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865 results for “Gene Mutation”
Bedrock radioactivity influences the rate and spectrum of mutation - Orthologous genes
<p>Alignments of the 2490 orthologous genes used in the article "Natural Bedrock radioactivity influences the rate and spectrum of mutation" to estimate the mutational spectrum and synonymous substitution rate.</p> <p>To compute accurate synonymous substitution rate, we removed genes with short sequences (<half of the alignment) and genes strongly supporting another phylogeny using ProfileNJ <a href="https://paperpile.com/c/Klqlpb/W5sS">(Noutahi et al. 2016)</a> with a bootstrap threshold of 90%, resulting in a subset of 769 genes listed in the file "List_769_1-to-1_orthologs_EvolutionRate.txt".</p> <p>Transcriptome paired-end reads used to define these orthologous genes have been deposited to the European Nucleotide Archive and are available under the study ID PRJEB14193.</p> <p>Sequences were aligned with Prank<a href="https://paperpile.com/c/Klqlpb/pilh"> (Löytynoja & Goldman 2008)</a> using a codon model and sites ambiguously aligned were removed with Gblocks <a href="https://paperpile.com/c/Klqlpb/c5kb">(Castresana 2000)</a>.</p>
gnomAD polymorphism and de novo mutation data for analysis of mutation rates in highly mutable gene classes
<p>We analyze the human mutation rate in three gene classes (IGK, RNU, and tRNA) which deviate from the expectations of a mutation rate model. We examine the distribution of allele frequencies for SNVs within these genes and we analyze the counts of de novo mutations stratified by whether the SNV was observed or not. </p> <p>{CHR}_IGK_SFS_v2_denovo.gz: allele frequencies, mutation rate estimates, and whether the de novo mutation was observed for IGK, RNU, and tRNA genes. Based on gnomAD v3. </p> <p>{CHR}_indiv_mu.csv: quality information for variants in these gene classes from the 1kg subset of gnomAD.</p> <p>"CHR", "POS", "REF", "ALT", "FILTER", "AC", "AN", "MQRankSum", "pab_max", "VQSLOD", "AB", "PN", "MR", "AR", "MG", "MC", "QUAL"</p> <p>all_variants_chr21_mu_h.csv.gz: all variants from chromosome 21 to use for comparing allele frequencies to those in our gene classes.</p> <p>21_indiv_mu_all.csv.gz: quality information from all variants on chromosome 21 from the 1kg subset of gnomAD to use for comparison with gene classes.</p> <p>"CHR", "POS", "REF", "ALT", "FILTER", "AC", "AN", "MQRankSum", "pab_max", "VQSLOD", "AB", "PN", "MR", "AR", "MG", "MC", "QUAL"</p> <p> </p>
Supplemental data for: Increased mutation and gene conversion within human segmental duplications
<p>Data used for figure generation and analysis in: <strong>Increased mutation and gene conversion within human segmental duplications</strong></p> <ol> <li>new-assemblies.zip contains all the new assemblies added in this work beyond the HPRC assemblies (Clint PTR, CHM1, HG00514, NA12878, HG03125). All other assemblies used in this analysis are available through the HPRC: <a href="https://github.com/human-pangenomics/HPP_Year1_Assemblies/blob/main/assembly_index/Year1_assemblies_v2_genbank.index">assembly_index/Year1_assemblies_v2_genbank.index</a>.</li> <li>all-sample.vcf is a vcf file with all the variant calls used in this analysis. </li> <li>alignments.zip contains all the syntenic alignments used for analysis. </li> <li>data.zip contains annotation data and other information used in analysis and figure making. </li> <li>Online tables 1-4 (Online-tables.xlsx)</li> </ol> <p>Code used in figure making and analysis is on <a href="https://github.com/mrvollger/sd-divergence-and-igc-figures">GitHub</a>.</p> <p>Snakemake pipelines used in the analysis are also on GitHub:</p> <ul> <li>Assembly alignment and IGC calling: https://github.com/mrvollger/asm-to-reference-alignment</li> <li>Variant calling from assembly alignments: https://github.com/mrvollger/sd-divergence</li> <li>Analysis of the triplet content of SNVs: https://github.com/mrvollger/mutyper_workflow</li> </ul>
Mutations in the telomerase reverse transcriptase promoter and PIK3CA gene are common events in penile squamous cell carcinoma of Italian and Ugandan patients
<p>Somatic mutations in the promoter region of TERT (TERTp) gene are highly frequent in penile carcinoma in Italian and Ugandan patients, predominantly in human papillomavirus (HPV) negative cancers (67.6%). TERTp and PIK3CA hotspot changes coexist in 15.8% of cases. The higher mutant allele frequencies (MAFs) of TERT -124A/-146A compared to PIK3CA E545K MAFs suggest an asynchronous mutation timing. The coexistence of TERTp and PIK3CA mutations may represent a novel co-actionable therapeutic target in penile carcinoma patients.</p>
Fig. 1 in First report of kdr mutations in the voltage-gated sodium channel gene in the arbovirus vector, Aedes aegypti, from Nouakchott, Mauritania
Fig. 1 The combinations of kdr point mutations S989P, V1016G, and F1534C in adult female Aedes aegypti mosquitoes in Nouakchott, Mauritania
Classification of Gene Mutations and Cancer-Types with BioBombe Compressed Gene Expression Features
<p>BioBombe analysis applied to gene expression data from The Cancer Genome Atlas (TCGA) PanCanAtlas.</p> <p>Then, the compressed features learned through the serial compression are fed into several machine learning algorithms.</p> <p>The algorithms are used to predict mutation status (for the top 50 most mutated genes in TCGA) and cancer-type using the compressed gene expression features.</p> <p>Method and results described in https://github.com/greenelab/BioBombe. We use the classification approach outlined in https://github.com/greenelab/pancancer</p>
datset related to article "THE NOVEL I213S MUTATION IN PSEN1 GENE IS LOCATED IN A HOTSPOT CODON ASSOCIATED WITH FAMILIAL EARLY-ONSET ALZHEIMER'S DISEASE"
<p><strong>Electropherogram of the proband psen1 exon 7</strong></p> <p><strong>ngs analysis of causal and risk genes associated to dementia</strong></p>
Datset related to article "G507D MUTATION IN FUS GENE CAUSES FAMILIAL AMYOTROPHIC LATERAL SCLEROSIS WITH A SPECIFIC GENOTYPE-PHENOTYPE CORRELATION"
<p><strong>NGS_analysis performed at Fondazione Besta carried out as part of the study reported at title</strong></p>
Dataset related to article"G507D MUTATION IN FUS GENE CAUSES FAMILIAL AMYOTROPHIC LATERAL SCLEROSIS WITH A SPECIFIC GENOTYPE-PHENOTYPE CORRELATION"
<p>NGS Analyses of patients included in the study reported at title followed at Fondazione Besta</p>
Dataset for: Ace and ace-like genes of invasive redlegged earth mite: Copy number variation, target-site mutations, and their associations with organophosphate insensitivity
<p class="MsoNormal">This repository contains the scripts and data required to replicate the analyses in Thia et al.'s, "Evolution of an acetylcholinesterase<em> </em>gene complex and its contribution toward organophosphate insensitivity in an invasive mite pest", submitted to <em>Pest Management Science</em>.</p> <p class="MsoNormal">In this work, Thia et al. use a combination of experimental selection and pool-seq genomic analyses to understand the genetic mechanisms underpinning organophosphate insensitivity in the redlegged earth mite, <em>Halotydeus destructor</em>. There is a special emphasis on disentangling the roles of copy number variation and target-site mutations in the acetylcholinesterase genes, <em>ace,</em> and radiated <em>ace</em>-like genes<span>.</span></p> <p class="MsoNormal">There are three major analyses: (1) an F<sub>ST</sub> genome scan to identify outlier loci between alive (insensitive) and dead (sensitive) mites; (2) an analysis of <em>ace </em>copy number variation between alive and dead mites; and (3) an analysis of candidate target-site mutations in the <em>ace</em> gene.</p>
Codeletion of 1p and 19q determines distinct gene methylation and expression profiles in IDH-mutated oligodendroglial tumors _ Dataset
<p>Overall design: Genome-wide DNA methylation profiling of oligodendroglial tumors (OTs) and five non tumoral brain tissue (NTBT) samples. The Illumina Infinium Human DNA methylation 450k Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in tumoral samples. Samples included 46 OTs and 5 NTBT.</p> <p>Bisulphite converted DNA from the 51 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip</p> <p>Extracted molecule: genomic DNA</p> <p>Platform: Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)</p> <p>Label protocol: Standard Illumina Protocol</p> <p>Hybridization protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol</p> <p>Scan protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting </p> <p>Data processing: BeadStudio software v3.2</p> <p>Data format: IDAT files</p>
A Global Study to Assess the Drug Dynamics, Efficacy, and Safety of Venglustat (GZ/SAR402671) in Parkinson's Disease Patients Carrying a Glucocerebrosidase (GBA) Gene Mutation
ClinicalTrials.gov study NCT02906020. IPD Sharing: YES. Countries: 16. Publications: 3.
Panitumumab and RAS, Diagnostically-useful Gene Mutation for mCRC
ClinicalTrials.gov study NCT02394795. IPD Sharing: YES. Countries: 1. Publications: 3.
A Study to Evaluate Rucaparib in Participants With Solid Tumors and With Deleterious Mutations in HRR Genes
ClinicalTrials.gov study NCT04171700. IPD Sharing: YES. Countries: 1. Publications: 1.
Data from: Gene network topology drives the mutational landscape of gene expression
Open the record for dataset details and reuse information.
Dataset for: Ace and ace-like genes of invasive redlegged earth mite: Copy number variation, target-site mutations, and their associations with organophosphate insensitivity
Open the record for dataset details and reuse information.
Data from: Large-scale mutation in the evolution of a gene complex for cryptic coloration
<p class="western">The types of mutations affecting adaptation in the wild are only beginning to be understood. In particular, whether structural changes shape adaptation by suppressing recombination or by creating new mutations is unresolved. Here we show that multiple, linked but recombining loci underlie cryptic color morphs of <i>Timema chumash </i>stick insects. In a related species, these loci are found in a region of suppressed recombination, forming a supergene. However, in seven species of <i>Timema </i>we find that a mega-base size 'supermutation' has deleted color loci in green morphs. Moreover, we find that balancing selection likely contributes more to maintaining this mutation than does introgression. Our results show how suppressed recombination and large-scale mutation can help package gene complexes into discrete units of diversity, such as morphs, ecotypes, or species.</p>
Data required for "Low mutation rate of spontaneous mutants enables detection of causative genes by comparing whole genome sequences"
<p>In the early 1900s,mutation breeding to select varieties with desirable traits using spontaneous mutation was actively conducted around the world, including Japan. In rice, the number of fixed mutations per generation was estimated to be 1.38-2.25. Although this low mutation rate was a major problem for breeding in those days, in the modern era with the development of NGS technology, it was conversely considered to be an advantage for efficient gene identification. In this paper, we proposed an in silico approach using next-generation sequencing (NGS) to compare the whole genome sequence of a spontaneous mutant with that of a closely related strain with a nearly identical genome, to find polymorphisms that differ between them, and to identify the causal gene by predicting the functional variation of the gene caused by the polymorphism. Using this approach, we found four causal genes for the dwarf mutation, the round shape grain mutation and the awnless mutation. Three of these genes were the same as those previously reported, but one was a novel gene involved in awn formation. The novel gene was isolated from Bozu-Aikoku, a mutant of Aikoku with the awnless trait, in which nine polymorphisms were predicted to alter gene function by their whole-genome comparison. Based on the information on gene function and tissue-specific expression patterns of these candidate genes, Os03g0115700/LOC_Os03g02460, annotated as a shortchain dehydrogenase/reductase SDR family protein, is most likely to be involved in the awnless mutation. Indeed, complementation tests by transformation showed that it is involved in awn formation. Thus, this method is an effective way to accelerate genome breeding of various crop species by enabling the identification of useful genes that can be used for crop breeding with minimal effort for NGS analysis.</p>
A complete list of filtered variants and gene lists of frequently and recurrently mutated genes in DLBCL, MCL, T-NHL, and BL, as well as pre-assembled CNV gene list
<p>A complete list of variants which passed filtering described in supplemental methods, that were found in both PDX model sample and patient’s sample from which it was derived (S1A) and variants which were gained (S1B) or lost (S1C) during PDX model derivation. Gene lists for filtration of variants in genes of special interest are included in the table (S1D). Gene list for filtration of CNV changes in genes of special interest is included in the table (S1E). Chr - Chromosome, REF - Reference allele, ALT - Alternative allele, AA change - Amino acid change, Patient AF - Allele frequency in the patient’s sample, Patient Depth – Read depth in patient’s sample, PDX AF- Allele frequency in PDX model sample, PDX Depth - Read depth in PDX sample, DLBCL - Diffuse Large B-cell lymphoma, MCL - Mantle Cell Lymphoma, TCL - T-cell lymphoma, BL – Burkitt Lymphoma, and CNV - Copy Number Variation.</p>
The effect of presence and absence of DNA repair genes on the rate and pattern of mutation in bacteria
<p>This repository contains the code, data, and outputs used in the manuscript "The effect of presence and absence of DNA repair genes on the rate and pattern of mutation in bacteria".</p> <ul> <li><strong>Script.py:</strong> This is a Python script for estimating the number of polymorphisms and mutation rates of bacterial clusters of orthologous genes found in ATGC_data.zip. It produces individual strain outputs to<em> Polymorphism_Results/</em> and<em> Rate_Results/ </em>directories.</li> <li><strong>ATGC_data.zip: </strong>This is a data set of bacterial clusters of orthologous genes downloaded from the ATGC database by Kristensen et al. (2017). The fasta files are utilised by <em>Script.py</em> and should be extracted to the same working directory, under <em>ATGC_data/.</em></li> <li><strong>mutation_rate_data.csv: </strong>This file contains the outputs of <em>Script.py </em>merged into a single file, alongside additional information regarding the presence and absence of particular repair genes, and the calculation of overall mutation rate and Watterson's corrected mutation rate.</li> <li><strong>Phylogenetic_Comparisons.xlsx:</strong> This file contains the averages of overall mutation rate, transition/transversion ratio, and GC-AT bias, for 50 phylogenetic comparisons under presence and absence of repair enzymes. </li> </ul>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.