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1,174
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1,174 results for “cancer genomics”
Metagenome-assembled genomes (MAGs), colorectal cancer (CRC)
<p>This archive contains (i) Metagenome assemblies of short-term enrichment cultures of CRC mucosal tissue microbiota, and (ii) Reconstructed metagenome-assembled genomes (MAGs) generated through binning of metagenome contigs.</p>
Genomic signature for malignant tumour progression in cervical cancer
<p>To investigate the clinical genomic signatures associated with tumor progression, we performed genomic sequencing on patients with cervical cancer, including primary, recurrent, and metastatic tumor tissues, and obtained their somatic mutation and copy number alteration profiles.</p>
Detection of genetic alterations in gastric cancer patients from Saudi Arabia using comparative genomic hybridization (CGH)
<p>Abstract</p> <p>Background: The present study was conducted to discover genetic imbalances such as DNA copy number variations (CNVs) associated with gastric cancer (GC) and to examine their association with different genes involved in the process of gastric carcinogenesis in Saudi population. </p> <p>Methods: Formalin-fixed paraffin-embedded (FFPE) tissues samples from 33 gastric cancer patients and 15 normal gastric samples were collected. Early and late stages GC samples were genotyped and CNVs were assessed by using Illumina HumanOmni1-Quad v.1.0 BeadChip. </p> <p>Results: Copy number gains were more frequent than losses throughout all GC samples compared to normal tissue samples. The mean number of the altered chromosome per case was 64 for gains and 40 for losses, and the median aberration length was 679115bp for gains and 375889bp for losses. We identified 7 high copy gain, 52 gains, 14 losses, 32 homozygous losses, and 10 copy neutral LOHs (loss of heterozygosities). Copy number gains were frequently detected at 1p36.32, 1q12, 1q22, 2p11.1, 4q23-q25, 5p12-p11, 6p21.33, 9q12-q21.11, 12q11-q12, 14q32.33, 16p13.3, 17p13.1, 17q25.3, 19q13.32, and losses at 1p36.23, 1p36.32, 1p32.1, 1q44, 3q25.2, 6p22.1, 6p21.33, 8p11.22, 10q22.1, 12p11.22, 14q32.12 and 16q24.2. We also identified 2 monosomy at chromosome 14 and 22, 52 partially trisomy and 22 whole chromosome 4 neutral loss of heterozygosities at 13q14.2-q21.33, 5p15.2-p15.1, 5q11.2-q13.2, 5q33.1-q34 and 3p14.2-q13.12. Furthermore, 11 gains and 2 losses at 1p36.32 were detected for 11 different GC samples and this region has not been reported before in other populations. Statistical analysis confirms significant association of H. pylori infection with T4 stage of GC as compare to control and other stages.</p>
An unsupervised deep learning framework with variational autoencoders for genome-wide DNA methylation analysis and biologic feature extraction applied to breast cancer
<p>Supplemental data for the paper titled "An unsupervised deep learning framework with variational autoencoders for genome-wide DNA methylation analysis and biologic feature extraction applied to breast cancer"</p>
Microscopy images - "An elevated rate of whole-genome duplications associated with carcinogen exposure in Black cancer patients"
<p>This repository contains microscopy data from the manuscript "An elevated rate of whole-genome duplications associated with carcinogen exposure in Black cancer patients" by Leanne M. Brown, Ryan A. Hagenson, Tilen Koklič, Iztok Urbančič, Janez Strancar, and Jason M. Sheltzer (preprint: 10.1101/2023.11.10.23298349; accepted for publication in Nature Communications).</p> <p> </p> <p>Each zip contains the set of images from individual multi-channel multi-position time-lapse experiment with different combinations of cells exposed to one nanomaterial. Files are named as: IMGxxxx_[ExperimentCode]_ROIxx_tile[TileNumber]_[Channel]_[CellType]_t[Timepoint].tif, where each of the varying elements in [..] denotes the following:</p> <ul> <li>[ExperimentCode]: tells which material the cells were exposed to - see decoding table in the file "material-codes.xlsx"</li> <li>[TileNumber]: two xy-tiles per condition</li> <li>[Channel]: cytoplasm of epi cells (LA4), membrane (MEM), cytoplasm of imu cells and tubulin (MHSTUB), nanomaterial (NANO)</li> <li>[CellType]: mono-culture of lung epithelial cells (epi), their coculture with macrophages (epiimu)</li> <li>[Timepoint]: consecutive number of the frame in the time-lapse</li> </ul> <p> </p>
Genomic and functional characterization of a mucosal symbiont involved in early-stage colorectal cancer
<p>Files Uploaded</p> <p>1. 16S Phylum level LDA analysis of colonoscopy biopsies </p> <p>16S_LDA_analysis_upload_20210710.tar.gz </p> <p>2. 16S DNA fastq files</p> <p>FASTQ_Generation_2019-03-16_17_29_28Z-167483978.zip</p> <p>3. Whole genome sequence analysis of b fragilis isolates from colonoscopy isolates</p> <p>WGS_b_fragilis_analysis_20210709_upload.tar.gz</p> <p>4. Sample sheet describing the b fragilis sample fastq files.</p> <p>16S sequencing sample sheet.docx</p> <p>5. b fragilis whole genome sequence fastq files</p> <p>Sample-*.fastq.gz</p>
Genomic Guided Therapy With Dasatinib or Nilutamide in Metastatic Castration-Resistant Prostate Cancer
ClinicalTrials.gov study NCT00918385. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Randomized Controlled Trial of Genomically Directed Therapy in Patients With Triple Negative Breast Cancer
ClinicalTrials.gov study NCT02101385. IPD Sharing: NO. Countries: 1. Publications: 2.
Adjuvant Cisplatin With Either Genomic-Guided Vinorelbine or Pemetrexed for Early Stage Non-Small-Cell Lung Cancer
ClinicalTrials.gov study NCT00545948. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Breast Cancer Genome Guided Therapy Study (BEAUTY)
ClinicalTrials.gov study NCT02022202. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Trial to Evaluate Genomic Expression Profiles to Direct Preoperative Chemotherapy in Early Stage Breast Cancer
ClinicalTrials.gov study NCT00636441. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Study Using a Genomic Predictor of Platinum Resistance to Guide Therapy in Stage IIIB/IV Non-Small Cell Lung Cancer
ClinicalTrials.gov study NCT00509366. IPD Sharing: Not stated. Countries: 1. Publications: 2.
HOPE-Genomics Intervention for the Improvement of Cancer Patient Knowledge of Genomics
ClinicalTrials.gov study NCT04905082. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Video Intervention to Improve Patient Understanding of Tumor Genomic Testing in Patients With Metastatic Cancer
ClinicalTrials.gov study NCT05215769. IPD Sharing: NO. Countries: 1. Publications: 1.
Lifecourse genome-wide association study meta-analysis refines the critical life stages for adiposity’s influence on breast cancer risk
Open the record for dataset details and reuse information.
Hemizygous loss of helicases promotes genomic instability and cancer development
Open the record for dataset details and reuse information.
Data from: Genomic analyses identify 15 susceptibility loci and reveal HDAC2, SOX2-OT, and IGF2BP2 in a naturally-occurring canine model of gastric cancer
Open the record for dataset details and reuse information.
Genomic features of lung cancer patients in Indonesia's National Cancer Center
<p><strong>Introduction:</strong> Advances in molecular biology bring advantages to lung cancer management. Moreover, high-throughput molecular tests are currently useful for revealing genetic variations among lung cancer patients. We investigated the genomics profile of the lung cancer patients at the National Cancer Centre of Indonesia.</p> <p><strong>Methods:</strong> A retrospective study enrolled 627 tissue biopsy samples using real time polymerase chain reaction (RT-PCR) and 80 circulating tumour DNA (ctDNA) liquid biopsy samples using next-generation sequencing (NGS) from lung cancer patients admitted to the Dharmais Cancer Hospital from January 2018 to December 2022. Data were obtained from medical records. Data statistically analysed with p<0.05 is considered significant.</p> <p><strong>Result:</strong> The <em>EGFR</em> test results revealed by RT-PCR were wild type (51.5%), single variant (38.8%), double variant (8.3%), and triple variant (1.4%), with 18.66% L85R, 18.22% Ex19del, and 11.08% L861Q variant. Liquid biopsy ctDNA using NGS showed only 2.5% <em>EGFR</em> wild type, 62.5% single variant and 35% co-variant, with <em>EGFR/TP53</em> and <em>EGFR/PIK3CA</em> as the highest.</p> <p><strong>Conclusion:</strong> EGFR variants are the most found in our centre. Liquid biopsy with ctDNA using NGS examination could detect broad variants and co-variants that will influence the treatment planning.</p>
Code and Data for "Genome-wide repeat landscapes in cancer and cell-free DNA" (Annapragada et.al., Science Translational Medicine, 2024)
<h1><strong>Code and Data for "Genome-wide repeat landscapes in cancer and cell-free DNA"</strong></h1> <div> <div> <p>Citation: <br>Annapragada, A.V. Niknafs, N. White, J.R. Bruhm, D.C., Cherry, C., Medina, J.E., Adleff, V., Hruban C., Mathios, D., Foda, Z.H., Phallen, J., Scharpf, R.B., Velculescu, V.E. Genome-wide repeat landscapes in cancer and cell-free DNA. <em>Science Translational Medicine</em>. 2024.</p> <p><a>The code to run the ARTEMIS pipeline and reproduce manuscript figures is publicly available at </a><a href="https://github.com/cancer-genomics/artemis2024">https://github.com/cancer-genomics/artemis2024</a></p> <p>This code also depends on c<a>ode that generates DELFI features for fragmentation-based analysis, which may be found at </a><a href="https://github.com/cancer-genomics/reproduce_lucas_wflow">https://github.com/cancer-genomics/reproduce_lucas_wflow</a> </p> <p>These github repositories have also been archived in this Zenodo as they were on 02/06/2024 (DELFI fragmentation) and 03/11/2024 (ARTEMIS).</p> </div> </div>
GNOSIS: an R Shiny app supporting cancer genomics survival analysis with cBioPortal
<p>GNOSIS Instructional videos.</p>
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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.