associated damage and mutagenesis by reactive oxygen species (ROS). However, somatic mtDNA mutations have historically been ...difficult to study because of technical limitations in accurately quantifying rare mtDNA mutations. We have applied the highly sensitive Duplex Sequencing methodology, which can detect a single mutation among >10(7) wild type molecules, to sequence mtDNA purified from human brain tissue from both young and old individuals with unprecedented accuracy. We find that the frequency of point mutations increases ~5-fold over the course of 80 years of life. Overall, the mutation spectra of both groups are comprised predominantly of transition mutations, consistent with misincorporation by DNA polymerase γ or deamination of cytidine and adenosine as the primary mutagenic events in mtDNA. Surprisingly, G → T mutations, considered the hallmark of oxidative damage to DNA, do not significantly increase with age. We observe a non-uniform, age-independent distribution of mutations in mtDNA, with the D-loop exhibiting a significantly higher mutation frequency than the rest of the genome. The coding regions, but not the D-loop, exhibit a pronounced asymmetric accumulation of mutations between the two strands, with G → A and T → C mutations occurring more often on the light strand than the heavy strand. The patterns and biases we observe in our data closely mirror the mutational spectrum which has been reported in studies of human populations and closely related species. Overall our results argue against oxidative damage being a major driver of aging and suggest that replication errors by DNA polymerase γ and/or spontaneous base hydrolysis are responsible for the bulk of accumulating point mutations in mtDNA.
Clinical oncology is being revolutionized by the increasing use of molecularly targeted therapies. This paradigm holds great promise for improving cancer treatment; however, allocating specific ...therapies to the patients who are most likely to derive a durable benefit continues to represent a considerable challenge. Evidence continues to emerge that cancers are characterized by extensive intratumour genetic heterogeneity, and that patients being considered for treatment with a targeted agent might, therefore, already possess resistance to the drug in a minority of cells. Indeed, multiple examples of pre-existing subclonal resistance mutations to various molecularly targeted agents have been described, which we review herein. Early detection of pre-existing or emerging drug resistance could enable more personalized use of targeted cancer therapy, as patients could be stratified to receive the therapies that are most likely to be effective. We consider how monitoring of drug resistance could be incorporated into clinical practice to optimize the use of targeted therapies in individual patients.
Mutated isocitrate dehydrogenase 1 (IDH1) defines a molecularly distinct subtype of diffuse glioma
. The most common IDH1 mutation in gliomas affects codon 132 and encodes IDH1(R132H), which harbours ...a shared clonal neoepitope that is presented on major histocompatibility complex (MHC) class II
. An IDH1(R132H)-specific peptide vaccine (IDH1-vac) induces specific therapeutic T helper cell responses that are effective against IDH1(R132H)
tumours in syngeneic MHC-humanized mice
. Here we describe a multicentre, single-arm, open-label, first-in-humans phase I trial that we carried out in 33 patients with newly diagnosed World Health Organization grade 3 and 4 IDH1(R132H)
astrocytomas (Neurooncology Working Group of the German Cancer Society trial 16 (NOA16), ClinicalTrials.gov identifier NCT02454634). The trial met its primary safety endpoint, with vaccine-related adverse events restricted to grade 1. Vaccine-induced immune responses were observed in 93.3% of patients across multiple MHC alleles. Three-year progression-free and death-free rates were 0.63 and 0.84, respectively. Patients with immune responses showed a two-year progression-free rate of 0.82. Two patients without an immune response showed tumour progression within two years of first diagnosis. A mutation-specificity score that incorporates the duration and level of vaccine-induced IDH1(R132H)-specific T cell responses was associated with intratumoral presentation of the IDH1(R132H) neoantigen in pre-treatment tumour tissue. There was a high frequency of pseudoprogression, which indicates intratumoral inflammatory reactions. Pseudoprogression was associated with increased vaccine-induced peripheral T cell responses. Combined single-cell RNA and T cell receptor sequencing showed that tumour-infiltrating CD40LG
and CXCL13
T helper cell clusters in a patient with pseudoprogression were dominated by a single IDH1(R132H)-reactive T cell receptor.
Using samples from Canada (N=1220) and the United States (N=1001), we examined how performing a variety of pro-environmental behaviors (PEBs) predicted life satisfaction. Controlling for demographic ...characteristics and perceptions of ecological threat, more frequent engagement in pro-environmental behaviors predicted higher life satisfaction. All but 2 of 39 PEBs were positively related to life satisfaction, suggesting that the relationship generalizes across behaviors. However, life satisfaction was more strongly predicted by behaviors that involved more social interaction, behaviors that were more easily observed, and by behaviors that involved direct costs in terms of money, time, and effort. Evidence for the role of direct costs was stronger than that for socialness or observability. In addition, perceptions of ecological threat negatively predicted life satisfaction, but this effect was partially suppressed by higher engagement in pro-environmental behavior. Results suggest that lifestyle changes that might be part of a sustainable society need not represent threats to well-being, and might even provide a means of enhancing well-being.
Next-generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA ...sequence in a single experiment, the error rate of ∼1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, we have developed a method termed Duplex Sequencing. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors result in mutations in only one strand and can thus be discounted as technical error. We determine that Duplex Sequencing has a theoretical background error rate of less than one artifactual mutation per billion nucleotides sequenced. In addition, we establish that detection of mutations present in only one of the two strands of duplex DNA can be used to identify sites of DNA damage. We apply the method to directly assess the frequency and pattern of random mutations in mitochondrial DNA from human cells.
We synthesize both optical RGB and synthetic aperture radar (SAR) remote sensing images from land cover maps and auxiliary raster data using generative adversarial networks (GANs). In remote sensing, ...many types of data, such as digital elevation models (DEMs) or precipitation maps, are often not reflected in land cover maps but still influence image content or structure. Including such data in the synthesis process increases the quality of the generated images and exerts more control on their characteristics. Spatially adaptive normalization layers fuse both inputs and are applied to a full-blown generator architecture consisting of encoder and decoder to take full advantage of the information content in the auxiliary raster data. Our method successfully synthesizes medium (10 m) and high (1 m) resolution images when trained with the corresponding data set. We show the advantage of data fusion of land cover maps and auxiliary information using mean intersection over unions (mIoUs), pixel accuracy, and Fréchet inception distances (FIDs) using pretrained U-Net segmentation models. Handpicked images exemplify how fusing information avoids ambiguities in the synthesized images. By slightly editing the input, our method can be used to synthesize realistic changes, i.e., raising the water levels. The source code is available at https://github.com/gbaier/rs_img_synth , and we published the newly created high-resolution data set at https://ieee-dataport.org/open-access/geonrw .
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