MobiDetails: online DNA variants interpretation.
Ontology highlight
ABSTRACT:
SUBMITTER: Baux D
PROVIDER: S-EPMC7868358 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:RegulationSpotter is a web-based tool for the user-friendly annotation and interpretation of DNA variants located outside of protein-coding transcripts (extratranscriptic variants). It is designed for clinicians and researchers who wish to assess the potential impact of the considerable number of non-coding variants found in Whole Genome Sequencing runs. It annotates individual variants with underlying regulatory features in an intuitive way by assessing over 100 genome-wide annotations. Additionally, it calculates a score, which reflects the regulatory potential of the variant region. Its dichotomous classifications, 'functional' or 'non-functional', and a human-readable presentation of the underlying evidence allow a biologically meaningful interpretation of the score. The output shows key aspects of every variant and allows rapid access to more detailed information about its possible role in gene regulation. RegulationSpotter can either analyse single variants or complete VCF files. Variants located within protein-coding transcripts are automatically assessed by MutationTaster as well as by RegulationSpotter to account for possible intragenic regulatory effects. RegulationSpotter offers the possibility of using phenotypic data to focus on known disease genes or genomic elements interacting with them. RegulationSpotter is freely available at https://www.regulationspotter.org.
| S-EPMC6602480 | biostudies-literature
Project description:BackgroundWith the availability of raw DNA generated from direct-to-consumer (DTC) testing companies, there has been a proliferation of third-party online services that are available to interpret the raw data for both genealogy and/or health purposes. This study examines the current landscape and downstream clinical implications of consumer use of third-party services.MethodsStudy participants were recruited online from social media platforms. A total of 321 survey respondents reported using third-party services for raw DNA interpretation.ResultsParticipants were highly motivated to explore raw DNA for ancestral information (67%), individual health implications (62%), or both (40%). Participants primarily used one of seven companies to interpret raw DNA; 73% used more than one. Company choice was driven by the type of results offered (51%), price (45%), and online reviews (31%). Approximately 30% of participants shared results with a medical provider and 21% shared with more than one. Outcomes of sharing ranged from disinterest/discounting of the information to diagnosis of genetic conditions. Participants were highly satisfied with their decision to analyze raw DNA (M = 4.54/5), yet challenges in understanding interpretation results were reported irrespective of satisfaction ratings.ConclusionConsumers face challenges in understanding the results and may seek out clinical assistance in interpreting their raw DNA results.
| S-EPMC5823680 | biostudies-literature
Project description:BackgroundMicroarray technology allows the analysis of genomic aberrations at an ever increasing resolution, making functional interpretation of these vast amounts of data the main bottleneck in routine implementation of high resolution array platforms, and emphasising the need for a centralised and easy to use CNV data management and interpretation system.ResultsWe present CNV-WebStore, an online platform to streamline the processing and downstream interpretation of microarray data in a clinical context, tailored towards but not limited to the Illumina BeadArray platform. Provided analysis tools include CNV analsyis, parent of origin and uniparental disomy detection. Interpretation tools include data visualisation, gene prioritisation, automated PubMed searching, linking data to several genome browsers and annotation of CNVs based on several public databases. Finally a module is provided for uniform reporting of results.ConclusionCNV-WebStore is able to present copy number data in an intuitive way to both lab technicians and clinicians, making it a useful tool in daily clinical practice.
| S-EPMC3024943 | biostudies-literature
Project description:Clinical interpretation of DNA sequence variants is a critical step in reporting clinical genetic testing results. Application of next-generation sequencing technology in molecular genetic testing has facilitated diagnoses of genetic disorders in clinical practice. However, the large number of DNA sequence variants detected in clinical specimens, many of which have never been seen before, make clinical interpretation challenging. Recommendations by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) have been widely adopted by clinical laboratories around the world to guide clinical interpretation of sequence variants. The ClinGen Sequence Variant Interpretation Working Group and various disease-specific variant curation expert panels have also developed specifications for the ACMG/AMP recommendations. Despite these efforts to standardize variant interpretation in clinical practice, different laboratories may subjectively use professional judgment to determine which criteria are applicable when classifying a variant. In addition, clinicians and researchers who are not familiar with the variant interpretation process may have difficulty understanding clinical genetic reports and communicating the clinical significance of genetic testing results. Here we provide a step-by-step protocol for clinical interpretation of sequence variants, including practical examples. By following this protocol, clinical laboratory geneticists can interpret the clinical significance of sequence variants according to the ACMG/AMP recommendations and ClinGen framework. Furthermore, this article will help clinicians and researchers to understand variant classification in clinical genetic testing reports and evaluate the quality of the reports. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Interpreting the clinical significance of sequence variants Support Protocol: Reevaluating the clinical significance of sequence variants.
| S-EPMC7431429 | biostudies-literature
Project description:Genome-wide association studies (GWAS) have identified a vast number of variants associated with various complex human diseases and traits. However, most of these GWAS variants reside in non-coding regions producing no proteins, making the interpretation of these variants a daunting challenge. Prior evidence indicates that a subset of non-coding variants detected within or near cis-regulatory elements (e.g., promoters, enhancers, silencers, and insulators) might play a key role in disease etiology by regulating gene expression. Advanced sequencing- and imaging-based technologies, together with powerful computational methods, enabling comprehensive characterization of regulatory DNA interactions, have substantially improved our understanding of the three-dimensional (3D) genome architecture. Recent literature witnesses plenty of examples where using chromosome conformation capture (3C)-based technologies successfully links non-coding variants to their target genes and prioritizes relevant tissues or cell types. These examples illustrate the critical capability of 3D genome organization in annotating non-coding GWAS variants. This review discusses how 3D genome organization information contributes to elucidating the potential roles of non-coding GWAS variants in disease etiology.
| S-EPMC9437546 | biostudies-literature
Project description:Continuous mixture interpretation methods that employ probabilistic genotyping to compute the Likelihood Ratio (LR) utilize more information than threshold-based systems. The continuous interpretation schemes described in the literature, however, do not all use the same underlying probabilistic model and standards outlining which probabilistic models may or may not be implemented into casework do not exist; thus, it is the individual forensic laboratory or expert that decides which model and corresponding software program to implement. For countries, such as the United States, with an adversarial legal system, one can envision a scenario where two probabilistic models are used to present the weight of evidence, and two LRs are presented by two experts. Conversely, if no independent review of the evidence is requested, one expert using one model may present one LR as there is no standard or guideline requiring the uncertainty in the LR estimate be presented. The choice of model determines the underlying probability calculation, and changes to it can result in non-negligible differences in the reported LR or corresponding verbal categorization presented to the trier-of-fact. In this paper, we study the impact of model differences on the LR and on the corresponding verbal expression computed using four variants of a continuous mixture interpretation method. The four models were tested five times each on 101, 1-, 2- and 3-person experimental samples with known contributors. For each sample, LRs were computed using the known contributor as the person of interest. In all four models, intra-model variability increased with an increase in the number of contributors and with a decrease in the contributor's template mass. Inter-model variability in the associated verbal expression of the LR was observed in 32 of the 195 LRs used for comparison. Moreover, in 11 of these profiles there was a change from LR > 1 to LR < 1. These results indicate that modifications to existing continuous models do have the potential to significantly impact the final statistic, justifying the continuation of broad-based, large-scale, independent studies to quantify the limits of reliability and variability of existing forensically relevant systems.
| S-EPMC6245789 | biostudies-literature
Project description:Genomic technologies are redefining the understanding of genotype-phenotype relationships and over the past decade, many bioinformatics algorithms have been developed to predict functional consequences of single nucleotide variants. This article presents the data from a comprehensive computational workflow adopted to assess the biomedical impact of the DNA variants resulting from the experimental study "Molecular analysis of sarcomeric and non-sarcomeric genes in patients with hypertrophic cardiomyopathy" (Bottillo et al., 2016) [1]. Several different independently methods were employed to predict the functional consequences of alleles that result in amino acid substitutions, to study the effect of some DNA variants over the splicing process and to investigate the impact of a sequence variant with respect to the evolutionary conservation.
| S-EPMC4802523 | biostudies-other
Project description:As the number of genes available for commercial sequencing increases and the promise of clinical whole-genome sequencing becomes a reality, the interpretation of the results of these tests becomes more challenging for the practicing neurologist as these studies have the potential to detect novel genetic variants. Such reports are becoming more frequent in general practice, and neurologists are often left to puzzle over the relevance of these "variants of unknown significance," as such genetic changes are often described, and how to communicate this information to the patients and their families. This article will briefly illustrate how clinicians can use such results in the care of their patients. Only genetic variants involving coding sequence will be considered, although similar methods may also be applied to changes such as noncoding alterations or copy number variations. It is also important to note that in some cases, particularly those involving tests that only sequence select exons, negative test results may also require special interpretation.
| S-EPMC3587691 | biostudies-literature
Project description:Our ability to determine the clinical impact of variants in 3' untranslated regions (UTRs) of genes remains poor. We provide a thorough analysis of 3'UTR variants from several datasets. Variants in putative regulatory elements including RNA-binding protein motifs, eCLIP peaks, and microRNA sites are up to 16 times more likely than other variants to have gene expression and phenotype associations. Heterozygous variants in regulatory motifs result in allele-specific protein binding in cell lines and allele-specific gene expression differences in population studies. In addition, variants in shared regions of alternatively polyadenylated isoforms and those proximal to polyA sites are more likely to affect gene expression and phenotype. Finally, pathogenic 3'UTR variants in ClinVar are 20 times more likely than benign variants to fall in a regulatory site. We incorporated these findings into RegVar, a software tool that interprets regulatory elements and annotations for any 3'UTR variant, and predicts whether the variant is likely to affect gene expression or phenotype. This tool will help prioritize variants for experimental studies and identify pathogenic variants in patients.
| S-EPMC10418266 | biostudies-literature
Project description:The mechanism of anaphora resolution is subject to large cross-linguistic differences. The most likely reason for this is the different sensitivity of pronouns to the range of factors that determine their reference. In the current study, we explored the mechanism of anaphora resolution in Polish. First, we explored preferences in the interpretation of null and overt pronouns in ambiguous sentences. More specifically, we investigated whether Polish speakers prefer to relate overt pronouns to subject or object antecedents. Subsequently, we tested the consequences of violating this bias when tracing the online sentence-interpretation process using eye-tracking. Our results show that Polish speakers have a strong preference for interpreting null pronouns as referring to subject antecedents and interpreting overt pronouns as referring to object antecedents. However, in online sentence interpretation, only overt pronouns showed sensitivity to a violation of the speaker's preference for a pronoun-antecedent match. This suggests that null pronoun resolution is more flexible than overt pronoun resolution. Our results indicate that it is much easier for Polish speakers to shift the reference of a null pronoun than an overt one whenever a pronoun is forced to refer to a less-preferred antecedent. These results are supported by naturalness ratings, which showed that null pronouns are considered equally natural regardless of their reference, while overt pronouns referring to subject antecedents are rated as considerably less natural than those referring to object antecedents. To explain this effect, we propose that the interpretation of null and overt pronouns is sensitive to different factors which determine their reference.
| S-EPMC8752000 | biostudies-literature