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ShareScore release 0.9.0
Dataset results
268 results for “liquid biopsy”
Data for methylome sequencing: Enriching and Profiling Methylomes for Tumor Classification and Liquid Biopsies
<p>We benchmarked and demonstrated the versatility of FLEXseq (Fragment Ligation EXclusive methylation sequencing) across different sample types: genomic DNA from the K562 (leukemia) cell line, DNA mix-in titrations of four immune cell types (B cells, T cells, monocytes, and neutrophils), DNA titrations of three cancer cell lines (breast invasive carcinoma [BRCA], colon adenocarcinoma [COAD], and glioblastoma [GBM]) mixed with those four immune cell mixtures separately, input titrations of cell-free (cf) DNA from one plasma sample and DNA from formalin-fixed paraffin-embedded (FFPE) tissues, cfDNA from 106 cerebrospinal fluids (CSF) and 42 other body fluids, and DNA from 37 FFPE tissues.</p> <p>We sequenced all the samples mentioned above using FLEXseq. Paired-end reads were quality and length trimmed with cutadapt version 3.5, and all high-quality sequencing reads were then aligned to the hg38 reference genome using Bismark v0.23.0. We then filtered out reads with unmethylated cytosine in the non-CpG context with filter_non_conversion function. Next, we used the bismark_methylation_extractor function to extract the methylation calls (removing single-nucleotide polymorphisms [SNP]).</p> <p>We also used the bam2pat function from wgbs_tools, to convert bam files into .pat files for deconvolution, keeping reads covering at least three CpG sites. The .pat files preserve fragment-level data and were de-identified by removing SNPs using the mask_pat function. </p> <p>We used CNVkit (v0.9.10) to analyze and visualize genome-wide copy numbers. Our inputs into CNVkit were Bismark/Bowtie 2 aligned BAM files deduplicated by Bismark based on end positions and fragment lengths. We then generated log2copy ratio plots for all body fluid and FFPE samples based on the pooled reference and visualized them across all bins using the DNAcopy R package.</p> <p> </p>
DEcancer: Proteomics Datasets of Liquid Biopsy Samples
<p>Two datasets used to build the DEcancer pipelines from open access data. The tables in the cancerseek folder are uploaded for convenience and can also be found from the supplementary data of <a href="https://doi.org/10.1016/j.isci.2019.04.035">Early Cancer Detection from Multianalyte Blood Test Results</a> paper. The nanoparticles dataset is processed with the Perseus software on the <a href="http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD017052">original data</a> from Blume <em>et al's</em> Rapid, deep and precise profiling of the plasma proteome with multi-nanoparticle protein corona. These are distinct datasets in that the nanoparticles is a cohort of patients from a high dimensional, low sample size proteomics dataset.</p>
Hybrid nanoplasmonic porous biomaterial scaffold for liquid biopsy diagnostics using extracellular vesicles: data and media
<p>Raw datasets and media accompanying the manuscript: <strong>Hybrid nanoplasmonic porous biomaterial scaffold for liquid biopsy diagnostics using extracellular vesicles</strong>, published in ACS Sensors</p>
Dataset related to the article "Binary classification of copy number alteration profiles in liquid biopsy with potential clinical impact in advanced NSCLC"
<p>This record contains original data used in the article "Binary classification of copy number alteration profiles in liquid biopsy with potential clinical impact in advanced NSCLC" to develop a linear support vector machine (SVM) classifier to predict chromosomal instability. </p> <p>We retrospectively evaluated the results of plasma NGS analysis performed at our Institution by using the AVENIO ctDNA Expanded Kit, a panel of 77 genes, which detects the major classes of genetic alterations. Binary classification, into “stable” (SCP) or “unstable” (UCP) chromosomal profiles, was initially performed by visual inspection of individual CNV alteration profiles by two independent professionals of our group. Then we decided to implement a support vector machine (SVM) classifier to automatically classify CNV profiles as SCP or UCP, beyond operators’ experience. We considered the segmented log2 ratios (.cns) files provided by the CNV kit software and computed three features (Segments, Size, Chromosomes). An alteration (“occurrence of instability”) in the CNV profile was defined each time we found a DNA segment of any size with absolute value of the log2 copy ratio exceeding a fixed cut-off. Two different cut-off values on log2 copy ratio were examined: 0.1 and 0.2. Once the cut-off was defined, three features were considered as covariates in the SVM classifier: 1) number of altered segments (Segments), 2) total length of altered regions (Size) and 3) number of affected chromosomes (Chromosomes).</p> <p>The “dataset_0.1.txt” and “dataset_0.2.txt” files are the original data matrices obtained by considering a cut-off of 0.1 and 0.2, respectively, on the absolute value of the log2 copy ratio.</p> <p>Rows represent available samples in our study (n=177). Columns contain the following variables: anonymized sample IDs (Sample), the class, “stable” or “unstable”, as assigned by two independent professionals of our group (Class), the corresponding binary label (Label: 0 for “stable”, 1 for “unstable”), the three features used as covariates in the SVM classifier and computed as described above (Segments, Size, Chromosomes).</p> <p><br>For the detailed results of our work, please refer to the full article.</p>
Data Set available for Liquid Biopsy of CML Diagnosis
<p><em><span>Chronic Myeloid Leukemia, CML, is caused in patients with myeloproliferative disorders by the presence of BCR::ABL1. The research discussed the integration of microfluidic chips with biosensors for the purpose of detecting biomarkers in peripheral blood thereby showing the raw experimental data set avaialble, liquid bipsy sample set available and Calculation for methods and data Simulation along with graphs, which could obviate the need for painful biopsies, thereby improving diagnostic accuracy and accessibility.</span></em></p>
Multimodal Fusion of Liquid Biopsy and CT Enhances Differential Diagnosis of Early-stage Lung Adenocarcinoma
<p>This research explores the potential of multimodal fusion for the differential diagnosis of early-stage lung adenocarcinoma (LUAD) (tumor sizes < 2 cm). It combines liquid biopsy biomarkers, specifically extracellular vesicle long RNA (evlRNA) and the computed tomography (CT) attributes.</p><p>It includes 4 files:</p><p>1. gene expression matrix : gene expression matrix for all samples (normalized read counts) .</p><p>2. evlRNA Rad features: 6 image features, 17 evlRNA features and labels</p><p>3. differentially expressed genes: Differentially expressed genes in LUAD patients compared with Benign individuals.</p><p>4. raw data: raw data used to for figure and table.</p>
Liquid Biopsy for Detection of Driver Mutation in NSCLC
ClinicalTrials.gov study NCT02778854. IPD Sharing: NO. Countries: 1. Publications: 1.
Liquid Biopsies and Imaging in Breast Cancer
ClinicalTrials.gov study NCT04223492. IPD Sharing: YES. Countries: 1. Publications: 1.
Liver Cancer and Immunotherapy in the Liquid Biopsy Era
ClinicalTrials.gov study NCT05810402. IPD Sharing: NO. Countries: 1. Publications: 25.
A Prospective Interventional Study on Early Screening for Lung Cancer Using Liquid Biopsy
ClinicalTrials.gov study NCT06422637. IPD Sharing: NO. Countries: 1. Publications: 0.
In Vivo Liquid Biopsy of Melanoma (Cytophone)
ClinicalTrials.gov study NCT06488365. IPD Sharing: NO. Countries: 1. Publications: 3.
Translating Single-cell Vulnerability Into Novel ALS Biomarkers and Therapeutic Targets: Towards a Liquid Nerve Biopsy
ClinicalTrials.gov study NCT07268833. IPD Sharing: Not stated. Countries: 1. Publications: 11.
Targeted Therapy With or Without Nephrectomy in Metastatic Renal Cell Carcinoma: Liquid Biopsy for Biomarkers Discovery
ClinicalTrials.gov study NCT02535351. IPD Sharing: Not stated. Countries: 1. Publications: 9.
RB Liquid Biopsy Biorepository
ClinicalTrials.gov study NCT04959097. IPD Sharing: YES. Countries: 1. Publications: 7.
Liquid Biopsy Using Exosomal miRNA Enables Risk Stratification of Potential Metastasis in Patients With Intrahepatic Cholangiocarcinoma.
ClinicalTrials.gov study NCT07224737. IPD Sharing: NO. Countries: 1. Publications: 13.
AssesSment of Early-deteCtion basEd oN liquiD Biopsy in GASTRIC Cancer, ASCEND-Gastric
ClinicalTrials.gov study NCT05224596. IPD Sharing: NO. Countries: 1. Publications: 30.
Peritoneal Lavage Liquid Biopsy in Patients With Gastric Cancer
ClinicalTrials.gov study NCT04943406. IPD Sharing: NO. Countries: 1. Publications: 14.
Prediction of Postoperative Treatment Efficacy and Recurrence Risk of High-risk GIST Based on Liquid Biopsy MRD
ClinicalTrials.gov study NCT05408897. IPD Sharing: NO. Countries: 1. Publications: 16.
Liquid Biopsy-informed Precision Oncology Study to Evaluate Utility of Plasma Genomic Profiling for Therapy Selection
ClinicalTrials.gov study NCT05585684. IPD Sharing: NO. Countries: 1. Publications: 0.
Liquid Biopsy With Immunomagnetic Beads Capture Technique for Malignant Cell Detection in Body Fluid
ClinicalTrials.gov study NCT02891642. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
ScienceDex guides
Understand access before you commit
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.