Search Results - EGA European Genome-Phenome Archive

Dataset for hematopoietic_malignancy-WHOLE_GENOME

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

Dataset EGAD00001008881

Dataset for hematopoietic_malignancy-EXON

Rare cancer sequencing data of 91 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008882

Dataset for hepatopancreaticobiliary_malignancy-EXON

Rare cancer sequencing data of 162 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008883

Dataset for melanoma-EXON

Rare cancer sequencing data of 76 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008890

Dataset for hepatopancreaticobiliary_malignancy-WHOLE_GENOME

Rare cancer sequencing data of 83 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008884

Dataset for leiomyosarcoma-EXON

Rare cancer sequencing data of 96 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008885

Dataset for liposarcoma-EXON

Rare cancer sequencing data of 29 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008886

Dataset for leiomyosarcoma-WHOLE_GENOME

Rare cancer sequencing data of 66 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008887

Dataset for liposarcoma-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 EGAD00001008888

Dataset for melanoma-WHOLE_GENOME

Rare cancer sequencing data of 22 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008889

Dataset for neuroendocrine_adrenal_tumor-EXON

Rare cancer sequencing data of 164 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008891

Dataset for NSCLC-EXON

Rare cancer sequencing data of 42 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008892

Dataset for NSCLC-WHOLE_GENOME

Rare cancer sequencing data of 34 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008894

Dataset for neuroendocrine_adrenal_tumor-WHOLE_GENOME

Rare cancer sequencing data of 112 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008893

Dataset for other_cancer-WHOLE_GENOME

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

Dataset EGAD00001008895

Dataset for other_cancer-EXON

Rare cancer sequencing data of 137 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008896

Dataset for soft_tissue_tumor-EXON

Rare cancer sequencing data of 246 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008897

Dataset for synovial_sarcoma-WHOLE_GENOME

Rare cancer sequencing data of 6 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008899

Dataset for synovial_sarcoma-EXON

Rare cancer sequencing data of 34 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008898

The immunopeptidome landscape associated with T cell infiltration, inflammation and immune-editing in lung cancer

WES sequencing of multiple regions per tumor from 8 lung cancer patients (LUSC, LCNEC and LUAD) and adjacent healthy lung tissue for each patient.

Dataset EGAD00001008950

Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here we are submitting two datasets that contain NGS files from gastrointestinal rare cancers (n=119): - Dataset 2 (87 patients): Intra-hepatic cholangiocarcinoma (n=47), Extra-hepatic, cholangiocarcinoma (n=16), Not specified Cholangiocarcinoma (n=9), Small bowel adenocarcinoma (n=6) and other rare GI cancer (n=9)

Dataset EGAD00001008968

Ovarian cancer EV RNA-seq

Dataset EGAD00001008972

RNA-seq derived from metastatic Castration-Resistant Prostate Cancer

Patients with progressive, metastatic castration-resistant prostate cancer (mCRPC) underwent metastatic tumor biopsy. 118 total samples including 14 paired samples (baseline and later progression). Various organ sites including soft tissue & bone were present. Published in DOI: 10.1200/JCO.2017.77.6880 Journal of Clinical Oncology 36, no. 24 (August 20, 2018) 2492-2503.

Dataset EGAD00001008991

Plasma whole genome sequencing from patients with stage IV colorectal cancer and microsatellite instability

This dataset contains plasma WGS data from patients with stage IV colorectal cancer (CRC, n = 16) and healthy individuals (n = 21) used in the Pointy manuscript. Patients with CRC provided written consent and samples were collected as performed as described previously (Clinical-Trials.gov number NCT01876511; Georgiadis et al., 2019, Le et al., 2017). Plasma samples from 21 healthy control individuals were procured through BioIVT. Cell-free DNA (cfDNA) was extracted from plasma using the QIAamp Circulating Nucleic Acid Kit. Libraries were prepared with 5 to 250 ng of cfDNA using the NEBNext DNA Library Prep Kit. Libraries were sequenced on HiSeq2000/2500.

Dataset EGAD00001008999

Detection of cancer cell transcriptomes

Single cell transcriptomes, generated using chromium 10X 3' sequencing, for two tumour types (AT/RT, and Ewing's sarcoma). For each individual, tumour and normal whole genome sequencing was also obtained using Illumina short read sequencing to an average depth of 30X. These data were used to validate the accuracy of a method for identifying cancer cell transcriptomes based on the allelic shift produced by copy number changes.

Dataset EGAD00001009005

Triple negative breast cancer matched patient and pdx dataset

PDX aCGH (txt), WES (fastq) and RNASeq (fastq) samples from mice treated with cisplatin. Primary samples and matched pdx samples from multiple passages. Models from the Marie Curie Instute (HBCx1, HBCx4B, HBCx8, HBCx10, HBCx12B, HBCx14, HBCx15, HBCx16, HBCx17, HBCx23, HBCx24, HBCx27, HBCx28, HBCx30, HBCx31, HBCx33, HBCx39, HBCx40, HBCx43, HBCx51, HBCx63, HBCx66, HBCx92, HBCx106) and the NKI (T127, T162, T241, T250, T283, T302, T336).

Dataset EGAD00001009046

Molecular Characterization for Nasopharyngeal Carcinoma (NPC)

Total RNA was isolated from 50 formalin-fixed paraffin-embedded nasopharyngeal cancer (NPC) specimens using the RecoverAll Total Nucleic Acid Isolation kit (Ambion). Tumor RNA libraries were prepared with 200ng RNA using the Illumina TruSeq Stranded Total RNA kit with Ribo-Zero Gold, and sequenced with >80 million 100 bp paired-end reads.

Dataset EGAD00001009047

WGS of high grade serous ovarian tumours and matched blood normals

FASTQ reads for 81 matched tumour-normal WGS pairs for high grade serous ovarian cancer patients. Scottish HGSOC samples were collected via local Bioresource facilities at Edinburgh, Glasgow, Dundee and Aberdeen and stored in liquid Nitrogen until required. HGSOC patients were determined from pathology records and were included in the study where there was matched tumour and whole blood samples. Tumour samples were divided into two for DNA and RNA extraction and slivers of tissue were taken, fixed in formalin and embedded in paraffin wax (FFPE). Samples were only included if they were confirmed as HGSOC and there was greater than 40% tumour cellularity throughout the tumour, determined using H&E staining of the FFPE sections and pathology review. Somatic DNA was extracted from the tumour and germline DNA was extracted from whole blood. Somatic DNA was extracted using the Qiagen DNeasy Blood and tissue kit (cat no 69504). The tissue was initially homogenised using a Qiagen Bioruptor, followed by the manufacturers recommended protocol (including RNase digestion step). Germline DNA was extracted from 1-3ml whole blood using the Qiagen FlexiGene kit (cat no 51206) following the manufacturers recommended protocol. The resulting DNA underwent quality control as follows: firstly, A260 and A280nm were measured on a Denovix DS-11 Fx to qualitatively illustrate A260/280nm and A260/230nm ratios as surrogate measures of DNA purity. A260/280 had to be 1.8 or greater and A260/230 had to be 2.0 or greater. Then, DNA was quantified using LifeTechnologies Qubit dsDNA BR kit (cat no Q32850) and we required a minimum of 50ul at 25ng/ul for WGS. Thirdly, DNA was diluted to 25ng/ul and a representative sample was loaded onto a 0.8% TAE gel, ran at 100v for 60mins and then imaged using a BioRad ChemiDoc imaging system to visualise the DNA quality.

Dataset EGAD00001009049

Comparison of single/pooled CTCs and bulk exome sequencing

Single cell technologies allow the interrogation of tumor heterogeneity, providing insights into tumor evolution and treatment resistance. To better understand whether circulating tumor cells (CTCs) could complement metastatic biopsies for tumor genomic profiling, we characterized 11 single CTCs and 10 pooled CTC samples at the mutational and copy number aberration (CNA) levels, and compared these results with matched synchronous tumor biopsies from 3 metastatic breast cancer patients with triple-negative (TNBC), HER2-positive and estrogen receptor-positive (ER+) tumors. Similar CNA profiles and the same patient-specific driver mutations were found in bulk tissue and CTCs for the HER2-positive and TNBC tumors, whereas different CNA profiles and driver mutations were identified for the ER+ tumor, which presented two distinct clones in CTCs defined by mutations in ESR1 Y537N and TP53, respectively. Furthermore, de novo mutational signatures derived from CTCs described patient-specific biological processes. These data suggest that tumor tissue and CTCs provide complementary clinically relevant information to map tumor heterogeneity and tumor evolution.

Dataset EGAD00001009052

PAMELA - 142 patients with HER2+ breast cancer

RNA sequencing data of 141 samples from 141 patients with HER2+ breast cancer treated withletrozole or tamoxifen (SOLTI-1114 PAMELA trial)

Dataset EGAD00001009054

RNAseq of breast cancer bone metastases PDX resistant of responder to IACS-010759 treatment

Fastq files from RNAseq of breast cancer bone metastases PDX after treatment with IACS-010759. Five PDX are resistants to treatment and 6 are responders.

Dataset EGAD00001009072

RNA-seq data from 164 advanced prostate tumors generated by the West Coast Dream Team including 42 paired samles

164 pairs of FASTQ files from metastatic Castration-Resistant Prostate Cancer (mCRPC) sequenced on HiSeq 4000 instruments. Patients were enrolled in the West Coast Dream Team study. Biopsies include various tissue sites including bone, soft tissue, and lymph node. 42 pairs prior to enzalutamide treatment and at progression from 21 patients are included.

Dataset EGAD00001009065

Garvan/St Vincent’s Prostate Cancer Tissue and Data

The cohort (n=53) consists of prostate cancer patients from Australia. For each patient, a pair of blood and tumour samples were collected. The sequencing data was mapped to hg38 reference. Blood BAMs are named with “-B” as suffix and tumour BAMs are named with “-T” as suffix.

Dataset EGAD00001009066

Southern African Prostate Cancer Study (SAPCS) Ethnic Disparity

The cohort (n=130) consists of prostate cancer patients from South Africa (n=123) and Brazil (n=7). For each patient, a pair of blood and tumour samples were collected. The sequencing data was mapped to hg38 reference. Blood BAMs are named with “-B” as suffix and tumour BAMs are named with “-T” as suffix.

Dataset EGAD00001009067

Sequence of breast cancer bone metastases PDX before and after palbociclib treatment resistance

RNAseq sequencing of 10 breast cancer bone metastasis PDX. Samples were obtained from 5 PDX that acquired palbociclib resistance (palboR) and 5 from the parentale PDX (palboS).

Dataset EGAD00001009068

WES of breast and larynx cancer cases

The dataset is based on 37 FFPE samples obtained from 12 patients diagnosed with breast or larynx cancer, For each patient 3 sample types were obtained P - primary tumor, L - malignant lymph node and C - benign lymph node (control). For patient G46 two malignant lymph nodes were used. DNA isolated from all samples was subject to exome selection using Agilent SureSelect Human All Exon V7. The obtained material was sequenced using NovaSeq 6000 platform with 2x150 reads. The sequencing was conducted by Novogene company.

Dataset EGAD00001009081

ESR1 mutations in tamoxifen-associated endometrial cancer versus spontaneous arisen endometrial tumors

An increased incidence of endometrial cancer has been described for patients that have received tamoxifen to treat breast cancer. Using samples from endometrial tumors, isolated from surgivcal specimens of patients who previously received tamoxifen treatment for breast cancer, we aimed to identify whether there are specific somatic mutations enriched in this population, relative to endometrial tumors from the general population. For this, WES was performed on matched endometrial tumors and healthy tissue (n=21).

Dataset EGAD00001009088

Dataset for soft_tissue_tumor-WHOLE_GENOME

Rare cancer sequencing data of 142 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008900

Dataset for upper_gastrointestinal_tumor-WHOLE_GENOME

Rare cancer sequencing data of 28 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008901

Dataset for upper_gastrointestinal_tumor-EXON

Rare cancer sequencing data of 85 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008902

Dataset for urologic_cancer-WHOLE_GENOME

Rare cancer sequencing data of 36 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008903

Dataset for urologic_cancer-EXON