7345 results for "canc*"

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• NGS sequencing data of archival FFPE tumor tissue

  The aim of the study was to identify mutations in key ovarian cancer genes (BRCA1, BRCA2,TP53, PTEN, ATM, ATR, NF1) in archival fresh-frozen paraffin embedded (FFPE) tumor tissue from platinum-resistant ovarian cancer patients enrolled in the phase I/II GANNET53 clinical trial. From the enrolled 133 patients, archival FFPE tissue was available and DNA was extracted thereof. The DNA samples passing quality control (n=118) were NGS sequenced using the SureSeq™ Ovarian Cancer Panel and the NGS Library Preparation kit (Oxford Gene Technology), which covers all exons of 7 key ovarian cancer genes for single nucleotide variants (SNV) and indels, and the Illumina MiSeq platform. For the paired-end runs, one Read 1 (R1) and one Read 2 (R2) FASTQ file were created for each sample. FASTQ files were compressed and created with the extension \.fastq.gz.

  Dataset EGAD50000001371

• Total RNAseq data from 8 patients with muscle invasive bladder cancer

  For this dataset we performed total RNAseq on blood samples from 8 patients with muscle invasive bladder cancer. The data consists of 8 sets of paired fastq files with accompanying UMI fastq files. Sequenced on the Illumina NoveSeq6000 platform using S2 flow cells (v1.5,2x150 cycles), with a mean yield of 313 million reads.

  Dataset EGAD50000001380

• Single cell RNAseq and TCRseq data from tumor and blood samples from 4 patients with muscle invasive bladder cancer

  For this dataset we performed single cell RNAseq paired with single cell TCR-seq on tumor and blood samples from 4 patients. This dataset contains 4 tumor samples as well as 4 blood samples. Each sample is made up of 2 sets of paired fastq files. The first pair contains reads corresponding to RNA transcripts (_Transcripts in file name), while the second pair contain reads corresponding to TCRs (_VDJ in file name). Sequenced on the Illumina NovaSeq6000 platform in a paired-end run using an SP flow cell (v1.5, 300 cycles).

  Dataset EGAD50000001381

• Bulk TCRseq data from 149 patients with bladder cancer

  For this dataset we performed bulk TCRseq on tumor and serial blood samples from patients with muscle invasive bladder cancer (n patients = 119, n blood = 209, n tumor = 28) or non-muscle invasive bladder cancer (n patients = 30, n blood = 56, n tumor = 19) for a total of 149 patients and 312 samples. Each sample consists of a paired fastq file. Sequenced on the Ilumina NovaSeq6000 platform using SP and S1 flow cells (v1.5, 2x101 cycles), with a mean yield of 42 million reads covering the CDR3β region.

  Dataset EGAD50000001382

• WES in Angolan and Cape Verdean triple-negative breast cancer samples

  WES (using the SureSelect Human All Exon V5 + UTRs target enrichment kit) in 23 Angolan and 7 Cape Verdean triple-negative breast cancer samples

  Dataset EGAD50000001482

• WES bam files associated with HNSCC patients in the LIONESS study

  This dataset contains 85 WES bam/bai files of HNSCC cancer patients as part of with the LIONESS study

  Dataset EGAD50000001487

• WGS of clonal organoids, bulk-tumor tissues, and matched blood samples derived from metastatic colorectal cancer patients

  This dataset consists of WGS fastq files from 58 clonal organoids and 18 fresh-frozen (FT) bulk-tissue samples from surgically resected primary and metastatic tumors before and after anticancer therapies in 6 patients with matched blood control samples from each patient. After DNA extraction from each sample using DNeasy Blood and Tissue Kit (Qiagen), library preparation was done using TruSeq DNA PCR-free kit. Then, paired-end fastq files were generated using Illumina NovaSeq 6000.

  Dataset EGAD50000001493

• single-cell RNA-seq profiling of 2 patient derived colorectal cancer organoids after treatment with a combination of different anticancer drugs

  This dataset consists of single-cell RNA-seq profiling of colorectal cancer organoids derived from two patients. The organoids were profiled both after 4 weeks of treatment and after a drug holiday of two weeks. There are 49 RNA sequence files generated using single cell RNA sequencing technology from 10X genomics.

  Dataset EGAD50000001495

• Oxford Nanopore long-read sequencing data of high-grade serous ovarian cancer

  This dataset comprises whole-genome Oxford Nanopore long-read sequencing data from six high-grade serous ovarian cancer (HGSOC) patients, including cryopreserved, pre-treatment tumor tissues and matched peripheral blood samples (12 samples in total). High-molecular-weight DNA was prepared using the SQK-LSK114 Ligation Sequencing Kit and sequenced on FLO-PRO114M flow cells (R10.4.1). Basecalling was conducted using the super-accurate (SUP) model, enabling simultaneous detection of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). The dataset includes BAM files containing base modification information for downstream genomic and epigenomic analyses.

  Dataset EGAD50000001509

• Liquid Biopsy High Grade Serous Ovarian Cancer WGS

  Liquid Biopsy High Grade Serous Ovarian Cancer WGS.

  Dataset EGAD50000001520

• Targeted Sequencing Data for RESOLVE Clinical Trial

  This is a Phase II clinical trial. This research study is studying a combination of targeted therapies as a possible treatment for estrogen-receptor positive (ER+) endometrial cancer and low-grade serous ovarian cancer. The drugs involved in this study are: - Abemaciclib (also known as Verzenio™) - Letrozole (also known as Femara®) - Metformin (also known as Glucophage®) - Zotatifin (also known as eFT226) - Gedatolisib (also known as PF-05212384)

  Dataset EGAD50000001711

• Mutation analysis using AVENIO Expanded in cfDNA

  High resolution mutation analysis using the AVENIO ctDNA Expanded Kit V2, which targets 77 cancer-associated genes, in cfDNA in metastatic breast cancer.

  Dataset EGAD50000001669

• Dataset of Study assessing the efficacy and safety of durvalumab plus olaparib plus fulvestrant in selected metastatic or locally advanced ER-positive, HER2-negative breast cancer patients.

  This dataset is made of 166 samples extracted from 1) FFPE blocks of the most recent biopsy (metastasis when applicable or primary tumor) of the breast tumor 2) Plasma samples and blood samples at baseline, at Day 1 Cycle2, Day 1 Cycle 3 and at progression or treatment discontinuation. Target sequencing has been perfomed using GREAT_A_v3 panel

  Dataset EGAD50000001665

• Transcriptomic dataset from a phase II study of pembrolizumab and epigenetic modification with azacitidine in platinum-resistant epithelial ovarian cancer

  This dataset includes sequence files from bulk RNA sequencing of tissue biospecimens from a phase II study investigating epigenetic priming followed by immune checkpoint blockade in platinum-resistant epithelial ovarian cancer (NCT02900560). There are 48 bulk RNA sequencing files from 24 specimens included in this dataset.

  Dataset EGAD50000001664

• Multi-omic dataset utilized in the analysis of a phase II study of epigenetic priming followed by nivolumab in lung cancer

  This dataset includes sequence files from whole exome sequencing and bulk RNA sequencing of tissue and blood biospecimens from a phase II clinical trial investigating epigenetic priming followed by immune checkpoint blockade in non-small cell lung cancer (NSCLC; NCT01928576). There are 78 whole exome sequencing files and 36 bulk RNA sequencing files included in this dataset.

  Dataset EGAD50000001336

• Shallow whole genome sequencing DETECT samples

  Shallow whole genome sequencing of samples from the paper Beddowes et al. A large-scale retrospective study in metastatic breast cancer patients using circulating tumour DNA and machine learning to predict treatment outcome and progression-free survival. Mol. One 2025. This includes 1048 longitudinal plasma samples from 149 patients and 35 normals. Samples were sequenced with shallow whole genome sequencing for copy number estimation. All the files are single-end fastq files.

  Dataset EGAD50000001333

• Total RNA-seq of CRPC and NEPC

  This dataset contains total RNA-seq of 10 patient samples: 5 castration resistant prostate cancer (CRPC) and 5 neuroendocrine prostate cancer (NEPC). Total RNA-seq was constructed using ribosomal RNA-depleted random hexamer-primed RNA library preparation kit and sequenced on Illumina at pair-end 150bp. Total RNA-seq allows for circular RNA and mRNA analyses. Each sample was sequenced on two separate lanes, therefore, two pairs of raw fastq files (4 files in total) are provided for each sample.

  Dataset EGAD50000001312

• RNA-seq of oropharynx cancer cases from University of Michigan

  This dataset consists of 67 bulk RNA-seq data (sorted aligned BAM files) from formalin-fixed paraffin-embedded (FFPE) oropharynx tumor samples from the University of Michigan (UM). Samples were collected as part of the UM Head and Neck SPORE between 2008-2014. Library preparation was performed using the ribo-depletion method with the FastSelect kit and sequenced on the NovaSeq 6000 at the UM Advanced Genomics Core, resulting in 150bp paired-end reads. Raw reads were trimmed using Cutadapt (v3.4) and aligned to hg38 and high-risk HPV genomes using STAR (v2.7.9a). 62 of 67 samples were determined to be HPV RNA-positive.

  Dataset EGAD50000001306

• Dataset for "HPV integration induces gene fusions" (Illumina)

  Illumina whole-genome sequencing data for "HPV integration induces gene fusions" We performed short read whole-genome sequencing of five HPV+ head and neck cancer samples using Illumina. The reads are submitted in bam or fastq file format.

  Dataset EGAD50000001305

• Dataset for "HPV integration induces gene fusions" (pacBio)

  pacBio whole-genome sequencing data for "HPV integration induces gene fusions" We performed long read whole-genome sequencing on four HPV+ head and neck cancer samples using pacBio HiFi. The sequence reads were submitted in fastq format.

  Dataset EGAD50000001304

• Dataset for "HPV integration induces gene fusions" (RNA)

  RNA-seq data for "HPV integration induces gene fusions" We performed RNA-seq analysis of five HPV+ head and neck cancer samples using Illumina short reads. Sequenced are submitted in bam format. We also sequenced one samples with pacBio long reads, and the reads are submitted in fastq format.

  Dataset EGAD50000001303

• Dataset for "HPV integration induces gene fusions" (ONT)

  ONT whole-genome sequencing data for "HPV integration induces gene fusions" . We sequenced five HPV-positive head and neck cancer samples using Oxford Nanopore platform. The sequences was submitted in fastq format.

  Dataset EGAD50000001302

• R compatible Seurat's objetc .rds files with count data and metadata from single cell RNA seq analysis to characterize the prostate cancer tumoral microenviroment of 31 fusion biopses.

  Pre-processed Seurat objects with cellular and functional annotation information from the scRNAseq study on PC fusion biopsy samples. The data consists of rds files composed of normalised counts matrices, normalised and scaled counts, functional enrichment counts at the cellular level and metadata with patient grouping and cellular annotation variables. There are 3 .rds files, one with the total cells (SCP_data_analysis), with the selection of cells annotated as cancerous (selected_cancer_analysis) and cancer-associated fibroblasts (selected_caf_analysis).

  Dataset EGAD50000001298

• Tumor Profiler Project - OV scDNA data additional samples

  The dataset contains 10x Chromium single-cell DNA sequencing data from 6 samples from 5 different patients with ovarian cancer. 4 samples were collected from the tumor, and 2 samples from ascites. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format. This dataset contains additional samples from patients not classified as having high-grade serous adenocarcinoma.

  Dataset EGAD50000001294

• Tumor Profiler Project - OV scRNA data additional samples

  The dataset contains 10x Chromium single-cell transcriptomics data from 6 samples from 4 different patients with ovarian cancer. 3 samples were collected from the tumor, 3 samples from ascites. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format. This dataset contains additional samples from patients not classified as having high-grade serous adenocarcinoma.

  Dataset EGAD50000001293

• De novo detection of somatic variants

  The Tumor Profiler Study is an observational trial combining a prospective diagnostic approach to assess the relevance of in-depth tumor profiling to support clinical decision-making with an exploratory approach to improve the biological understanding of the disease. This dataset contains scDNA-seq data for 3 ovarian cancer samples from the Tumor Profiler Study used to validate LongSom. LongSom is a computational workflow leveraging high-quality long-read scRNA-seq data to call de novo somatic single-nucleotide variants (SNVs), including in mitochondria (mtSNVs), copy-number alterations (CNAs), and gene fusions, to reconstruct tumor clonal heterogeneity.

  Dataset EGAD50000001292

• Tumor Profiler Project - OV scDNA data

  The dataset contains 10x Chromium single-cell DNA sequencing data from 42 samples from 38 different patients with ovarian cancer. 35 samples were collected from the tumor, and 7 samples from ascites. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format.

  Dataset EGAD50000001291

• Tumor Profiler Project - OV scRNA data

  The dataset contains 10x Chromium single-cell transcriptomics data from 43 samples from 38 different patients with ovarian cancer. 36 samples were collected from the tumor, 7 samples from ascites. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format.

  Dataset EGAD50000001290

• Genetic differences between primary colorectal cancer and its paired synchronous and metachronous metastases

  This study contains data obtained from 210 CRC samples (87 pairs and 36 singletons for whom only one of the sample pair was available). Our sample set consisted of 105 primary tumor and 105 metastatic samples. Data are analysis-ready BAM files. Sequencing libraries were prepared with the SureSelect Human All Exon V8 kit by Agilent. Sequencing was done on NovaSeq X Plus instrument (Illumina, San Diego, CA, USA) using 150-bp paired-end reads.

  Dataset EGAD50000001460

• TSO500 sequencing of ovarian tumour samples

  This dataset consists of 8 ovarian cancer DNA sample libraries prepared using the Illumina TruSight Oncology 500 Kit (Illumina, cat no. 20076480) following the manufacturer's protocol. Library quality and quantity were assessed with High Sensitivity/D5000 Screentape Assay (Agilent Technologies, cat no. 5067-5592) on 4150/4200 Tapestation Quant-IT/Qubit dsDNA HS (Qiagen, cat no. Q32851) assay according to the supplier’s recommendations. Libraries were then pooled together in equal ratios and sequenced using PE-150bp mode on NovaSeq S1 flow cell 300 cycles kit (Illumina, 20028317) or S4 flow cell 300 cycles kit (Illumina, 20028312) aiming for 100 million reads per sample. The dataset contains sequence reads in fastq file format.

  Dataset EGAD50000001451

• The dataset for Detection of brain cancer using genome-wide cell-free DNA fragmentomes

  The dataset for “Detection of brain cancer using genome-wide cell-free DNA fragmentomes” includes 310 bam files from whole genome next-generation sequencing on the Illumina Novaseq 6000. The dataset analyzed include plasma cfDNA samples from patients with cancer, patients with neurological conditions, and healthy individuals.

  Dataset EGAD50000001445

• ST lobular manuscript dataset

  Spatial transcriptomics analysis for 43 breast cancer lobular samples. Note that there are 2 runs per sample Images and read counts will be made availalble on Zenodo upon publication.

  Dataset EGAD50000001467

• WGS data from MTB-Guided Targeted Treatments paper

  WGS data from biliary tract cancer samples (Beaudry et al, 2025; n=55)

  Dataset EGAD50000001418

• SCANDARE TNBC transcriptomics data

  SCANDARE (NCT03017573) is a multicentric biobanking study, enrolling adult patients with newly diagnosed head and neck squamous cell carcinoma (HNSCC), triple negative breast cancer (TNBC), ovarian and cervical cancer. Tumor tissue and blood samples are collected at several time points during patient's journey, including at diagnosis, post-neoadjuvant chemotherapy in case of neoadjuvant treatment, at surgery, at recurrence and at disease progression following treatment initiated at recurrence. Since its launch in 2017 at Institut Curie, SCANDARE has enabled the longitudinal collection and preservation of samples for in-depth analyses. Here, we describe molecular alterations in 124 frozen samples (n=84 at baseline and n=40 paired at post-NAC surgery) from 91 TNBC patients using total RNAseq technology, with FASTQ files deposited in the dataset.

  Dataset EGAD50000001416

• Tumor Profiler Project - OV bulk transcriptomics data

  The dataset contains bulk transcriptomics data from 39 samples from 36 different patients with ovarian cancer. 34 samples were collected from the tumor, 5 samples from ascites. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format.

  Dataset EGAD50000001413

• Tumor Profiler Project - OV cell-free DNA data additional samples

  The dataset contains amplicon sequencing data from 7 samples from 7 different patients with ovarian cancers. Cell free DNA was collected from plasma. Sequencing was performed on an Ion Torrent platform and the sequencing data is provided in bam format. These samples are from patients not classified as having high-grade serous adenocarcinoma.

  Dataset EGAD50000001412

• Tumor Profiler Project - OV bulk transcriptomics data additional samples

  The dataset contains bulk transcriptomics data from 4 samples from 3 different patients with ovarian cancer. 3 samples were collected from the tumor, 1 sample from ascites. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format. These samples are from patients not classified as as having high-grade serous adenocarcinoma.

  Dataset EGAD50000001411

• Tumor Profiler Project - OV cell-free DNA data

  The dataset contains amplicon sequencing data from 48 samples from 35 different patients with ovarian cancers. Cell free DNA was collected from plasma. Sequencing was performed on an Ion Torrent platform and the sequencing data is provided in bam format.

  Dataset EGAD50000001410

• Whole Exome Sequencing of Human Gastro-esophageal Cancer PDXs

  The dataset includes 51 whole exome sequencing datasets generated using Illumina paired-end sequencing technology. These data derive from 26 patient-derived xenograft (PDX) tumors and their matched normal tissues, which consist of either normal gastric mucosa or blood samples. In one case (GTR0607), the matched normal tissue data are unavailable. As a result, the dataset comprises 102 FASTQ files, providing raw sequencing reads for comprehensive genomic analysis.

  Dataset EGAD50000001407

• PCR-Free Shallow Whole Genome Sequencing for Chromosomal Copy Number Detection

  Archival peripheral blood or bone marrow plasma samples from non small-cell lung cancer, B-cell lymphoma and acute myeloid leukemia patients, and healthy donors. Shallow whole genome sequencing of 100 Samples by two distinct library preparation methods (PCR = 45, PCR-Free = 55). sWGS done for Chromosomal CN detection.

  Dataset EGAD50000001404

• Sequencing dataset for the Predictive Endocrine ResistanCe Index (PERCI) in Breast Cancer cases

  Sequencing dataset for the Predictive Endocrine ResistanCe Index (PERCI) in Breast Cancer cases of the WSG-ADAPT trial (NCT01779206). The Oncomine Comprehensive v3 assay (ThermoFisher) and a customized amplicon-based NGS-Panel (DERv2) was performed.

  Dataset EGAD50000001595

• Targeted Illumina sequencing of 3399 plasma cfDNA samples and 1988 leukocyte DNA samples from 1995 metastatic prostate cancer patients

  Blood samples were collected from eight clinical trials and a British Columbia-based biobank. All plasma cfDNA and leukocyte DNA samples were processed with uniform methodology, and underwent targeted sequencing using a custom hybridization capture panel and Illumina instruments. Four different generations of custom hybridization capture panel were used, all providing coverage of the complete coding regions of 72 prostate cancer genes, and later panel generations also providing exhaustive coverage of the AR locus (including introns and flanking regulatory regions), as well as a genome-wide SNP grid for copy number analysis.

  Dataset EGAD50000001594

• RNAseq dataset of ovarian cancer patients

  Dataset of transcriptomics data from a cohort of individuals diagnosed with ovarian cancer. This dataset includes RNAseq sequencing data from 68 individuals. A total of 109 tumor samples were sequenced. Samples were prepared with the Illumina TruSeq Stranded RNA library. Sequencing data are paired end.

  Dataset EGAD50000001556

• Clinical Utility of BRCA Research by Inocras, CMC and SMC (CUBRICS)

  This dataset consists of whole-genome sequences from 1,364 Korean breast cancers, with transcriptome data available for most cases

  Dataset EGAD50000001546

• Active-Seq of CRC patients

  This dataset contains 48 fastq files of samples derived from CRC patients, including colorectal cancer tissue, normal adjacent tissue and cfDNA samples, processed with the Illumina platform NovaSeq6000.

  Dataset EGAD50000001746

• Targeted panel sequencing of two patient-derived melanoma cell lines

  Targeted panel sequencing was conducted on patient-derived cell lines: Mel-DCC-11 (the parental line, sensitive to the BRAF inhibitor) and Mel-DCC-11-R (resistant to the BRAF inhibitor). The parental cell line was generated from disseminated cancer cells (DCCs) obtained from a lymph node sample of a melanoma patient. The resistant cell line was generated from the parental one through exposure to Vemurafenib. Normal peripheral blood lymphocytes from the same patient served as the control for comparison. Sequencing on NovaSeq6000. Fastq files.

  Dataset EGAD50000001745

• WGBS dataset for lymphnode metastasis samples from prostate cancer

  This dataset contains WGBS sequencing data of lymphnode metastasis samples from prostate cancer. Sequencing was performed on Illumina HiSeq X Ten. The sequencing was always paired.

  Dataset EGAD50000001183

• Colorectal cancer peritoneal metastasis

  This dataset consist of 72 samples profiled on whole exome sequencing and 94 samples profiled on whole transcriptome sequencing. The Agilent SureSelect Human All Exon v6 kit (Agilent Technologies) was used for whole exome sequencing. For RNA-seq experiments, library preparation was conducted using the Tru-Seq Stranded Total RNA with Ribo-Zero Gold kit protocol (Illumina). Libraries were sequenced on a HiSeq4000 sequencer using the paired-end 150 bp read option. Sequences in cram format was provided.

  Dataset EGAD50000001199

• Labcorp® Plasma Detect™ assay: whole genome sequencing analyses of plasma cfDNA, white blood cells and FFPE tumor tissue

  The dataset "Labcorp® Plasma Detect™ assay: whole genome sequencing analyses of plasma cfDNA, white blood cells and FFPE tumor tissue" includes CRAM and CRAI files derived from WGS of 555x plasma cfDNA, 209x white blood cells (normal DNA) and 209x FFPE tumor tissue (tumor DNA) samples for 209 stage III colorectal cancer patients. WGS (150bp PE) was performed on a NovaSeq 6000 with a target depth of coverage of 80x for tumor DNA, 40x for normal DNA and 30x for cfDNA. Reads were aligned to GRCh37 (plasma cfDNA) or GRCh38 (tumor/normal DNA).

  Dataset EGAD50000001180

• WGS data of 100 Breast Cancer patients from SV Based ctDNA Detection study

  Whole Genome Sequencing data of 100 Breast Cancer patients from "Ultrasensitive Detection and Monitoring of Circulating Tumor DNA using Structural Variants in Early-Stage Breast Cancer" study.

  Dataset EGAD50000001175