Search Results - EGA European Genome-Phenome Archive

Whole exome Sequencing (WES) of multiple tumor biopsies, patient-derived spheroids and leukocyte DNA from colorectal cancer patients (BAM files)

WES was performed using the KAPA-Hyper prep kit from Illumina (Roche, Basel, Switzerland) for library construction, followed by exome capture using Niblegen SeqCap EZ Human Exome Library v3.0 (Roche). Reads were mapped using BWA MEM against the humane reference genome HG19.

Dataset EGAD00001003821

RRBS sequencing data of ovarian cancer, breast cancer, control tissues, and white blood cell DNA.

The dataset comprises 8 breast cancer, 11 ovarian cancer, 1 benign tumour, 18 normal tissue, 2 endometrium, and 23 white blood cell samples. Genome wide methylation analysis was performed by Reduced Representation Bisulfite Sequencing (RRBS) on Illumina HiSeq 2500. Data is provided as FASTQ files

Dataset EGAD00001003822

Somatic mutation analysis based on Whole exome Sequencing (WES) of multiple tumor biopsies, patient-derived spheroids and leukocyte DNA from colorectal cancer patients (vcf files)

Somatic mutations were called using whole exome Sequencing (WES) data from colorectal cancer samples (dataset EGAD00001003821) using MuTect2, with matched constitutional WES-data obtained from leukocytes samples as reference.

Dataset EGAD00001003823

Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks

Whole genome sequencing data on 10 human cancer cell lines

Dataset EGAD00001003824

Exome sequencing data from tumor progression cohort

This dataset, named Stockholm tumor progression cohort, contains exome-sequencing samples of matched primary and metastasis samples from 20 metastatic breast cancer patients. All patients have one or more sequenced normal samples as well. The total number of samples is 125. The dataset has been used, apart from other studies, to explore tumor evolution patterns in metastatic breast cancer at Karolinska Institute Stockholm.

Dataset EGAD00001003837

microRNA-seq of human serum from a longitudinal study of 66 women with no history of cancer

This dataset includes microRNA sequencing data from 198 human serum samples, representing a subset of 66 women with no history of cancer who participated in the UKCTOCS study and with serum samples collected at three timepoints over a period of up to 5 years. Small RNA libraries prepared from the serum samples were sequenced with 50-bp single end reads on an Illumina HiSeq 2000 instrument. Data is provided as FASTQ files.

Dataset EGAD00001004348

Exome sequencing to evaluate HER2/ERBB2 mutations in cancer

ERBB2/HER2 transmembrane and juxtamembrane domain mutations in cancer. Exome sequencing of tumor and matched blood and 2 blood samples from relatives.

Dataset EGAD00001004351

Whole Exome Sequencing

The Whole Exome Sequencing dataset contains 30 whole exome sequencing files (tumor, germ line DNA) and phenotype metadata for 15 patients on the phase II clinical trial of neoadjuvant immune checkpoint blockade in high-risk resectable melanoma at MD Anderson Cancer Center (NCT02519322). Included are data from baseline samples.

Dataset EGAD00001004352

Molecular portraits of breast cancer diagnosed during pregnancy

The aim of this study was to compare the mutational landscape of breast cancer diagnosed during pregnancy (BCP) and breast cancer from age/stage non-pregnant patients (controls). We present whole genome sequencing data (Illumina HiSeq X ten platform) of tumor and matched normal tissues from 35 BCP patients and 20 controls. This work provides important novel biological insights and a unique resource to study the biology of breast cancer in young women and how pregnancy could modulate tumor biology.

Dataset EGAD00001004353

Dataset for "Genomic landscape of oral cancers" (Illumina WGS)

Dataset EGAD00001004356

Summary statistics for cervical cancer GWAS

Summary statistics from GWAS meta-analysis of cervical cancer

Dataset EGAD00001004361

DNA sequencing for gastric cancer ascites

Whole-exome sequencing (WES) was performed on a total of 34 PC specimens, with 15 cases having matched gDNAs extracted from blood.

Dataset EGAD00001004364

RNA sequencing for gastric cancer ascites

Whole transcriptome sequencing (RNA-seq) was performed on 39 PC specimens. Among them, 21 specimens also had WES data.

Dataset EGAD00001004365

Dataset for "Genomic landscape of oral cancers" (Illumina RNA)

Dataset EGAD00001004366

Organoid Derivation Project TGS: Release 1

Targeted gene sequencing of cancer driver genes to determine the driver mutations present in newly-derived cancer organoid models

Dataset EGAD00001004368

Locally advanced rectal cancer samples

Fastq files from exome sequencing of paired normal/tumor (pre and post-nCRT) samples from 7 patients with rectal tumors. All samples were sequenced on a 5500xl SOLiD sequencing platform (Thermo Fisher Scientific).

Dataset EGAD00001004378

Dynamics of multiple resistance mechanisms in plasma DNA during EGFR‐targeted therapies in non‐small cell lung cancer - sWGS

Shallow whole‐genome sequencing dataset on samples from three patients who underwent histological transformation to small‐cell lung cancer. Samples included in this dataset include normal buffy coat samples, plasma samples collected at diagnosis of NSCLC as well as prior to small‐cell transformation and after SCLC transformation and progression on cisplatin and irinotecan.

Dataset EGAD00001004379

Infiltrative and drug-resistant slow-cycling cells support metabolic heterogeneity in glioblastoma

Glioblastoma patient derived Fast/Slow cycling cancer stem cell RNA sequencing. Consists of 3 patient cell lines and 6 files

Dataset EGAD00001004380

Ovarian Cancer Organoid Biobank

WGS of ovarian cancer organoids, tumor samples and blood references. Ovarian cancer (OC) is a heterogeneous disease usually diagnosed at a late stage. Experimental in vitro models that faithfully capture the hallmarks and tumor heterogeneity of OC are limited and hard to establish. We present a novel protocol that enables efficient derivation and long-term expansion of OC organoids. Utilizing this protocol, we have established 56 organoid lines from 32 patients, representing the spectrum of ovarian neoplasms, including non-malignant borderline tumors, as well as mucinous, clear-cell, endometrioid, low- and high-grade serous carcinomas. OC organoids recapitulate histological and genomic features of the pertinent lesion from which they were derived, illustrating intra- and inter-patient heterogeneity, and can be genetically modified. We show that OC organoids can be used for drug screening assays and capture different tumor subtype responses to the gold standard platinum-based chemotherapy, including acquisition of chemoresistance in recurrent disease. Finally, OC organoids can be xenografted, enabling in vivo drug sensitivity assays. Taken together, this demonstrates their potential application for research and personalized medicine.

Dataset EGAD00001004387

A Study to Evaluate Denosumab in Young Patients With Primary Breast Cancer (D-Beyond)

This is a prospective, single arm phase IIa trial in which patients with early breast cancer will receive pre-operatively two doses of denosumab 120mg subcutaneously one week apart (maximum 12 days) followed by surgery. Tumor, normal breast tissue and blood samples will be collected at baseline and at surgery. Post-operative treatment will be at the discretion of the investigator.Primary objective: to determine if a short course of RANKL inhibition with denosumab can induce a decrease in tumor proliferation rates as determined by Ki67 immunohistochemistry (IHC) in newly diagnosed, early stage breast cancer in pre-menopausal women.

Dataset EGAD00001004391

PDAC

ctDNA and protein markers for earlier detection of pancreatic cancers

Dataset EGAD00001004399

Prostate cancer datasets WGS

Low pass WGS: 48 samples (5 blood samples from 6 patient data): 22 Tumour cores and 26 normal/benign cores (Next Seq )

Dataset EGAD00001004466

Prostate cancer datasets WES

WES: 48 samples (5 blood samples from 6 patient data): 22 Tumour cores and 26 normal/benign cores (HiSeq)

Dataset EGAD00001004467

Prostate cancer datasets RNA Seq

Total RNA Seq: 15 Samples (2 patients (MF1 and MF3)) (HiSeq) and Poly A RNA Seq: 27 Samples (4 patients Normal and Tumour ) (HiSeq)

Dataset EGAD00001004468

Exome sequencing of a novel cervical cancer cell line

In this work, we establish and characterized a low-passage cervix cancer cell line from a Brazilian patient with squamous cell carcinoma. The dataset contains three samples from the same patient (blood, tumor tissue and the primary cell line). The technology used was exome sequencing and the file type available is fastq files.

Dataset EGAD00001004480

Targeted sequencing of cell-free DNA and white blood cells from 24 men with metastatic prostate cancer

This dataset consists of aligned DNA sequencing data in BAM file format from cell-free DNA and white blood cells from 24 men with metastatic prostate cancer. One cell-free DNA sample and one white blood cell sample is available for each patient, resulting in 48 total BAM files in this dataset. The sequencing was performed using a hybrid capture-based targeted panel of 73 prostate cancer driver genes.

Dataset EGAD00001004486

Longitudinal breast cancer cohort in SMC

Whole transcriptome sequencing (WTS) of a longitudinal breast cancer (BC) cohort consisting of 146 cases (281 tumors, 109 pairs), including 52 (38%) that achieved pathologic complete responses (pCR) and 85 (62%) that harbored residual diseases at time of surgery.

Dataset EGAD00001004487

UIC HNSCC RNA-Seq and miRNA-Seq Data

This dataset contains matched RNA-Seq and miRNA-Seq fastq files from 109 match samples of 34 human Papillomavirus-negative Head and Neck cancer patients, including 72 lymph nodes, 29 tumor and 8 normal samples.

Dataset EGAD00001004489

Recalibrated whole-exome sequencing alignment data of papillary thyroid cancer of Saudi Arabia

The dataset consists of samples from papillary thyroid cancer patients. A total of 11 DNA samples from blood/normal and cancer tissue are subjected to whole exome sequencing using Illumina. The fastq files generated were aligned with reference genome ‘hg19’, duplicates were marked, realignment around indels and quality recalibration were performed to produce good quality variants. The recalibrated “.bam” files are included with this dataset.

Dataset EGAD00001004490

Familial Breast cancer dataset

Illumina HiSeqXTen platform sequencing data of whole genome libraries prepared from 156 matched tumour-normal samples from 78 donors

Dataset EGAD00001004494

Single cell multiomics sequencing and analyses of human colorectal cancer

Whole genome sequencing data of tumor tissues, adjacent normal tissues, and peripheral blood from CRC patients.

Dataset EGAD00001004495

Microsatellite unstable colorectal cancers

Mapped data for 10 Colon MSI cancer samples

Dataset EGAD00001004500

Genomic and transcriptomic determinants of therapy resistance and immune landscape evolution during anti-EGFR treatment in colorectal cancer

Genomic and transcriptomic data from a cohort of 35 RAS wild-type colorectal cancers. All 35 cases were DNA sequenced at baseline (BL) before treatment with single agent cetuximab. Progressive disease (PD)-biopsies were taken shortly after radiological progression and successfully exome sequenced from 24/35 cases. mRNA sequencing is available for 25 Baseline and 15 PD samples. ctDNA from 9 cases that progressed after prolonged cetuximab benefit were also deep sequenced.

Dataset EGAD00001004501

Ovarian Cancer Organoid Biobank - RNASeq data

Ovarian cancer (OC) is a heterogeneous disease usually diagnosed at a late stage. Experimental in vitro models that faithfully capture the hallmarks and tumor heterogeneity of OC are limited and hard to establish. We present a novel protocol that enables efficient derivation and long-term expansion of OC organoids. Utilizing this protocol, we have established 56 organoid lines from 32 patients, representing the spectrum of ovarian neoplasms, including non-malignant borderline tumors, as well as mucinous, clear-cell, endometrioid, low- and high-grade serous carcinomas. OC organoids recapitulate histological and genomic features of the pertinent lesion from which they were derived, illustrating intra- and inter-patient heterogeneity, and can be genetically modified. We show that OC organoids can be used for drug screening assays and capture different tumor subtype responses to the gold standard platinum-based chemotherapy, including acquisition of chemoresistance in recurrent disease. Finally, OC organoids can be xenografted, enabling in vivo drug sensitivity assays. Taken together, this demonstrates their potential application for research and personalized medicine.

Dataset EGAD00001004509

Pancreatic organoid - case samples

This dataset contains 31 pancreatic organoid samples used in the 'organoid data of pancreatic cancers ' study

Dataset EGAD00001004528

MCO colorectal cancer genomics at UNSW

This dataset contains DNA sequencing data from 95 colorectal cancer and matched-normal samples. The dataset contains targeted deep sequencing of selected regulatory elements in 95 cancer and matched-normal samples, and data for one sample that was additionally whole-genome sequenced (cancer and matched-normal).

Dataset EGAD00001004582

A compendium of mutational signatures due to environmental exposures

Whole-genome-sequencing (WGS) of human tumours has revealed distinct mutation patterns that hint at the causative origins of cancer. We examined mutational-signatures in 324 WGS of human induced pluripotent stem cells (iPSCs) following exposure to known or suspected environmental carcinogens. 79 agents were tested with or without metabolic activation at concentrations that produced measurable cytotoxicity; 41 yielded characteristic substitution mutational signatures. Some exhibit similarity with signatures found in human tumours. Additionally, 6 agents produced double-substitution signatures and 8 produced indel signatures. Investigating mutation asymmetries across genome topography reveals fully functional mismatch and transcription-coupled repair pathways in iPSCs. Primary adducts induced by environmental carcinogens can be resolved by disparate repair/replicative pathways, resulting in an assortment of signature outcomes even for a single mutagen. This compendium of experimentally-induced mutational-signatures permits further exploration of roles of environmental agents in cancer aetiology, and underscores how human stem cell DNA is directly vulnerable to environmental agents.

Dataset EGAD00001004583

Extreme intratumor heterogeneity and driver evolution in mismatch repair deficient gastro-esophageal cancer

The dataset includes multi-region exome sequencing (MSeq) of four resected treatment naïve mismatch repair deficient gastro-esophageal cancers. Paired-end sequencing was performed on the Illumina HiSeq 2500 or NovaSeq 6000 with a target depth of 200X. Seven primary tumor regions along with tumor-adjacent non malignant tissue were subjected to MSeq. An additional two lymph node metastases were also included from each of two cases.

Dataset EGAD00001004594

7825 results for "canc*"

in 69.57 milliseconds.