Search Results - EGA European Genome-Phenome Archive

NICHE - RNA-seq of MMR proficient and MMR deficient early stage colon cancers

The dataset includes 77 FASTQ files from single-end total RNA sequencing on Illumina HiSeq2500 for 39 patients.

Dataset EGAD00001006042

Guardians of the genome: protecting DNA from endogenous sources of damage

Mutational signatures are imprints of cell-intrinsic and extrinsic pathophysiological processes that have occurred through tumorigenesis. Experimental efforts to explore signature etiologies have produced a compendium of signatures of exogenous mutagens previously. Here, we unearth major sources of endogenous DNA damage and the genes that are critical to mitigating this innate stream of DNA damage under normal, physiological circumstances. We performed whole genome sequencing of 173 subclones of CRISPR-Cas9 knockouts of 43 genes in a human induced pluripotent stem cell system, in the absence of any added DNA damage. We reveal substitution and indel signatures that arise from those genes which are essential guardians of the genome. By detailed dissection and comparisons to cancer-derived signatures, we demonstrate interminable sources of constitutive DNA damage, and some mechanistic knowledge into how guardian genes preserve the genome. Based on these experimental insights, we develop and benchmark a tool for clinical classification of tumor samples.

Dataset EGAD00001006055

Whole-Exome Sequencing of Tumor Biopsies from a Colorectal Cancer Patient with Two Distinct Primary Tumors and Matched Metastases

Colorectal cancer (CRC) is a heterogeneous disease in which rare genetic alterations, such as neurotrophic receptor tyrosine kinase (NTRK) fusions, have emerged as clinically relevant therapeutic targets. Here, we report the case of a 69-year-old man with an advanced colorectal carcinoma comprising two intermixed but histologically distinct components: a predominant (>90%) poorly differentiated solid carcinoma and a conventional adenocarcinoma with mucinous features. Whole-exome sequencing (WES) of microdissected tumor regions (two primary tumors and two matched metastases) along with germline DNA analysis revealed profound genetic divergence between the two tumor components. This case illustrates the coexistence of two genetically independent yet spatially inseparable CRCs following distinct evolutionary trajectories—one driven by an NTRK1 fusion and microsatellite instability (MSI), and the other by canonical KRAS and SMAD4 alterations.

Study EGAS50000001385

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NICHE - RNA-seq of MMR proficient and MMR deficient early stage colon cancers

Guardians of the genome: protecting DNA from endogenous sources of damage

Whole-Exome Sequencing of Tumor Biopsies from a Colorectal Cancer Patient with Two Distinct Primary Tumors and Matched Metastases

Genome and transcriptome sequence data from an alveolar soft part sarcoma patient

Genome and transcriptome sequence data from a gastroesophageal junction adenocarcinoma patient

Genome and transcriptome sequence data from a colon adenocarcinoma patient

Genome and transcriptome sequence data from an unknown tissue unknown histology patient

Genome and transcriptome sequence data from an osteosarcoma patient

Genome and transcriptome sequence data from a squamous cell carcinoma patient

Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient