Search Results - EGA European Genome-Phenome Archive

Dataset for urologic_cancer-RNA

Rare cancer sequencing data of 75 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008851

Dataset for GIST-RNA

Rare cancer sequencing data of 50 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008852

Dataset for upper_gastrointestinal_tumor-RNA

Rare cancer sequencing data of 44 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008853

Dataset for liposarcoma-RNA

Rare cancer sequencing data of 40 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008854

Dataset for colorectal_cancer-RNA

Rare cancer sequencing data of 97 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008855

Dataset for colorectal_cancer-WHOLE_GENOME

Rare cancer sequencing data of 54 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008872

Dataset for gynecologic_cancer-RNA

Rare cancer sequencing data of 48 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008856

Dataset for cancer_of_unknown_primary-RNA

Rare cancer sequencing data of 58 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008857

Dataset for melanoma-RNA

Rare cancer sequencing data of 49 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008858

Dataset for soft_tissue_tumor-RNA

Rare cancer sequencing data of 243 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008859

Dataset for hematopoietic_malignancy-RNA

Rare cancer sequencing data of 47 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008860

Dataset for bone_cancer-EXON

Rare cancer sequencing data of 87 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008865

Dataset for bone_cancer-WHOLE_GENOME

Rare cancer sequencing data of 48 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008866

Dataset for breast_cancer-WHOLE_GENOME

Rare cancer sequencing data of 12 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008867

Dataset for breast_cancer-EXON

Rare cancer sequencing data of 94 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008868

Dataset for cancer_of_unknown_primary-EXON

Rare cancer sequencing data of 62 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008870

Dataset for cancer_of_unknown_primary-WHOLE_GENOME

Rare cancer sequencing data of 46 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008869

Dataset for colorectal_cancer-EXON

Rare cancer sequencing data of 119 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008871

Dataset for Ewing_sarcoma_PNET-EXON

Rare cancer sequencing data of 30 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008873

Dataset for Ewing_sarcoma_PNET-WHOLE_GENOME

Rare cancer sequencing data of 18 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008874

Dataset for GIST-EXON

Rare cancer sequencing data of 64 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008875

Dataset for GIST-WHOLE_GENOME

Rare cancer sequencing data of 18 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008876

Dataset for gynecologic_cancer-EXON

Rare cancer sequencing data of 55 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008877

Dataset for gynecologic_cancer-WHOLE_GENOME

Rare cancer sequencing data of 38 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008878

Dataset for head_and_neck_cancer-WHOLE_GENOME

Rare cancer sequencing data of 56 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008879

Clonal somatic copy number altered driver events inform drug sensitivity in high-grade serous ovarian cancer.

This dataset consists of shallow whole genome sequencing data and amplicon sequencing data for 26 ovarian cancer patients (21 high-grade serous ovarian cancer, 4 low-grade serous ovarian cancer and 1 clear cell ovarian cancer). The data are provided as single end FASTQ files for the shallow whole genome sequencing data (31 libraries) and paired end FASTQ files for the amplicon sequencing data (98 libraries).

Dataset EGAD00001008716

RNA and whole-exome sequencing of 22 patients with non-small cell lung cancer

Whole exome sequencing from pre-treatment samples and matched blood normals from 22 patients. Of these individuals, on-treatment samples are available for a subset of 18 patients. RNA sequencing from pre-treatment samples from 21 patients. Of these individuals, on-treatment samples are available for a subset of 15 patients.

Dataset EGAD00001008733

scRNA mCRC PDO

Chromium 10x scRNA of 6 metastatic colorectal cancer organoids

Dataset EGAD00001008734

cfMeDIP data for 72 VPC samples for validation

We analyzed the cell free DNA methylomes using 72 plasma samples from patients with mCRPC prostate cancer in the VPC project for validation. Methylation was profiled using the methylated DNA immunoprecipitation coupled to next generation sequencing (MeDIP) technology. Files from multiple lanes exists per sample.

Dataset EGAD00001008737

CITE-seq for peripheral blood samples of 5 breast cancer patients

We have 5 breast cancer patients who received VEN therapy. We collected their peripheral blood samples before and after long-term Venetoclax treatment. We apply CITE-seq protocol to these samples. This collection contains the all CITE-seq data for patients.

Dataset EGAD00001008751

Novel method for efficient establishment, expansion and drug response profiling of high-grade serous ovarian cancer organoids

HGSOC patient-derived organoids and their tissue of origin

Dataset EGAD00001008753

Genomics characterization of BRAF-V600E colorectal cancer patients treated with anti-BRAF/EGFR

WES files (fastQ) from 19 germline DNA, 22 tumor DNA, 5 patient-derived xenograft (PDX) DNA, and 9 plasma cfDNA) samples from 28 CRC-BRAF-mutated patients collected at baseline to anti-BRAF/EGFR therapies.

Dataset EGAD00001008755

Salivary Gland Cancer TSO500 dataset

DNA was extracted from archival tissue of 119 patients with various SGC subtypes and sequenced using a targeted NGS panel encompassing 523 cancer related genes (TruSight Oncology 500, TSO500). This dataset belongs to the publication entitled: 'Identification of fusion genes and targets for genetically matched therapies in a large cohort of salivary gland cancer patients'.

Dataset EGAD00001008759

Bulk RNAseq

Bulk tumor RNAseq FASTQ files from 124 samples from patients with hormone sensitive or castration resistant prostate cancer.

Dataset EGAD00001008760

Raw count table

Raw count matrix of the 124 bulk tumor RNAseq samples from patients with hormone sensitive or castration resistant prostate cancer.

Dataset EGAD00001008762

Clinical data

Clinical data from this cohort of patients, including hormone sensitive or castration resistant prostate cancer, overall survival, NMF subtypes, tumor TMB, prior treatment status, PD-L1 IC and TC scores from SP142 and SP263 as well as percentage of CD8 IHC at tumor center.

Dataset EGAD00001008761

Germline WES data of pediatric cancer patients

This dataset includes bam files (aligned to hg38) from the germline of pediatric cancer patients.

Dataset EGAD00001008763

APOBEC mutagenesis is a common process in normal human small intestine

The single base substitution mutational signatures SBS2 and SBS13, likely caused by APOBEC cytosine deaminases, are common in many human cancer types. However, the stimulus activating APOBEC mutagenesis is unknown and understanding of when it occurs in the progression from normal to cancer cell is limited. Here, as part of a wider survey of human tissues, we whole genome sequenced 342 microdissected normal epithelial crypts from the small intestines of 39 individuals. SBS2/13 mutations were present in 17% normal small intestine crypts and were likely due to APOBEC3A activity. Localised clusters of SBS2/13 mutations (kataegis) were also commonly found. APOBEC mutation burdens were variable between individuals and between crypts from the same individual. Crypts with SBS2/13 often had immediate crypt neighbours without SBS2/13, suggesting that the underlying cause of SBS2/13 is cell-intrinsic rather than a widely distributed microenvironmental exposure, or needs to be permitted by cell-intrinsic conditions. APOBEC mutagenesis occurred throughout the human lifespan, including in young children, and was episodic with a small number of episodes occurring during the life history of a single cell. The results indicate that APOBEC mutagenesis is more common in the small intestine epithelium than in many other cell types, and is an episodic process in vivo initiated or permitted by cell intrinsic factors.

Dataset EGAD00001008764

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