5731 results for "canc*"

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• clonealign: direct library preparation+ single-cell DNA-sequencing

  Direct library preparation+ single-cell DNA-sequencing of (i) patient derived triple negative breast cancer xenograft (ii) primary tumour and ascites ovarian cancer cell lines at tumour recurrence.

  Dataset EGAD00001004553

• BS-seq in plasma of CRC patients

  We performed whole genome bisulfite sequencing of plasma DNA in 11 colorectal cancer patients to study the colonic DNA in plasma.

  Dataset EGAD00001004568

• Genome and transcriptome sequence data from a mucinous colloid carcinoma of the pancreas patient

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

  Dataset EGAD00001004598

• Somatic mutations in facial skin from countries of contrasting skin cancer risk

  The incidence of non-melanoma skin cancer is 17-fold lower in Singapore compared to the UK1, despite Singapore receiving 2-3 times more year-round ultraviolet radiation (UV)2,3. The ageing epidermis of the skin comprises competing somatic mutant clones4,5, from which such cancers develop. We question if differences in keratinocyte skin cancer incidence are reflected in the mutational landscape by comparing ageing facial epidermis from donors of Singapore and the UK. We find UK skin to be a highly competitive, densely mutated landscape with 4-fold greater mutation burden compared to Singaporean skin and differences in clonal selection by country. We disproportionately observe multiple features common to keratinocyte skin cancers6,7,8 in UK skin, such as UV mutagenesis, copy number aberration and hotspot mutations (in particular TP53 R248W). We conclude that keratinocyte skin cancer incidence is reflected in the somatic clones of non-cancerous epidermis. Finally, we re-analyse squamous cell carcinoma exomes from Korea9 to show, even in low incidence populations, carcinogenesis is driven by UV damage.

  Dataset EGAD00001009666

• The mutational landscape of skin tumours in CYLD cutaneous syndrome determined

  Patients with germline mutations in CYLD can develop hundreds of benign skin tumours called cylindromas. The development of multiple tumours within a single patient at sun-protected and sun-exposed sites, varying tumour histological patterns and grades of malignancy allow for the testing of several genetic hypothesis in relation to cutaneous carcinogenesis. By adopting the unprecedented approach of whole genome sequencing of multiple benign skin tumours within individuals in multigenerational families, we set out to study the impact of mutational diversity on models such as multistep carcinogenesis as well as non-sequential carcinogenesis. Using non-negative matrix factorisation (NMF) to discover mutational signatures, we found distinct mutational signatures in identical benign tumours (N=2 patients; n=11 tumours) at sun exposed and sun protected skin tumours within a mother and her daughter. We found recurrent mutations in epigenetic modifying genes in CCS tumours which are known to have an oncogenic dependency on Wnt signalling. We also demonstrate that cutaneous tumours that metastasize to the lung carry a a UV signature, supporting the origin from the skin. Distinct malignant tumours, such as BCC and malignant spiradenocarcinoma carried unique driver mutations. These findings add new dimensions to the existing paradigms of UV-induced skin cancer and highlight the utility of studying rare disease to gain novel insights into genetic mechanisms of tumour formation.

  Dataset EGAD00001004573

• Mannheim Liquid Biopsy Unit, Heidelberg University & DKFZ

  The dataset consists of sequenced cell free DNA (cfDNA) samples from colorectal cancer patients. The samples were sequenced on an Illumina MiSeq machine using a custom amplicon sequencing approach. These amplicons were designed to cover the most common mutation hotspots in colorectal cancer. The data include 138 cfDNA samples from 34 different patients. For each patient several samples are available derived from blood drawn at different time points during treatment. In addition the data include samples from 22 histology slides and 30 samples derived from HT29/HCT116 cell lines that were used as controls.

  Dataset EGAD00001004574

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

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

  Dataset EGAD00001004600

• Metabolic reprogramming towards OXPHOS identifies a novel therapeutic target for mantle cell lymphoma

  Metabolic reprogramming is linked to cancer cell growth and proliferation, metastasis, and therapeutic resistance in a multitude of cancers. Targeting dysregulated metabolic pathways to overcome resistance, an urgent clinical need in all relapsed/refractory cancers, remains difficult. Through genomics analysis of clinical specimens, we show that metabolic reprogramming towards oxidative phosphorylation (OXPHOS) and glutaminolysis is associated with therapeutic resistance to the Bruton’s tyrosine kinase inhibitor ibrutinib in mantle cell lymphoma (MCL), an incurable B-cell lymphoma with poor clinical outcomes. Inhibition of OXPHOS with a novel, clinically applicable small molecule, IACS-010759, which targets complex I of the mitochondrial electron transport chain, results in significant growth inhibition in vitro and in vivo in ibrutinib-resistant patient-derived cancer models. This work suggests that targeting metabolic pathways to subvert therapeutic resistance is a clinically viable approach to treat highly refractory malignancies.

  Dataset EGAD00001004577

• Probabilistic cell type assignment of single-cell transcriptomic data reveals spatiotemporal microenvironment dynamics in human cancers

  Dataset EGAD00001004585

• MCO colorectal cancer genomics at UNSW

  This dataset contains DNA sequencing data from 95 colorectal cancer and matched-normal samples. The dataset contains targeted deep sequencing of selected regulatory elements in 95 cancer and matched-normal samples, and data for one sample that was additionally whole-genome sequenced (cancer and matched-normal).

  Dataset EGAD00001004582

• A compendium of mutational signatures due to environmental exposures

  Whole-genome-sequencing (WGS) of human tumours has revealed distinct mutation patterns that hint at the causative origins of cancer. We examined mutational-signatures in 324 WGS of human induced pluripotent stem cells (iPSCs) following exposure to known or suspected environmental carcinogens. 79 agents were tested with or without metabolic activation at concentrations that produced measurable cytotoxicity; 41 yielded characteristic substitution mutational signatures. Some exhibit similarity with signatures found in human tumours. Additionally, 6 agents produced double-substitution signatures and 8 produced indel signatures. Investigating mutation asymmetries across genome topography reveals fully functional mismatch and transcription-coupled repair pathways in iPSCs. Primary adducts induced by environmental carcinogens can be resolved by disparate repair/replicative pathways, resulting in an assortment of signature outcomes even for a single mutagen. This compendium of experimentally-induced mutational-signatures permits further exploration of roles of environmental agents in cancer aetiology, and underscores how human stem cell DNA is directly vulnerable to environmental agents.

  Dataset EGAD00001004583

• Extreme intratumor heterogeneity and driver evolution in mismatch repair deficient gastro-esophageal cancer

  The dataset includes multi-region exome sequencing (MSeq) of four resected treatment naïve mismatch repair deficient gastro-esophageal cancers. Paired-end sequencing was performed on the Illumina HiSeq 2500 or NovaSeq 6000 with a target depth of 200X. Seven primary tumor regions along with tumor-adjacent non malignant tissue were subjected to MSeq. An additional two lymph node metastases were also included from each of two cases.

  Dataset EGAD00001004594

• 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 EGAD00001004597

• Genome and transcriptome sequence data from a metastatic leiomyosarcoma patient

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

  Dataset EGAD00001004601

• Genome and transcriptome sequence data from a osteosarcoma patient

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

  Dataset EGAD00001004628

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

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

  Dataset EGAD00001004626

• Genome and transcriptome sequence data from a metastatic basal cell carcinoma of frontal scalp patient

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

  Dataset EGAD00001004621

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

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

  Dataset EGAD00001004620

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

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

  Dataset EGAD00001004619

• Genome and transcriptome sequence data from a metastatic mmmt of the endometrium patient

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

  Dataset EGAD00001004618

• 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 EGAD00001004643

• Genome and transcriptome sequence data from a anorectal gastrointestinal stromal tumor patient

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

  Dataset EGAD00001004617

• Genome and transcriptome sequence data from a ganglioglioma of the left temporal lobe patient

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

  Dataset EGAD00001004615

• Genome and transcriptome sequence data from a metastatic squamous cell carcinoma of the cheek patient

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

  Dataset EGAD00001004603

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

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

  Dataset EGAD00001004622