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243 results for “mutational profiling”
SMDP: SARS-CoV-2 Mutation Distribution Profiler for rapid estimation of mutational histories of unusual lineages
<p>Supplementary information relating to the manuscript titled "SMDP: SARS-CoV-2 Mutation Distribution Profiler for rapid estimation of mutational histories of unusual lineages" that has been published on the preprint server arXiv.</p> <ul> <li>PersistentInfectionScore.nb: Mathematica code used to process the data and generate Figure 2</li> <li>PersistentInfectionScore.pdf: pdf version of the above file</li> <li>Supplementary_tables_Harari_et_al_2022.xlsx: raw data from (<a href="https://www.nature.com/articles/s41591-022-01882-4#Sec19">Harari et al. 2022</a>) that was used to generate mutation distributions</li> </ul>
Functional precision profiling reveals non-mutational rewiring of kinase signaling networks in colorectal cancer
<p>Multi-omics profiling of colorectal cancer (CRC) patients and associated patient-derived organoids. Tumor organoids were characterized in steady-state and perturbed using kinase inhibitors.</p>
Structural modelling results to accompany the paper "Uncommon mutational profiles of metastatic colorectal cancer detected during routine genotyping using next generation sequencing: an update"
<p>This repository contains the results of modelling missense mutants in KRAS, NRAS and BRAF observed in our study in the corresponding protein structures. Modelling was performed using FoldX.</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>
Mutational Profiling in Epithelial Ovarian Cancer: A Meta-Analysis of 435 Patients Dataset
<p><strong>Data Description</strong></p> <p>0 represents no mutation, 1 represents a mutation</p> <p>Survive relates to the survival outcome of the patient. SurviveTime is in days (7300 chosen for alive patients).</p> <p>Ovarian Cancer Patients</p> <ul> <li>361 count</li> <li>TP53, BRCA1, BRCA2, KMT2C, CDK12, CSMD3, TTN, MUC16, NF1, PALB2, RB1, PTEN, FOXM1, BRIP1, KRAS, RASA1, CHEK2, RAD50, RAD51C/D, MRE11A, NBN, FANCE, FANCD2, ATR, ATM, MSH2, PMS2, MLH1, MSH6, FAT1, FAT2, FAT3, FAT4</li> </ul> <p>Uterine Cancer Patients</p> <ul> <li>437 count</li> <li>MSH6, CDK12, PMS2, BRIP1, FAT1, CSMD3, FAT4, BRCA2, MUC16, PALB2, KRAS, BRCA1, MSH2, PTEN, TP53, NF1, KMT2C, FAT3, FANCD2, ATM, NBN, ATR, CHEK2, FANCE, MLH1</li> </ul> <p>Cervical Cancer Patients</p> <ul> <li>174 count</li> <li>CSMD3, CDK12, FAT1, BRIP1, RB1, FAT4, BRCA2, MUC16, PALB2, KRAS, TP53, PTEN, KMT2C, FAT3, BRCA1, NF1, ATM, FANCD2, NBN, ATR, MLH1</li> </ul>
TCGA RNA-Seq normalized rsem data, TCGA clinical data and mutational signature profiles
<p>Normalized rsem RNA-Seq data for each of the 33 TCGA tumor types named as "<em>tumortype</em>rnaSeq.tar", a file containing TCGA clinical data ("cliDat_tcga_18.tar") and a text file with single base substitution mutational signatures for each sample from COSMIC (https://cancer.sanger.ac.uk/cosmic, “signatureProfileSample.txt.zip”).</p>
Data from: Dissimilarity of individual microsatellite profiles under different mutation models: empirical approach
Microsatellites (simple sequence repeats, SSRs) still remain popular molecular markers for studying neutral genetic variation. Two alternative models outline how new microsatellite alleles evolve. Infinite alleles model (IAM) assumes that all possible alleles are equally likely to result from a mutation, while stepwise mutation model (SMM) describes microsatellite evolution as stepwise adding or subtracting single repeat units. Genetic relationships between individuals can be analyzed in higher precision when assuming the SMM scenario with allele size differences as a proxy of genetic distance. If population structure is not predetermined in advance, an empirical data analysis usually includes (a) estimating proximity between individual SSR profiles with a selected dissimilarity measure and (b) determining putative genetic structure of a given set of individuals using methods of clustering and/or ordination for the obtained dissimilarity matrix. We developed new dissimilarity indices between SSR profiles of haploid, diploid, or polyploid organisms assuming different mutation models and compared the performance of these indices for determining genetic structure with population data and with simulations. More specifically, we compared SMM with a constant or variable mutation rate at different SSR loci to IAM using data from natural populations of a freshwater bryozoan Cristatella mucedo (diploid), wheat leaf rust Puccinia triticina (dikaryon), and wheat powdery mildew Blumeria graminis (monokaryon). We show that inferences about population genetic structure are sensitive to the assumed mutation model. With simulations, we found that Bruvo's distance performs generally poorly, while the new metrics are capturing the differences in the genetic structure of the populations.
Data from: Differential neuropsychological profile of ALS patients with and without C9orf72 mutation
<p><b>Objective</b>. To determine whether the neuropsychological profiles of ALS patients with (ALSC9+) and without (ALSC9-) <i>C9orf72</i> expansion are different we administered a battery of neuropsychological tests to 741 ALS patients (68 ALSC9+ and 673 ALSC9-) and 129 controls.</p> <p><b>Methods</b>. The study population includes 741 ALS patients who were consecutively diagnosed at the Turin ALS expert center in the period 2010-2018 and who underwent both cognitive/behavioral and genetic testing. Patients' neuropsychological patterns were compared (a) at the same degree of cognitive and behavioral deficit according to the revised ALS-FTD Consensus Criteria; and (b) at the same level of motor impairment according to the King's staging system.</p> <p><b>Results</b>. Despite being about 7 years younger, ALSC9+ patients had significant lower scores in tests exploring executive functions, and verbal memory both when classified as cognitively normal and when diagnosed in the intermediate cognitive categories. Considering the clinical perspective, ALSC9+ patients showed significantly lower scores compared to ALSC9- patients at King's stage 1 and 3 in almost all the examined neuropsychological domains, while at King's stage 2 ALSC9+ patients were more severely affected only in the verbal memory domain. Behavioral function was comparably impaired in the two cohorts.</p> <p><b>Conclusions</b>. ALSC9+ patients show a different neuropsychological profile compared to ALSC9- ones, being more impaired in executive functions and verbal memory domains at all King's stages. Verbal memory emerged as a particularly vulnerable function in ALSC9+, with worse performances even when patients were still classified as cognitively normal.</p>
Ex Vivo Drug Sensitivity Testing and Mutation Profiling
ClinicalTrials.gov study NCT03860376. IPD Sharing: Not stated. Countries: 1. Publications: 2.
A Phase I Study to Investigate the Safety, Tolerability and Pharmacokinetic Profile of of GSK2118436 in Japanese Subjects With BRAF Mutation Positive Solid Tumors
ClinicalTrials.gov study NCT01582997. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Predicting Non-small Cell Lung Cancer (NSCLC) Lymph Node Metastasis: Integrating Circulating Tumor DNA (ctDNA) Mutation/ Methylation Profiling With Positron Emission Tomography-computed Tomography (PE
ClinicalTrials.gov study NCT06358222. IPD Sharing: NO. Countries: 1. Publications: 6.
Definition of Mutational Profile of Papillary Thyroid Tumors by Mass-ARRAY
ClinicalTrials.gov study NCT05766098. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: Dissimilarity of individual microsatellite profiles under different mutation models: empirical approach
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Data from: Differential neuropsychological profile of ALS patients with and without C9orf72 mutation
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Supplemental material from: ESR1 mutations associated with EIS change conformation of ligand receptor complex and alter transcriptome profile
Estrogen insensitivity syndrome (EIS) arises from rare mutations in estrogen receptor α (ERα, encoded by ESR1 gene) resulting in the inability of estrogen to exert its biological effects. Due to the rarity, mutations in ESR1 gene and the underlying molecular mechanisms of EIS have not been thoroughly studied. Here, we investigate known ESR1 mutants, Q375H and R394H, associated with EIS patients using in vitro and in vivo systems. Comparison of the transcriptome and DNA methylome from stable cell lines of both Q375H and R394H clinical mutants show a differential profile compared to WT ERα resulting in loss of estrogen-responsiveness. Molecular dynamic simulation shows that both ESR1 mutations change the ERα conformation of the ligand receptor complexes. Furthermore, we generated a mouse model Esr1-Q, harboring the human mutation using CRISPR/Cas9 genome editing. Female and male Esr1-Q mice are infertile and have similar phenotypes to αERKO mice. Overall phenotypes of the Esr1-Q mice correspond to those observed in the Q375H patient. Finally, we explore the effects of a synthetic progestogen and a GnRH inhibitor in the Esr1-Q mice for potentially reversing the impaired female reproductive tract function. These findings provide an important basis for understanding the molecular mechanistic consequences associated with EIS.
AlphaFold2 Modeling and Molecular Dynamics Simulations of the Conformational Ensembles for the SARS-CoV-2 Spike Omicron JN.1, KP.2 and KP.3 Variants : Mutational Profiling of Binding Energetics Reveals Epistatic Drivers of the ACE2 Affinity and Escape Hotspots of Antibody Resistance
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Supplementary Material from: "Wnt/B-catenin activation and TP53 mutations associate with distinct immune profiles in advanced thyroid cancer"
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A Molecular Profiling Study of Patients With EGFR Mutation-positive Locally Advanced or Metastatic NSCLC Treated With Osimertinib
ClinicalTrials.gov study NCT03239340. IPD Sharing: YES. Countries: 5. Publications: 0.
Supplemental material from: ESR1 mutations associated with EIS change conformation of ligand receptor complex and alter transcriptome profile
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Transcriptional profiling of STAT1 gain-of-function reveals common and mutation-specific fingerprints
GEO Series GSE166392. Homo sapiens. 70 samples. Type: Expression profiling by high throughput sequencing.
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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.