8255 results for "canc*"

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• Discovery of new fusion transcripts in a cohort of pediatric solid cancers at relapse

  This study aims to dissect further the complexity of fusion landscape in recurrent pediatric cancers. A retrospective study on RNA-sequencing data of 48 pediatric patients at relapse with different malignancies was conducted in order to detect and validate several fusions and predict their probable oncogenic potential and targetability. We obtained a high validation rate of 90% of selected candidates which will serve both clinical and research needs to detect and prioritize experimental validation studies leading to the development of new therapeutic options.

  Study EGAS00001003236

• Mutational_burden_in_oesophagus_following_chemotherapy_and_radiotherapy_treatment_WGS

  We wish to assess the changes in signature and mutational burden in patients who have undergone either chemotherapy or chemotherapy + radiotherapy. Using duplex sequencing will assess the mutational landscape in oesophageal epithelia in patients who have undergone these treatment regimes.

  Study EGAS00001007415

• The_effects_of_chemotherapy_and_radiation_in_human_oesophageal_epithelium

  Human oesophagus is a patchwork of competing mutant clones. We wish to see how this patchwork is altered under the extreme selection pressures of chemotherapy and radiotherapy both individually and combined. We will sequence 2mm2 contiguous pieces of oesophageal epithelium from patients who have undergone chemotherapy and radiotherapy to assess how the mutational landscape has changed.

  Study EGAS00001007417

• Mutant p53 confers gain-of-function transcriptional activity in liver cancer

  Mutant p53 confers gain-of-function transcriptional activity in liver cancer

  Study EGAS00001005779

• MutWP5__CRUK_Mutographs_of_Cancer__Lung__PD37920__WG_

  Sequencing of LCM-derived microbiopsies from explanted lung from COPD patient. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Deep sampling throughout multiple regions of the lung will determine whether there are differences in smoking-related mutation burden in different portions of the lung. Whole-genome sequencing will be conducted on samples identified as promising from the initial targeted data. Results from this portion of the study will be compared to other individuals with smoking-related diseases (COPD, pulmonary fibrosis, lung cancer), and normal, non-smoking lungs.

  Study EGAS00001003320

• RNA sequencing data of 142 samples from 142 patients with HER2+ breast cancer treated with letrozole or tamoxifen (SOLTI PAMELA trial)

  PAMELA (NCT01973660) is a non-randomized, open-label, multicentric, prospective translational research study in stage I-IIIA HER2+ breast cancer designed to evaluate the ability of the PAM50 intrinsic subtypes to predict pCR in the breast (pCRB) following 18 weeks of neoadjuvant lapatinib and trastuzumab (+/- hormonal therapy if hormone receptor [HR] positive). Patients with HR+ disease received letrozole (if postmenopausal) or tamoxifen (if pre-menopausal). The primary objective was to compare the pCRB rates of the HER2-E versus the non-HER2-E subtypes in the intent-to-treat population.

  Study EGAS00001006410

• RRBS data from TRACERx non-small cell lung cancer (NSCLC) tumours and matched normal adjacent tissue.

  TRACERx (TRAcking Cancer Evolution through therapy (Rx)) is a prospective cohort study designed to investigate intratumor heterogeneity (ITH) in relation to clinical outcome, and to determine the clonal nature of driver events and evolutionary processes in early stage non-small cell lung cancer (NSCLC).

  Study EGAS00001008071

• Multiple_myeloma_precursor_genomics

  Whole genome sequencing of up to 45 multiple myeloma precursor samples and matched normals pairs.

  Study EGAS00001006312

• DERMATLAS__SG_basal_cell_adenoma_and_adenocarcinoma_WES

  Virtually no other tumour type is associated with so many different forms as skin cancer. Histologically, tumours of the skin may arise from epithelium, including epidermis, hair follicle, sebaceous or sweat gland, melanocytes, dermal-associated mesenchymal structures or tissue resident immune cells, making for a diversity of clinical presentations. Importantly, many skin tumour types have an extremely poor prognosis. Many skin tumour subtypes have never undergone molecular profiling, or if they have, targeted sequencing has been used and the number of cases analyzed has been so limited that deriving firm conclusions about the profile of driver genes, DNA mutational signatures and germline alleles has not been possible For 70 key skin tumour subtypes defined by the World Health Organization, that have not undergone extensive genetic analysis previoulsy, we propose to perform whole exome and transcriptome sequencing, from a range of body sites, to build a genomic atlas of dermatological tumours, including detailed maps of SNVs, copy number alterations, genome-wide methylation and expression profiles. The cases in this cohort are SG basal cell adenomas and adenocarcinomas.

  Study EGAS00001007745

• XClone for analyzing somatic copy number alterations

  Somatic copy number alterations (CNAs) are major mutations that contribute to the development and progression of various cancers. Despite a few computational methods proposed to detect CNAs from single-cell transcriptomic data, the technical sparsity of such data makes it challenging to identify allele-specific CNAs, particularly in complex clonal structures. In this study, we present a statistical method, XClone, that strengthens the signals of read depth and allelic imbalance by effective smoothing on cell neighborhood and gene coordinate graphs to detect haplotype-aware CNAs from scRNA-seq data. By applying XClone to multiple datasets with challenging compositions, we demonstrated its ability to robustly detect different types of allele-specific CNAs and potentially indicate whole genome duplication, therefore enabling the discovery of corresponding subclones and the dissection of their phenotypic impacts.

  Study EGAS00001007854

• Effect_of_platinum_on_whole_blood_NanoSeq

  Whole-genome NanoSeq to assess the effect of platinum chemotherapy on the mutation burden and signatures found in whole blood.

  Study EGAS00001006454

• Detection of human brain cancers using genomic and immune cell characterization of cerebrospinal fluid through CSF-BAM

  Detection of human brain cancers using genomic and immune cell characterization of cerebrospinal fluid through CSF-BAM

  Study EGAS00001008199

• Direct Detection of Early-stage Cancers Using Circulating Tumor DNA

  Early detection and intervention are likely to be the most effective means for reducing morbidity and mortality of human cancer. However, development of methods for noninvasive detection of early-stage tumors has remained a challenge. We have developed an approach called targeted error correction sequencing (TEC-Seq) that allows ultrasensitive direct evaluation of sequence changes in circulating cell-free DNA using massively parallel sequencing. We have used this approach to examine 58 cancer-related genes encompassing 81 kb. Analysis of plasma from 44 healthy individuals identified genomic changes related to clonal hematopoiesis in 16% of asymptomatic individuals but no alterations in driver genes related to solid cancers. Evaluation of 200 patients with colorectal, breast, lung, or ovarian cancer detected somatic mutations in the plasma of 71, 59, 59, and 68%, respectively, of patients with stage I or II disease. Analyses of mutations in the circulation revealed high concordance with alterations in the tumors of these patients. In patients with resectable colorectal cancers, higher amounts of preoperative circulating tumor DNA were associated with disease recurrence and decreased overall survival. These analyses provide a broadly applicable approach for noninvasive detection of early-stage tumors that may be useful for screening and management of patients with cancer.

  Study EGAS00001002577

• Res1_PC9_exp2_MC_01_04_22

  8 cell pellet samples for genomic DNA extraction. CRISPR PCR1 and PCR2 indexing - Please use standard Kosuke primers.

  Study EGAS00001006170

• Somatic Inactivation of Breast Cancer Predisposition Genes in Tumours Associated with Pathogenic Germline Variants

  Breast cancers (BC) from susceptibility gene carriers, including BRCA1/2, PALB2 and RAD51C, have been shown to have bi-allelic loss in the respective genes and be associated with triple-negative (TN) BC and distinctive somatic mutational signatures. Tumour sequencing thus presents an orthogonal approach to assess the role of candidate genes in BC development.

  Study EGAS00001006532

• Non-coding RNAs in breast cancer

  Using RNA CaptureSeq we annotated non-coding RNAs transcribed from genome intervals surrounding breast cancer risk signals in a range of mammary-derived tissue and cell lines.

  Study EGAS00001003353

• Childhood_Cancer_Paediatric_Behjati_SRF_Targeted_Nanoseq_TE_96389176_Managed_Access

  An exploratory study using targeted NanoSeq on a bait set of common paediatric cancer genes and cancer predisposition genes to assess mutations, mutational signatures, treatment effect, risk of relapse and to study the development of childhood cancer.

  Study EGAS00001007424

• Atypical tetrasomy 18 in a hepatoblastoma patient

  Constitutive aneuploidy often underlies developmental defects, while copy-number alterations are recurrent somatic events in cancers. Rarely, mosaic aneuploidy links developmental defects and cancer development, yet its molecular basis remains elusive. We report the first cancer case in a tetrasomy 18 patient—a female who developed hepatoblastoma at age two and remains recurrence-free 24 months post-surgery and chemotherapy. Whole-genome sequencing and Fluorescent in situ hybridization (FISH) uncovered a complex rearrangement with eight breakpoints between 18p11.32 to 18q12.1, present in 10% of liver and blood cells. Haplotype analysis revealed a pre-zygotic origin, with mosaicism arising from early rescue by loss of the rearranged chromosome. Strikingly, all tumor cells retained this rearranged chromosome. Single-nucleus RNA-seq of liver and hepatoblastoma tissue traced the aneuploidy’s evolution during gametogenesis, organogenesis, and tumorigenesis. This study provides insights into mechanisms of aneuploidy-driven cancer, highlighting the interplay of mosaicism, developmental defects, and tumor evolution in a rare genetic syndrome.

  Study EGAS00001008072

• WES of Colorectal cancer organoid-stroma biobank cohort

  In colorectal cancers (CRC) the tumor microenvironment plays a key role for prognosis and therapy efficacy. Patient-derived tumor organoids (PDTOs) show enormous potential for preclinical testing, however, in purely epithelial cultures features including the ‘consensus molecular subtypes’ (CMS) are largely eradicated. To better reflect cell heterogeneity, we established the CRC organoid-stroma biobank of matched PDTOs and cancer-associated fibroblasts (CAFs) from 30 patients. Context-specific phenotyping showed that xenotransplantation or co-culture with CAFs restores the individual transcriptomic status and instructs subtype-specific stromal gene expression. Furthermore, co-culture exposed CMS4-specific resistance to Gefitinib and SN-38 and revealed prognostic gene expression signatures. Chemogenomic library screening identified patient- and therapy-dependent mechanisms of stromal resistance including MET as common target. Our results demonstrate that CRC phenotypes are encrypted in the cancer epithelium in a plastic fashion that strongly depends on the context. Consequently, CAFs are essential for faithful representation of molecular subtypes and therapy responses ex vivo.

  Study EGAS00001007301

• Intra-prostatic tumour evolution, steps in metastatic spread and histogenomic associations revealed by integration of multi-region whole genome sequencing with histopathological features

  We performed whole genome sequencing on 42 prostate cancer samples from the prostate, seminal vesicles and regional lymph nodes of five treatment-naive patients with locally advanced disease who underwent radical prostatectomy. Using cancer cell fractions computed from single nucleotide variants and copy number alterations, we reconstructed the tumour phylogenies, which in turn allowed us to infer key molecular steps in the progression of prostate cancer in these individuals. We mapped the clonal composition of cancer sampled across the prostate in each individual and inferred the routes of spread of cancer cells within the prostate and to seminal vesicles and lymph nodes.

  Study EGAS00001007438

• V4_panel_bait_design_test

  Targeted gene screen of FFPEs, cell lines and primary tumours for testing the new V4 Cancer gene panel.

  Study EGAS00001001808

• Genomic evolution and transcriptional changes in the evolution of prostate cancer into neuroendocrine and ductal carcinoma types (RNAseq)

  Prostate cancer is typically of acinar adenocarcinoma type but can occasionally present as neuro-endocrine and/or ductal type carcinoma. These are associated with clinically aggressive disease and the former often arises on a background of androgen deprivation therapy, although it can al-so arise de novo. Two prostate cancer cases were sequenced by exome capture from archival tis-sue. Case 1 was de novo small cell neuroendocrine carcinoma and ductal adenocarcinoma with 3 longitudinal samples over 5 years. Case 2 was a single time point after development of treatment related neuroendocrine prostate carcinoma. Case 1 showed whole genome doubling in all sam-ples and focal amplification of AR in all samples except the first time point. Phylogenetic analysis revealed a common ancestry for the ductal and small cell carcinoma. Case 2 showed 13q loss (involving RB1) in both adenocarcinoma and small cell carcinoma regions, and 3p gain, 4p loss, 17p loss (involving TP53) in the latter. By using highly curated samples, we demonstrate for the first time that small cell neuroendocrine and ductal prostatic carcinoma can have a common an-cestry and the process of evolution over time. We highlight whole genome doubling in a patient with prostate cancer relapse, reinforcing its poor prognostic nature.

  Study EGAS00001007428

• PDX_models_from_Latin_America_RNAseq

  Acral melanoma (AM) is a subtype of cutaneous melanoma that occurs on glabrous skin of the hands and feet (palms, soles and nail apparatus) and which is relatively more common in non-European descent populations such as those of Latin America. Compared to other subtypes, it is poorly studied and experimental models that faithfully reproduce human AM features are urgently needed. We report the generation and preliminary characterisation of a collection of patient-derived xenografts of acral melanomas (AM-PDX) from Latin-American patients. PDX came from Brazilian and Mexican patients cared for at the Instituto Nacional de Câncer (INCA) and the Instituto Nacional de Cancerologia (INCan). The majority of the samples are acral lentiginous melanomas, ulcerated, with > 4mm Breslow depth and > 2 mitosis / mm2. Samples were mechanically fragmented and subcutaneously implanted in NSG mice and then collected for molecular analysis.

  Study EGAS00001008150

• Whole_genome_sequencing_of_rhabdomyosarcoma_tumouroids

  The aim of this study is to investigate the genomic landscape of human cancer.

  Study EGAS00001008270

• Metastatic_Prostate_Follow_Up_2

  Validation/deeper sequencing for metastatic prostate cancer samples

  Study EGAS00001000756