8213 results for "canc*"

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• Genome and transcriptome sequence data from a non-small cell lung cancer patient

  Genome and transcriptome sequence data from a non-small cell lung cancer patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016085

• Genome and transcriptome sequence data from a primary unknown patient

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

  Dataset EGAD00001016086

• Genome and transcriptome sequence data from a acral lentiginous melanoma patient

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

  Dataset EGAD00001016087

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

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

  Dataset EGAD00001016088

• Genome and transcriptome sequence data from a metastatic breast cancer patient

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

  Dataset EGAD00001016089

• Genome and transcriptome sequence data from a lung cancer patient

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

  Dataset EGAD00001016091

• Genome and transcriptome sequence data from a poorly differentiated adenocarcinoma more consistent with metastatic melanoma patient

  Genome and transcriptome sequence data from a poorly differentiated adenocarcinoma more consistent with metastatic melanoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016092

• Genome and transcriptome sequence data from a lung adenocarcinoma patient

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

  Dataset EGAD00001016093

• Genome and transcriptome sequence data from a clear cell ovarian cancer patient

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

  Dataset EGAD00001016094

• Genome and transcriptome sequence data from a metastatic cervical cancer patient

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

  Dataset EGAD00001016095

• Genome and transcriptome sequence data from a metastatic hepatocellular carcinoma patient

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

  Dataset EGAD00001016096

• Genome and transcriptome sequence data from a metastatic cholangiocarcinoma patient

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

  Dataset EGAD00001016097

• Genome and transcriptome sequence data from a endometrial carcinosarcoma patient

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

  Dataset EGAD00001016098

• Genome and transcriptome sequence data from a mucosal melanoma patient

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

  Dataset EGAD00001016099

• Genome and transcriptome sequence data from a metastatic undifferentiated pleomorphic sarcoma patient

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

  Dataset EGAD00001016100

• Genome and transcriptome sequence data from a recurrent peritoneal mesothelioma patient

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

  Dataset EGAD00001016101

• Ancestry and somatic profile predict acral melanoma origin and prognosis – WXS

  Acral melanoma, which is not ultraviolet (UV)-associated, is the most common type of melanoma in several low- and middle-income countries including Mexico. Latin American samples are significantly underrepresented in global cancer genomics studies, which directly affects patients in these regions as it is known that cancer risk and incidence may be influenced by ancestry and environmental exposures. To address this, we characterise the genome and transcriptome of 123 acral melanoma tumours from 92 Mexican patients, a population notable because of its genetic admixture. Compared with other studies of melanoma, we found fewer frequent mutations in classical driver genes such as BRAF, NRAS or NF1. While most patients had predominantly Amerindian genetic ancestry, those with higher European ancestry had increased frequency of BRAF mutations and a lower median number of structural variants. The tumours with activating BRAF mutations have a transcriptional profile more similar to cutaneous non-volar melanocytes, suggesting that acral melanomas in these patients may arise from a distinct cell of origin compared to other tumours arising in these locations. KIT mutations were found in a subset of these tumours, and quadruple wild-type samples (non BRAF/NRAS/NF1/KIT) differed from mutated samples in their structural genomic profile and overall and recurrence-free survival patterns. Transcriptional profiling defined three expression clusters; these characteristics were associated with recurrence-free and overall survival. We highlight potential novel low-frequency drivers, such as PTPRJ, NF2 and RDH5. Our study enhances knowledge of this understudied disease and underscores the importance of including samples from diverse ancestries in cancer genomics studies.

  Dataset EGAD00001015755

• Ancestry and somatic profile predict acral melanoma origin and prognosis – RNA

  Acral melanoma, which is not ultraviolet (UV)-associated, is the most common type of melanoma in several low- and middle-income countries including Mexico. Latin American samples are significantly underrepresented in global cancer genomics studies, which directly affects patients in these regions as it is known that cancer risk and incidence may be influenced by ancestry and environmental exposures. To address this, we characterise the genome and transcriptome of 123 acral melanoma tumours from 92 Mexican patients, a population notable because of its genetic admixture. Compared with other studies of melanoma, we found fewer frequent mutations in classical driver genes such as BRAF, NRAS or NF1. While most patients had predominantly Amerindian genetic ancestry, those with higher European ancestry had increased frequency of BRAF mutations and a lower median number of structural variants. The tumours with activating BRAF mutations have a transcriptional profile more similar to cutaneous non-volar melanocytes, suggesting that acral melanomas in these patients may arise from a distinct cell of origin compared to other tumours arising in these locations. KIT mutations were found in a subset of these tumours, and quadruple wild-type samples (non BRAF/NRAS/NF1/KIT) differed from mutated samples in their structural genomic profile and overall and recurrence-free survival patterns. Transcriptional profiling defined three expression clusters; these characteristics were associated with recurrence-free and overall survival. We highlight potential novel low-frequency drivers, such as PTPRJ, NF2 and RDH5. Our study enhances knowledge of this understudied disease and underscores the importance of including samples from diverse ancestries in cancer genomics studies.

  Dataset EGAD00001015756

• PEACE (Posthumous Evaluation of Advanced Cancer Environment) whole exome sequencing data

  PEACE (Posthumous Evaluation of Advanced Cancer Environment) whole exome sequencing data

  Dataset EGAD00001015763

• Genomics Define Malignant Transformation in Myeloma Precursor Conditions

  Multiple myeloma (MM) is consistently preceded by monoclonal gammopathy of undetermined significance (MGUS) and smoldering multiple myeloma (SMM). While these precursor conditions are asymptomatic, they are not entirely benign and carry a lifelong risk of progression to MM. Unlike other cancers defined by pathology, malignant transformation from MGUS or SMM to MM has so far relied on demonstration of clinical end-organ damage as morphology and cytogenetics cannot reliably distinguish them. In this study, using genomic data from 374 patients with MGUS or SMM (277 training, 97 validation), to our knowledge, we demonstrate for the first time the ability to identify malignant transformation in MGUS and SMM. We introduce the concept of genomic MM and genomic MGUS to differentiate the subsets of MGUS and SMM that are biologically malignant with genomic features indistinguishable from MM from the subset that is premalignant and unlikely to progress to malignancy. Importantly, we find that most SMM has biological features of malignant transformation indistinguishable from MM. As expected, this subset that we consider having genomic MM is associated with a high risk of progression to MM although some patients remained progression-free beyond 5 years. Conversely, 60% of MGUS and 10% of SMM have no evidence of malignant transformation (genomic MGUS), with no progression during follow-up. Integration of genomic features with the 2/20/20 International Myeloma Working Group model significantly improved the prediction of progression among genomic MM. These findings support the use of genomic criteria to refine the classification and the risk stratification in myeloma precursor conditions.

  Dataset EGAD00001015768

• Single-cell RNA sequencing of breast cancer lung metastasis and adjacent normal tissue

  This dataset contains single-cell RNA sequencing data from two samples: L1 (breast cancer metastasis to lung) and N3 (adjacent normal lung tissue) from a female patient. The samples were processed using 10X Chromium 3' technology and sequenced on Illumina NextSeq 500. This data supports the study "Endocrine therapy reprogramming of breast cancer facilitates metastatic escape via upregulation of P-Rex1/Rac1 signalling" which investigates how endocrine therapy reprograms breast cancer cells, leading to upregulation of P-Rex1/Rac1 signalling pathways that facilitate metastatic escape. The single-cell analysis reveals cellular reprogramming mechanisms in endocrine therapy-resistant breast cancer cells that form metastases in the lung.

  Dataset EGAD00001015769

• Resolution of tumour cell populations enhances specificity of treatment options for precision cancer medicine

  This dataset comprises FASTQ files for single-cell RNA-seq and single-cell ATAC-seq data. These data were generated using 10x Genomics' multiome kit. In this cohort, there are 25 samples from 17 human cancer patients.

  Dataset EGAD00001015782

• MethylScan data of plasma samples

  10ng from each cfDNA sample was used as the input material. For gDNA samples, 1.5-2ug each was first sonicated by Covaris R230 system (Woburn, MA). Next, size-selection with 0.8x-1.5x two-step Ampure XP beads was performed to enrich the 150-200bp fragments. 200ng of the size-selected gDNA was used as input material. The pre-capture library construction was performed with NEB UltraII DNA library prep kit for Illumina (Ipswich, MA) and the adapter was the methylated EM-seq adapter. Before the first PCR amplification, the gDNA samples were subjected to bisulfite conversion by QIAGEN Epitect kit, and cfDNA samples were subjected to enzymatic conversion by NEBNext enzymatic methyl-seq kit if the hybrid capture panel designed for converted DNA was used downstream. Twist panel hybrid capture was performed with their standard protocol (Twist Bioscience, South San Francisco, CA). The concentration of the post-capture library after the second PCR amplification was measured by Qubit 1xdsDNA HS kit (ThermoFisher, Waltham, MA). Their quality was examined by TBE-UREA PAGE and Bioanalyzer before sequencing. Libraries were then sequenced with 150bp paired-end reads on Illumina machines by Genewiz, Inc. (South Plainfield, NJ, USA). This dataset contains MethylScan data of the plasma samples from 248 noncancer individuals and 27 cancer patients (17 liver and 10 GI-tract cancers).

  Dataset EGAD00001015815

• 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

• Genome and transcriptome sequence data from a metastatic breast cancer patient

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

  Dataset EGAD00001015832

• Genome and transcriptome sequence data from a breast cancer patient

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

  Dataset EGAD00001015833

• Genome and transcriptome sequence data from a metastatic breast cancer patient

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

  Dataset EGAD00001015834

• 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

• Genome and transcriptome sequence data from a metastatic breast cancer patient

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

  Dataset EGAD00001015836

• Genome and transcriptome sequence data from a right buccal mucosa squamous cell cancer patient

  Genome and transcriptome sequence data from a right buccal mucosa squamous cell cancer patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016102

• Genome and transcriptome sequence data from a nras mutated metastatic melanoma patient

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

  Dataset EGAD00001016103

• Genome and transcriptome sequence data from a squamous cell lung carcinoma patient

  Genome and transcriptome sequence data from a squamous cell lung carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016104

• Genome and transcriptome sequence data from a lung adenocarcinoma patient

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

  Dataset EGAD00001016105

• Genome and transcriptome sequence data from a squamous cell carcinoma of the right oro/hypopharynx patient

  Genome and transcriptome sequence data from a squamous cell carcinoma of the right oro/hypopharynx patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016106

• Genome and transcriptome sequence data from a primary unknown - suspected metastatic scc of lung vs thymus patient

  Genome and transcriptome sequence data from a primary unknown - suspected metastatic scc of lung vs thymus patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016107

• Genome and transcriptome sequence data from a gallbladder adenocarcinoma, nos patient

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

  Dataset EGAD00001016108

• Genome and transcriptome sequence data from a uroepithelial carcinoma patient

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

  Dataset EGAD00001016109

• Genome and transcriptome sequence data from a metastatic intrahepatic cholangiocarcinoma patient

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

  Dataset EGAD00001016110

• Genome and transcriptome sequence data from a metastatic adenocarcinoma (endometrioid vs. clear cell) patient

  Genome and transcriptome sequence data from a metastatic adenocarcinoma (endometrioid vs. clear cell) patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016111

• Genome and transcriptome sequence data from a urothelial carcinoma patient

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

  Dataset EGAD00001016112

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

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

  Dataset EGAD00001016113

• Genome and transcriptome sequence data from a adenocarcinoma of the lung patient

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

  Dataset EGAD00001016114

• Genome and transcriptome sequence data from a metastatic melanoma patient

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

  Dataset EGAD00001016115

• Extensive and differential platinum chemotherapy mutagenesis in livers of children - RNA

  Bulk RNA sequencing of normal liver and liver tumours from children. Five of the children had liver cancer and samples was taken at surgery. Two children had non-liver type of cancer and liver samples were obtained postmortem.

  Dataset EGAD00001016117