1,181 research outputs found
GeneDistillerâDistilling Candidate Genes from Linkage Intervals
Background: Linkage studies often yield intervals containing several hundred positional candidate genes. Different manual or automatic approaches exist for the determination of the gene most likely to cause the disease. While the manual search is very flexible and takes advantage of the researchers â background knowledge and intuition, it may be very cumbersome to collect and study the relevant data. Automatic solutions on the other hand usually focus on certain models, remain ââblack boxesâ â and do not offer the same degree of flexibility. Methodology: We have developed a web-based application that combines the advantages of both approaches. Information from various data sources such as gene-phenotype associations, gene expression patterns and protein-protein interactions was integrated into a central database. Researchers can select which information for the genes within a candidate interval or for single genes shall be displayed. Genes can also interactively be filtered, sorted and prioritised according to criteria derived from the background knowledge and preconception of the disease under scrutiny. Conclusions: GeneDistiller provides knowledge-driven, fully interactive and intuitive access to multiple data sources. It displays maximum relevant information, while saving the user from drowning in the flood of data. A typical query takes less than two seconds, thus allowing an interactive and explorative approach to the hunt for the candidate gene
MutationDistiller: user-driven identification of pathogenic DNA variants
MutationDistiller is a freely available online tool for user-driven analyses of Whole Exome Sequencing data. It offers a user-friendly interface aimed at clinicians and researchers, who are not necessarily bioinformaticians. MutationDistiller combines Mutation- Tasterâs pathogenicity predictions with a phenotypebased approach. Phenotypic information is not limited to symptoms included in the Human Phenotype Ontology (HPO), but may also comprise clinical diagnoses and the suspected mode of inheritance. The search can be restricted to lists of candidate genes (e.g. virtual gene panels) and by tissue-specific gene expression. The inclusion of GeneOntology (GO) and metabolic pathways facilitates the discovery of hitherto unknown disease genes. In a novel approach, we trained MutationDistillerâs HPO-based prioritization on authentic genotypeâphenotype sets obtained from ClinVar and found it to match or outcompete current prioritization tools in terms of accuracy. In the output, the program provides a list of potential disease mutations ordered by the likelihood of the affected genes to cause the phenotype. MutationDistiller provides links to gene-related information from various resources. It has been extensively tested by clinicians and their suggestions have been valued in many iterative cycles of revisions. The tool, a comprehensive documentation and examples are freely available at https://www.mutationdistiller.org
MutationTaster2021
Here we present an update to MutationTaster, our DNA variant effect prediction tool. The new version uses a different prediction model and attains higher accuracy than its predecessor, especially for rare benign variants. In addition, we have integrated many sources of data that only became available after the last release (such as gnomAD and ExAC pLI scores) and changed the splice site prediction model. To more easily assess the relevance of detected known disease mutations to the clinical phenotype of the patient, MutationTaster now provides information on the diseases they cause. Further changes represent a major overhaul of the interfaces to increase user-friendliness whilst many changes under the hood have been designed to accelerate the processing of uploaded VCF files. We also offer an API for the rapid automated query of smaller numbers of variants from within other software. MutationTaster2021 integrates our disease mutation search engine, MutationDistiller, to prioritise variants from VCF files using the patient's clinical phenotype. The novel version is available at https://www.genecascade.org/MutationTaster2021/. This website is free and open to all users and there is no login requirement
MutationTaster2021
Here we present an update to MutationTaster, our DNA variant effect prediction tool. The new version uses a different prediction model and attains higher accuracy than its predecessor, especially for rare benign variants. In addition, we have integrated many sources of data that only became available after the last release (such as gnomAD and ExAC pLI scores) and changed the splice site prediction model. To more easily assess the relevance of detected known disease mutations to the clinical phenotype of the patient, MutationTaster now provides information on the diseases they cause. Further changes represent a major overhaul of the interfaces to increase user-friendliness whilst many changes under the hood have been designed to accelerate the processing of uploaded VCF files. We also offer an API for the rapid automated query of smaller numbers of variants from within other software. MutationTaster2021 integrates our disease mutation search engine, MutationDistiller, to prioritise variants from VCF files using the patient's clinical phenotype. The novel version is available at https://www.genecascade.org/MutationTaster2021/. This website is free and open to all users and there is no login requirement
RegulationSpotter: annotation and interpretation of extratranscriptic DNA variants
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, âfunctionalâ or ânon-functionalâ, 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
Systematic Comparison of Three Methods for Fragmentation of Long-Range PCR Products for Next Generation Sequencing
Next Generation Sequencing (NGS) technologies are gaining importance in the routine clinical diagnostic setting. It is thus desirable to simplify the workflow for high-throughput diagnostics. Fragmentation of DNA is a crucial step for preparation of template libraries and various methods are currently known. Here we evaluated the performance of nebulization, sonication and random enzymatic digestion of long-range PCR products on the results of NGS. All three methods produced high-quality sequencing libraries for the 454 platform. However, if long-range PCR products of different length were pooled equimolarly, sequence coverage drastically dropped for fragments below 3,000 bp. All three methods performed equally well with regard to overall sequence quality (PHRED) and read length. Enzymatic fragmentation showed highest consistency between three library preparations but performed slightly worse than sonication and nebulization with regard to insertions/deletions in the raw sequence reads. After filtering for homopolymer errors, enzymatic fragmentation performed best if compared to the results of classic Sanger sequencing. As the overall performance of all three methods was equal with only minor differences, a fragmentation method can be chosen solely according to lab facilities, feasibility and experimental design
A systematic, large-scale comparison of transcription factor binding site models
Background The modelling of gene regulation is a major challenge in biomedical
research. This process is dominated by transcription factors (TFs) and
mutations in their binding sites (TFBSs) may cause the misregulation of genes,
eventually leading to disease. The consequences of DNA variants on TF binding
are modelled in silico using binding matrices, but it remains unclear whether
these are capable of accurately representing in vivo binding. In this study,
we present a systematic comparison of binding models for 82 human TFs from
three freely available sources: JASPAR matrices, HT-SELEX-generated models and
matrices derived from protein binding microarrays (PBMs). We determined their
ability to detect experimentally verified ârealâ in vivo TFBSs derived from
ENCODE ChIP-seq data. As negative controls we chose random downstream exonic
sequences, which are unlikely to harbour TFBS. All models were assessed by
receiver operating characteristics (ROC) analysis. Results While the area-
under-curve was low for most of the tested models with only 47 % reaching a
score of 0.7 or higher, we noticed strong differences between the various
position-specific scoring matrices with JASPAR and HT-SELEX models showing
higher success rates than PBM-derived models. In addition, we found that while
TFBS sequences showed a higher degree of conservation than randomly chosen
sequences, there was a high variability between individual TFBSs. Conclusions
Our results show that only few of the matrix-based models used to predict
potential TFBS are able to reliably detect experimentally confirmed TFBS. We
compiled our findings in a freely accessible web application called ePOSSUM
(http:/mutationtaster.charite.de/ePOSSUM/) which uses a Bayes classifier to
assess the impact of genetic alterations on TF binding in user-defined
sequences. Additionally, ePOSSUM provides information on the reliability of
the prediction using our test set of experimentally confirmed binding sites
dolls/puppets as miniatures - more than small
Weitere Hrsg.: Jana Mikota, Philipp SchmerheimDer Themenschwerpunkt der zweiten Ausgabe von de:do lautet: Puppen als Miniaturen â mehr als klein. Puppen und ihre Kontexte beanspruchen hier, âmehrâ als nur verkleinerte Varianten oder Repliken menschlicher Lebenswelten zu sein. Nicht von ungefĂ€hr gelten sie als ein âFundort der GröĂeâ (Bachelard).
Als âkleine Formateâ generieren sie Bilder und Narrative der eigenen Art, die in Funktion und Wirkung offen sind: so bewegen sie sich zwischen Abbildung, Verdichtung und Transformation von RealitĂ€t, sind Ausdruck von SehnsĂŒchten und/oder KontrollbedĂŒrfnissen ihrer ErschafferInnen, lösen Bezauberung, Verwunderung oder Befremden aus und ermöglichen ganzheitliche WeltzugĂ€nge und Erkenntnis ĂŒber innere ZusammenhĂ€nge. Einmal mehr erweisen sich Puppen als Miniaturen und im Kontext miniaturisierter Welten als hybride Objekte, aufgeladen mit vielerlei Symbolik und BedeutungsĂŒberschuss.
Die Zusammenschau der höchst unterschiedlichen BeitrĂ€ge im vorliegenden Heft vermittelt eine Ahnung von möglichen SpannungsverhĂ€ltnissen â zwischen âkleinâ und âgroĂâ, âSichtbaremâ und âVerstecktemâ, âRealitĂ€tâ und âFiktionâ, âMimesisâ und âPoetikâ. Das heterogene Themenspektrum unterstreicht die subtile Bedeutung der Puppe als einem besonderen Markenzeichen der âkleinen Formâ in vielerlei Disziplinen. Die BeitrĂ€ge stammen aus so unterschiedlichen FĂ€chern bzw. interdisziplinĂ€r offenen Fachkulturen wie ArchĂ€ologie, Anthropologie, Volkskunde, Kinder- und Jugendliteratur, Kunstgeschichte, Spielzeugkunde, Animationsfilm, Bildende Kunst, Mode-Design, Forensik.
Ein Interview mit einer jungen KĂŒnstlerin, Miszellen und Rezensionen ergĂ€nzen die Themenvielfalt.The focus topic of the second edition of the journal denkste: puppe / just a bit of: doll (de:do), a multidisciplinary, peer reviewed online journal for human-doll discourses is: dolls/puppets as miniatures - more than small. Dolls/puppets and their contexts claim to be âmoreâ than just miniaturized variants or replicas of human worlds. Thus, it is not by chance that they are regarded as a âplace to find greatnessâ (Bachelard). As âsmall formatsâ, they generate images and narratives of their own kind which are open in function and effect: they oscillate between representation, condensation and transformation of reality, expressing longings and/or control needs of their creators and triggering enchantment, amazement or alienation while enabling a holistic access to the world and insight into inner contexts. Arguing in this line, dolls/puppets prove to be miniatures and â in the context of miniaturized worlds âhybrid objects, charged with all sorts of symbolism and excess of meaning. The synopsis of the highly diverse contributions in this issue gives us an idea of possible tensions â between âsmallâ and âlargeâ, âvisibleâ and âhiddenâ, ârealityâ and âfictionâ, âmimesisâ and âpoeticsâ. The heterogeneous range of topics underlines the subtle significance of the doll/puppet as a special trademark of the âsmall formâ in many disciplines. The contributions come from subjects as diverse as diverse as archeology, anthropology, folklore, childrenâs and youth literature, art history, toy studies, animated film, fine arts, fashion design, forensics. An interview with a young artist, miscellaneous aspects as well as reviews complete the variety of topics
Heterozygous Loss-of-Function SEC61A1 Mutations Cause Autosomal-Dominant Tubulo-Interstitial and Glomerulocystic Kidney Disease with Anemia
Autosomal-dominant tubulo-interstitial kidney disease (ADTKD) encompasses a group of disorders characterized by renal tubular and interstitial abnormalities, leading to slow progressive loss of kidney function requiring dialysis and kidney transplantation. Mutations in UMOD, MUC1, and REN are responsible for many, but not all, cases of ADTKD. We report on two families with ADTKD and congenital anemia accompanied by either intrauterine growth retardation or neutropenia. Ultrasound and kidney biopsy revealed small dysplastic kidneys with cysts and tubular atrophy with secondary glomerular sclerosis, respectively. Exclusion of known ADTKD genes coupled with linkage analysis, whole-exome sequencing, and targeted re-sequencing identified heterozygous missense variants in SEC61A1âc.553A>G (p.Thr185Ala) and c.200T>G (p.Val67Gly)âboth affecting functionally important and conserved residues in SEC61. Both transiently expressed SEC6A1A variants are delocalized to the Golgi, a finding confirmed in a renal biopsy from an affected individual. Suppression or CRISPR-mediated deletions of sec61al2 in zebrafish embryos induced convolution defects of the pronephric tubules but not the pronephric ducts, consistent with the tubular atrophy observed in the affected individuals. Human mRNA encoding either of the two pathogenic alleles failed to rescue this phenotype as opposed to a complete rescue by human wild-type mRNA. Taken together, these findings provide a mechanism by which mutations in SEC61A1 lead to an autosomal-dominant syndromic form of progressive chronic kidney disease. We highlight protein translocation defects across the endoplasmic reticulum membrane, the principal role of the SEC61 complex, as a contributory pathogenic mechanism for ADTKD
A principal component meta-analysis on multiple anthropometric traits identifies novel loci for body shape
Large consortia have revealed hundreds of genetic loci associated with anthropometric traits, one trait at a time. We examined whether genetic variants affect body shape as a composite phenotype that is represented by a combination of anthropometric traits. We developed an approach that calculates averaged PCs (AvPCs) representing body shape derived from six anthropometric traits (body mass index, height, weight, waist and hip circumference, waist-to-hip ratio). The first four AvPCs explain >99% of the variability, are heritable, and associate with cardiometabolic outcomes. We performed genome-wide association analyses for each body shape composite phenotype across 65 studies and meta-analysed summary statistics. We identify six novel loci: LEMD2 and CD47 for AvPC1, RPS6KA5/C14orf159 and GANAB for AvPC3, and ARL15 and ANP32 for AvPC4. Our findings highlight the value of using multiple traits to define complex phenotypes for discovery, which are not captured by single-trait analyses, and may shed light onto new pathways
- âŠ