Search Results - EGA European Genome-Phenome Archive

Genome and transcriptome sequence data from a metastatic colorectal cancer patient

Genome and transcriptome sequence data from a metastatic colorectal cancer patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001015835

On-target mutations confer resistance to WRN helicase inhibitors in Microsatellite Unstable Cancer Cells

This study investigates genetic dependencies and resistance mechanisms to Werner helicase inhibitors (WRNi) in microsatellite-unstable (MSI) cancer models. To define determinants of WRN dependency and acquired resistance, we performed genome-wide CRISPR-Cas9 knockout screens, CRISPR base-editing mutagenesis screens targeting WRN, targeted sequencing of resistance-associated variants, bulk RNA sequencing, and whole-genome sequencing. The datasets deposited in EGA comprise raw sequencing files from CRISPR-Cas9 knockout screens, CRISPR base-editing screens, targeted DNA sequencing, RNA-seq experiments, and whole-genome sequencing of parental and drug-treated cell populations, including models with spontaneously acquired resistance. These data enable investigation of WRN synthetic lethality, genetic modifiers of WRNi response, and genomic alterations emerging under selective pressure.

Dataset EGAD00001015822

Systemic mutagen exposures reported by normal kidney cell genomes - peripheral blood samples (NanoSeq)

Lifestyle, environmental and other exposures to exogenous mutagens generate somatic mutations in normal human cells in vivo and increase cancer risk. However, the global repertoire of exogenous mutagen exposures is uncertain. Using single-molecule duplex sequencing of normal kidney (n=319) and blood (n=272) samples from 10 countries, we show that kidney proximal tubule cells exhibit higher mutation rates than most normal cell types despite low cell division rates. Compared to cells from kidney glomeruli, medulla, distal tubules, or peripheral blood, proximal tubule cells show marked enrichment of mutational signatures due to the exogenous carcinogenic mutagens, aristolochic acids, and of several signatures of unknown causes. The results suggest the existence of multiple, common, systemically circulated mutagens affecting human populations and indicate that the genomes of kidney proximal tubule cells report such exposures with high sensitivity.

Dataset EGAD00001015824

Systemic mutagen exposures reported by normal kidney cell genomes - bulk kidney samples (NanoSeq)

Lifestyle, environmental and other exposures to exogenous mutagens generate somatic mutations in normal human cells in vivo and increase cancer risk. However, the global repertoire of exogenous mutagen exposures is uncertain. Using single-molecule duplex sequencing of normal kidney (n=319) and blood (n=272) samples from 10 countries, we show that kidney proximal tubule cells exhibit higher mutation rates than most normal cell types despite low cell division rates. Compared to cells from kidney glomeruli, medulla, distal tubules, or peripheral blood, proximal tubule cells show marked enrichment of mutational signatures due to the exogenous carcinogenic mutagens, aristolochic acids, and of several signatures of unknown causes. The results suggest the existence of multiple, common, systemically circulated mutagens affecting human populations and indicate that the genomes of kidney proximal tubule cells report such exposures with high sensitivity.

Dataset EGAD00001015825

Systemic mutagen exposures reported by normal kidney cell genomes - kidney cancer samples (whole-genome sequencing)

Lifestyle, environmental and other exposures to exogenous mutagens generate somatic mutations in normal human cells in vivo and increase cancer risk. However, the global repertoire of exogenous mutagen exposures is uncertain. Using single-molecule duplex sequencing of normal kidney (n=319) and blood (n=272) samples from 10 countries, we show that kidney proximal tubule cells exhibit higher mutation rates than most normal cell types despite low cell division rates. Compared to cells from kidney glomeruli, medulla, distal tubules, or peripheral blood, proximal tubule cells show marked enrichment of mutational signatures due to the exogenous carcinogenic mutagens, aristolochic acids, and of several signatures of unknown causes. The results suggest the existence of multiple, common, systemically circulated mutagens affecting human populations and indicate that the genomes of kidney proximal tubule cells report such exposures with high sensitivity.

Dataset EGAD00001015826

Systemic mutagen exposures reported by normal kidney cell genomes - microdissected kidney samples (NanoSeq)

Lifestyle, environmental and other exposures to exogenous mutagens generate somatic mutations in normal human cells in vivo and increase cancer risk. However, the global repertoire of exogenous mutagen exposures is uncertain. Using single-molecule duplex sequencing of normal kidney (n=319) and blood (n=272) samples from 10 countries, we show that kidney proximal tubule cells exhibit higher mutation rates than most normal cell types despite low cell division rates. Compared to cells from kidney glomeruli, medulla, distal tubules, or peripheral blood, proximal tubule cells show marked enrichment of mutational signatures due to the exogenous carcinogenic mutagens, aristolochic acids, and of several signatures of unknown causes. The results suggest the existence of multiple, common, systemically circulated mutagens affecting human populations and indicate that the genomes of kidney proximal tubule cells report such exposures with high sensitivity.

Dataset EGAD00001015827

Systemic mutagen exposures reported by normal kidney cell genomes - matched normal samples (whole-genome sequencing)

Lifestyle, environmental and other exposures to exogenous mutagens generate somatic mutations in normal human cells in vivo and increase cancer risk. However, the global repertoire of exogenous mutagen exposures is uncertain. Using single-molecule duplex sequencing of normal kidney (n=319) and blood (n=272) samples from 10 countries, we show that kidney proximal tubule cells exhibit higher mutation rates than most normal cell types despite low cell division rates. Compared to cells from kidney glomeruli, medulla, distal tubules, or peripheral blood, proximal tubule cells show marked enrichment of mutational signatures due to the exogenous carcinogenic mutagens, aristolochic acids, and of several signatures of unknown causes. The results suggest the existence of multiple, common, systemically circulated mutagens affecting human populations and indicate that the genomes of kidney proximal tubule cells report such exposures with high sensitivity.

Dataset EGAD00001015828

Common early-life exposure of the colorectal epithelium to the microbiome-derived mutagen colibactin

Colibactin is a mutagen produced by bacterial strains in the colorectal microbiomes of some healthy people. It generates somatic mutations characterised by the mutational signatures SBS88 and ID18 in normal human colorectal epithelial cells in vivo. Increasing prevalence of colibactin mutagenesis during the 20th century is hypothesised to have caused recent international increases in early-onset colorectal cancer incidence. Here, we establish the early-life prevalence, timing, mutation burdens and distribution through the colon of colibactin mutagenesis by sequencing normal colorectal epithelial cell genomes to detect SBS88 and ID18 in children and adolescents from the UK and Denmark biopsied between 2016 and 2024. Colibactin mutagenesis was found in ~40% individuals. It starts soon after birth and often ceases by age five years, although some children show longer exposures. Mutation burdens are higher in the left than right colon and show substantial variation between exposed individuals, in some causing >100-fold increases in total mutation loads compared to unexposed children of the same age. Therefore, colorectal mutagenesis by colibactin is currently common in some populations, occurs during early childhood and can produce markedly elevated somatic mutation burdens. The future public health implications of this widespread mutagen exposure will depend on clarification of its role in colorectal cancer causation.

Dataset EGAD00001015830

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Genome and transcriptome sequence data from a metastatic colorectal cancer patient

On-target mutations confer resistance to WRN helicase inhibitors in Microsatellite Unstable Cancer Cells

Systemic mutagen exposures reported by normal kidney cell genomes - peripheral blood samples (NanoSeq)

Systemic mutagen exposures reported by normal kidney cell genomes - bulk kidney samples (NanoSeq)

Systemic mutagen exposures reported by normal kidney cell genomes - kidney cancer samples (whole-genome sequencing)

Systemic mutagen exposures reported by normal kidney cell genomes - microdissected kidney samples (NanoSeq)

Systemic mutagen exposures reported by normal kidney cell genomes - matched normal samples (whole-genome sequencing)

Common early-life exposure of the colorectal epithelium to the microbiome-derived mutagen colibactin

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a breast cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a squamous cell carcinoma of esophagus patient

Genome and transcriptome sequence data from a breast cancer patient

Genome and transcriptome sequence data from a high grade mucinous endometrial adenocarcinoma patient

Genome and transcriptome sequence data from a de novo breast cancer patient

Genome and transcriptome sequence data from a glioblastoma patient

Genome and transcriptome sequence data from a metastatic pulmonary adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic leiomyosarcoma patient

Genome and transcriptome sequence data from a metastatic neuroendocrine carcinoma of the pancreas patient

Genome and transcriptome sequence data from a metastatic pancreatic adenocarcinoma patient

Genome and transcriptome sequence data from a pancreatic cancer patient

Genome and transcriptome sequence data from a metastatic endometrial cancer patient

Genome and transcriptome sequence data from a pancreatic cancer patient