8224 results for "canc*"

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• ProstOmics: spatial and bulk multi-omics of prostate cancer

  In this ERC-funded ProstOmics project we have used spatial and bulk multi-omics on fresh frozen prostate cancer samples to investigate cancer biology and find for biomarkers to improve patient treatment. All tissue material were collected from prostate cancer patients undergoing radical prostatectomy who had not received any prior cancer-specific treatment.Of the 498 prostate tissue samples (114 patients) included in our project, 176 samples (N=37 patients) have been analyzed with bulk transcriptomics (RNA-seq). Some of these 176 samples were also analyzed with spatial transcriptomics (n=32, N=8, Visium 10x RNA-seq) and DNA methylomics (n=96, N=24, array). All datasets include metadata for histopathological evaluation. Patient metadata include information of age at surgery, time (months) until reported relapse, pre-surgery PSA and post-surgery T-stage.

  Study EGAS50000000413

• an integrated molecular study of clear cell renal cell carcinoma (ccRCC) including whole-genome/exome and RNA sequencing as well as array-based gene expression/copy-number/methylation analyses

  an integrated molecular study of clear cell renal cell carcinoma (ccRCC) including whole-genome/exome and RNA sequencing as well as array-based gene expression/copy-number/methylation analyses

  Study EGAS00001000509

• Cell-free DNA fragmentome profiles predict immunotherapy response

  Mutation-based liquid biopsy approaches face challenges in accurately identifying the cellular origin of variants, which complicates the determination of circulating tumor DNA (ctDNA) molecular response. We hypothesized that these limitations could be addressed by utilizing genome-wide cell-free DNA (cfDNA) fragmentome methods. To this end, we performed whole-genome sequencing of 528 serial cfDNA samples and quantified the cfDNA tumor fraction (TF) using DELFI-TF, a tumor- and mutation-naive machine learning cfDNA fragmentome classifier, across two prospective clinical protocols for immunotherapy-treated non-small cell lung cancer (NSCLC). DELFI-TF values were validated independently by hybrid capture fixed gene panel next-generation sequencing, and the landmark cfDNA fragmentome molecular response (fMR) was determined within 3-9 weeks from the initiation of immunotherapy. Individuals with fMR attained significantly longer progression-free and overall survival than those without fMR (logrank p=2.7e-14 and p=3e-9), including in patients with mutation-based molecular progression (logrank p=1.2e-4 and p=2e-3). Our findings suggest that analyses of the cfDNA fragmentome can provide a clinically meaningful measure of circulating tumor fraction and validate the clinical sensitivity of plasma-only cfDNA fragmentome-based molecular response as an early indicator of immunotherapy response.

  Study EGAS50000001837

• Ouro-seq: Improved Recovery of Full-Length circRNAs from Samples with Limited RNA Content Using Short-Amplicon Suppression

  Circular RNAs (circRNAs) represent an emerging class of RNAs with potential roles in disease pathogenesis and promising biomarker applications. However, their detection in samples with limited RNA content, such as liquid biopsies, remains challenging due to extremely low abundance. Here, we introduce Ouro-seq, a novel long-read sequencing protocol optimized for full-length circRNA recovery. We applied Ouro-seq to urine and self-sampled cervical swab (CVS) samples from cervical cancer patients and plasma from lung cancer patients and healthy controls. Our approach significantly outperformed conventional methods, recovering 2-5 times more and substantially longer circRNA molecules. Unexpectedly, while plasma samples predominantly contained exonic circRNAs, urine and CVS were dominated by previously under characterized intergenic circRNA. We identified extensive alternative circularization and splicing events. Functional annotation revealed distinct specialization patterns among circRNA subtypes, with exonic circRNAs exhibiting enhanced miRNA sponging potential and circRNAs from unplaced genomic scaffolds showing greater peptide-coding capacity. This study significantly advances our understanding of circRNA biology in liquid biopsies and establishes Ouro-seq as a valuable tool for comprehensive circRNA characterization with potential applications in biomarker discovery and disease monitoring.

  Study EGAS50000001356

• UNICORN Data Access Committee

  The UNICORN Data Access Committee reviews and manages requests for controlled access to genomic, transcriptomic and associated clinical data generated within the UNICORN colorectal cancer study.

  Dac EGAC50000001116

• High-grade serous ovarian cancer is associated with increased TP53 mutation burden in uterine lavage

  High grade serous ovarian cancer (HGSC) has low survival partly due to the lack of methods for detection, diagnosis, and risk prediction. TP53 mutations, which drive HGSC, are found in gynecological tissues as the result of somatic evolution, but it is unknown whether an excess of mutations is linked to ovarian cancer. Here we investigate if TP53 mutation burden measured in uterine lavage, a minimally invasive gynecological liquid biopsy, can discriminate between patients with and without HGSC. We used ultradeep TP53 duplex sequencing (>15,000x duplex depth) to detect TP53 mutations in uterine lavage collected pre-operatively in 278 patients undergoing gynecological surgery for pelvic masses (average risk) or cancer risk-reduction (high risk). All lavages contained multiple TP53 mutant clones, which were used to quantify TP53 mutation burden frequency (MBF). Average risk patients with HGSC had significantly higher TP53 MBF independently of age and other risk factors (77% sensitivity, 89% specificity, AUC =0.88). Excluding tumor TP53 clonal mutations from the lavage MBF calculation maintains this association, suggesting that it is the overall TP53 somatic mutation burden (rather than the discovery of the specific tumor driver mutation) that identifies HGSC. These results demonstrate that TP53 somatic mutations are common in uterine lavage but more abundant in patients with HGSC, highlighting a connection between TP53 somatic evolution and ovarian cancer. Uterine lavage offers a minimally invasive approach that could be valuable to identify patients with HGSC.

  Study EGAS50000001910

• Arcagen - Gynecologic cancer domain

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here we are submitting the dataset that contain NGS files from patients with rare ovarian cancer and primary peritoneal cancer and/or fallopian-tube cancer, including low grade serous carcinoma, mucinous adenocarcinoma, clear cell adenocarcinoma; and other rare cancers such as sex cord tumors, germ cell tumor, yolk sac tumor, and malignant/immature teratoma (n=94).

  Study EGAS50000000900

• Circulating cell-free DNA methylation profiling for detection, distinction, and estrogen receptor status classification of advanced breast cancer

  We developed cell-free DNA (cfDNA) methylation signatures for minimally invasive breast cancer detection, distinction, and estrogen receptor (ER) status classification with cell-free Methylated DNA Immunoprecipitation and Sequencing (cfMeDIP-seq). We profiled peripheral blood plasma from 87 patients with mBC spanning ER-positive/HER2-negative (ER+/HER2-), HER2-positive, and triple-negative breast cancer (TNBC).

  Study EGAS50000001675

• Single-cell transcriptome and TCR profiles of T cells from supercentenarians

  Our previous study identified CD4 cytotoxic T lymphocytes (CD4 CTLs) as a hallmark of supercentenarians. Using single-cell immune profiling, we found that CD4 CTLs begin expanding around age 100, characterized by sequential CD27/CD28 loss without exhaustion. These cells showed strong clonal expansion and shared CDR3beta sequences with tumor-infiltrating T cells, especially from lung cancer. These findings suggest that CD4 CTLs adapt to persistent antigens and may contribute to cancer surveillance in extreme aging.

  Study JGAS000815

• Whole Exome Sequencing and RNA Sequencing data

  Whole Exome Sequencing and RNA Sequencing data for SCLC samples used in the study "A targetable dependency on nonsense-mediated decay for cellular homeostasis and immune control in small cell lung cancer"

  Dataset EGAD50000002962