Search Results - EGA European Genome-Phenome Archive

Genomic data used in "ACT-Discover: identifying karyotype heterogeneity in pancreatic cancer evolution using ctDNA"

Dataset EGAD00001010250

lymphoma plasma cfRNA

Dataset contains total RNA sequencing data from plasma of 65 different human donors: 30 diffuse large B-cell lymphoma (DLBCL) and 13 primary mediastinal large B-cell lymphoma (PMBCL) patients, and 22 cancer-free controls. Samples were sequenced on a NovaSeq 6000 and are provided in FASTQ format.

Dataset EGAD00001010259

Evaluation of triple negative breast cancer with heterogeneous immune infiltration

This dataset contains the raw RNA-seq data (FASTQ files) of the samples used in the study title: "Evaluation of triple negative breast cancer with heterogeneous immune infiltration". The dataset is composed of 3 patients with 6 samples per patient (3 with high TILs and 3 with low TILs).

Dataset EGAD00001010280

Tumour evolvability metrics predict recurrence in advanced localised prostate cancer (tumour data)

There is a need for quantitative measurements of evolutionary metrics in controlled clinical trials with long term follow-up information. This is particularly true in advanced localised prostate cancer, which can recur more than a decade after diagnosis. Here we mapped genomic intra-tumour heterogeneity in 642 tumour samples from 114 patients who took part in the IMRT and DELINEATE clinical trials, for which full clinical information and 12y median follow-up was available. We concomitantly assessed phenotypic (morphological) heterogeneity using Deep Learning in 1,923 histological sections from 250 IMRT patients (fully overlapping with the genetic set). This study shows that combining genomics with AI-aided histopathology in clinical trials leads to novel clinical biomarkers. This EGA repository contains data produced from tumour samples using low coverage whole genome sequencing and a prostate cancer specific gene panel data following compression of unique molecular identifiers.

Dataset EGAD00001010274

UCSF-CASCADE analysis of metastatic prostate cancer

Targeted cancer therapy inevitably selects for tumor cells that harbor some form of therapy resistance. This phenomenon is a principle reason why advanced prostate cancer, which can be treated with agents targeting androgen signaling dependency and DNA repair failure, is a lethal condition. The influence of a patient's clinical history and disease evolution on how their disseminated tumors develop resistance has been difficulty to study, because few autopsy studies have been performed in heavily treated patients with DNA-repair deficient metastatic castration-resistant prostate cancer (mCRPC). Here, we assessed how resistance to targeted cancer therapies evolved in an autopsy cohort of 54 mCRPC tumors from six men. This dataset includes targeted sequencing, exome sequencing, and RNA-seq conducted on these biopsies.

Dataset EGAD00001010275

Bulk RNAseq of Neuroblastoma patient's tumors

This dataset contains 9 bulk RNAseq of neuroblastoma patient's tumors used to compare with derived PDXs and/or single-cell data in the Thirant C et al, Nature Communications, 2023. They were intially produced for the Berlanga P., Cancer Discovery, 2022.

Dataset EGAD00001010287

Mutation analysis of 77 genes in cfDNA from metastatic CRC patients

Aligned NGS data (BAM) of 77 frequently mutated genes in cancer using the AVENIO Expanded platform.

Dataset EGAD00001010294

Biomarker analysis and treatment dynamics following preoperative ipilimumab plus nivolumab in locally advanced urothelial cancer from the phase 1B NABUCCO study

In the current analysis of the full NABUCCO trial population (cohorts 1 and 2), we aimed to explore both potential biomarkers for response to combination ICB, as well as treatment dynamics to gain a better understanding of the effects of ICB on the urothelial cancer tumor microenvironment (TME).

Study EGAS50000001781

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Genomic data used in "ACT-Discover: identifying karyotype heterogeneity in pancreatic cancer evolution using ctDNA"

lymphoma plasma cfRNA

Evaluation of triple negative breast cancer with heterogeneous immune infiltration

Tumour evolvability metrics predict recurrence in advanced localised prostate cancer (tumour data)

UCSF-CASCADE analysis of metastatic prostate cancer

Bulk RNAseq of Neuroblastoma patient's tumors

Mutation analysis of 77 genes in cfDNA from metastatic CRC patients

Biomarker analysis and treatment dynamics following preoperative ipilimumab plus nivolumab in locally advanced urothelial cancer from the phase 1B NABUCCO study

Genome and transcriptome sequence data from a melanoma patient

Genome and transcriptome sequence data from a follicular lymphoma patient

Genome and transcriptome sequence data from a neuroendocrine tumor patient

Genome and transcriptome sequence data from a thymic cancer patient

Genome and transcriptome sequence data from a small cell lung carcinoma patient

Genome and transcriptome sequence data from a pancreatic cancer patient

Genome and transcriptome sequence data from a nasopharyngeal carcinoma patient

Genome and transcriptome sequence data from a colorectal carcinoma patient

Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient

Genome and transcriptome sequence data from a urachal adenocarcinoma patient

Genome and transcriptome sequence data from a liposarcoma patient

Genome and transcriptome sequence data from a gastrointestinal stromal tumor patient

Genome and transcriptome sequence data from a granulosa cell ovarian tumor patient

Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic triple negative breast cancer patient

Genome and transcriptome sequence data from a papillary thyroid carcinoma patient