8253 results for "canc*"

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• NGS sequencing data of archival FFPE tumor tissue

  The aim of the study was to identify mutations in key ovarian cancer genes (BRCA1, BRCA2,TP53, PTEN, ATM, ATR, NF1) in archival fresh-frozen paraffin embedded (FFPE) tumor tissue from platinum-resistant ovarian cancer patients enrolled in the phase I/II GANNET53 clinical trial. From the enrolled 133 patients, archival FFPE tissue was available and DNA was extracted thereof. The DNA samples passing quality control (n=118) were NGS sequenced using the SureSeq™ Ovarian Cancer Panel and the NGS Library Preparation kit (Oxford Gene Technology), which covers all exons of 7 key ovarian cancer genes for single nucleotide variants (SNV) and indels, and the Illumina MiSeq platform. For the paired-end runs, one Read 1 (R1) and one Read 2 (R2) FASTQ file were created for each sample. FASTQ files were compressed and created with the extension .fastq.gz.

  Dataset EGAD50000001371

• Tissue architecture and immune niches govern ctDNA release in colorectal cancer

  Circulating tumor DNA (ctDNA) is central to liquid biopsy-based cancer detection, yet its release into the bloodstream varies widely and remains poorly understood. To define the tissue-level determinants of ctDNA shedding in colorectal cancer (CRC), we integrated tumor-informed plasma sequencing with detailed histopathology, immunophenotyping, spatial transcriptomics, and in situ mutation detection in resectable stages (I–III). ctDNA detectability increased with tumor burden, and high ctDNA shedders exhibited a distinct architectural and microenvironmental phenotype characterized by expanded necrotic pseudolumina, frequent epithelial barrier disruption, and dense myeloid infiltration. Spatial profiling revealed stress-associated malignant programs and a myeloid-rich immune-luminal niche. In situ sequencing confirmed plasma-detected mutations within pseudoluminal debris, identifying these structures as focal reservoirs of shed DNA. These findings provide a mechanistic framework linking tissue architecture, immune remodelling, and spatially organized cell death to ctDNA release with implications for refining liquid biopsy applications.

  Study EGAS50000001941

• Type 1 interferon perturbates clonal competition by reshaping human blood development

  We studied hematopoietic stem cells, progenitors and immune cells from patients with myeloproliferative neoplasms (MPN) at baseline and following interferon-⍺ (IFN⍺) treatment, the only therapy to deplete mutated stem cells. We deployed single-cell multi-omics methods that distinguish the IFN⍺ effects on mutated stem cells from the admixed wildtype HSCs, with respect to their differentiation, transcriptomes, immunophenotypes, and chromatin accessibility.

  Study EGAS50000002009

• FGFR2b Prevalence in Biliary Tract Cancers

  Patients with intrahepatic cholangiocarcinoma (iCCA) often have limited effective treatment options after first-line therapy. Actionable driver mutations are present in only a small subset of patients with iCCA; therefore, therapeutic strategies such as antibody–drug conjugates (ADCs) that do not exclusively rely on presence of specific oncogenic mutations may be particularly attractive. However, there is a critical lack of knowledge regarding prevalent and actionable cell-surface targets in iCCA. We applied a novel isoform-resolved proteogenomic discovery framework for profiling cell surface targets and identified FGFR2b, a splicing isoform of FGFR2, as a therapeutic target in iCCA that is highly-expressed, tumor-enriched, localized to the membrane, and associated with prognosis. FGFR2b is the dominant isoform in iCCA, and it was present in all patients with FGFR2 fusions. These findings provide a strong rationale for further research and therapeutic development of FGFR2b-targeted biologics, including therapeutic antibodies and ADCs, in iCCA.

  Study EGAS50000002012

• Spatial Biology of Cancer of Unknown Primary

  Dac EGAC50000000720

• Studying ctDNA signal in plasam whole genome sequencing from high risk Breast Cancer patients

  We apply fragmentomics and minimal residue disease tools to find out signals from ctDNA in high risk Breat Cancer patients.

  Study EGAS50000001830

• Transcriptomics for IMMU-BC1 cohort

  The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes metastatic Triple Negative Breast Cancer (mTNBC) patients, naïve of treatment in the metastatic settings, treated in 1st line with chemotherapy or chemo-immunotherapy This dataset contains transcriptomics data processed with the STAR pipeline. Two sequencing kits were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA quantities. It contains gene-level counts.

  Dataset EGAD50000002269

• Variant calling for IMMU-BC1 cohort

  The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes metastatic Triple Negative Breast Cancer (mTNBC) patients, naïve of treatment in the metastatic settings, treated in 1st line with chemotherapy or chemo-immunotherapy This dataset contains whole exome sequencing data from tumor and matching germline samples processed with the Vegan pipeline. It includes SNP and CNV calling.

  Dataset EGAD50000002270

• Biopsy and resection samples of HCC and non-tumor tissue

  A total of 16 patients with primary liver cancer, who first underwent diagnostic biopsy and then surgical resection shortly afterwards (median 27 days) were included. Tumor and non-tumor biopsy and resection tissue were analyzed by RNA sequencing. Total RNA from frozen tumor- and non-tumor tissue from biopsy and resection specimens was extracted using the ZR-Duet DNA and RNA MiniPrep Plus kit (Zymo Research) according to the manufacturer’s instructions. Prior to extraction, frozen tissues were crushed in liquid nitrogen to facilitate lysis. Extracted RNA was quantified using the Qubit Fluorometer (Thermo Fisher Scientific). 200 ng total RNA was used for RNAseq library prep with the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) according to the manufacturer’s specifications. Paired-End sequencing was performed on a Novaseq 6000 (Illumina) with 51 cycles at the Genomics Facility Basel according to the manufacturer’s guidelines.

  Dataset EGAD50000002291

• Study cfDNA molecular profiling for finding cancer signal in high risk Breast Cancer patients

  Whole genome sequencing of the matching blood from high risk breast cancer patients

  Dataset EGAD50000002653

• Study cfDNA molecular profiling for finding cancer signal in high risk Breast Cancer patients

  cfmedip methylation profiling CM from plasma cfDNA of high risk breast cancer patients

  Dataset EGAD50000002654

• FGFR2b Project Biliary Tract Cancer RNA Sequencing Data

  FASTQ files of RNA Sequencing data for the FGFR2b project.

  Dataset EGAD50000002899

• Germline WES of serrated polyposis syndrome

  The serrated polyposis syndrome (SPS) is a disease with a mainly unknown inherited genetic basis characterized by the presence of multiple and/or large serrated polyps in the colon and a higher associated risk for colorectal cancer (CRC). The objective of the present study was to identify new SPS/CRC germline predisposition genes by using whole-exome sequencing in two affected SPS patients from the same family.

  Study EGAS50000000765

• SOLTI- Arianna trial

  The main hypothesis of the study is that enzalutamide induces a significant proliferative arrest in HR+/HER2-negative breast cancer falling into the PAM50 HER2-E subtype. Patient population included males or pre/post-menopausal women with advanced HR+/HER2- ABC resistant to endocrine therapy, received ENZ 160 mg/day until disease progression. Patients were assigned to different cohorts according to PAM50 intrinsic subtypes identified in the pre-treatment tumor biopsy: Cohort A included pts with HER2-E and Cohort B pts with Luminal A/B tumors. Centralized molecular assessment was done at pre-treatment and C1D15.

  Study EGAS50000001979

• Study cfDNA molecular profiling for finding cancer signal in high risk Breast Cancer patients

  EM-seq methylation profiling MC of plasma cfDNA of high risk breast cancer patients

  Dataset EGAD50000002655

• Study cfDNA molecular profiling for finding cancer signal in high risk Breast Cancer patients

  Plasma cfDNA WGS profiling of high risk breast cancer patients.

  Dataset EGAD50000002656

• IMMUcan BC2 cohort

  The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with confirmed localized TNBC (stages I to III) treated with neo-adjuvant therapy Comprehensive profiling data are integrated with longitudinally collected clinical information. Cellular profiling of the same tumor samples was performed using multiplex immunofluorescence imaging, imaging mass cytometry, and H&E staining.

  Study EGAS50000001938

• Impact of Mutated CTCF DNA binding sites of Topologically associating domains on nearby Cancer Gene Regulation: A Multi-Omics Analysis

  Cutaneous squamous cell carcinoma (cSCC) is the most common lethal malignancy world-wide. Due in most part to the extremely high mutational burden (TMB) in cSCC, making sense of it’s non-coding and regulatory regional genomic variation has lagged that of other far less common cancers. This study presents the first investigation of mutations at CCCTC-binding factor binding sites (CTCFbs) of Topologically associating domains (TAD) across defined cSCC progression stages—primary non-metastatic (PNM), primary metastat-ic (PM), and lymph node metastasis (LNM).

  Study EGAS50000001686

• RNA-seq from ASCENT cohort

  Bulk RNA sequencing data generated from primary resected non-small cell lung cancer (NSCLC) tumour tissue collected through the ASCENT study.

  Study EGAS50000001969

• IMC-F106C-101 dose escalation

  Brenetafusp is an ImmTAC bispecific (PRAME×CD3) targeting the cancer testis antigen PRAME. In this phase 1 study (NCT04262466), 126 HLA-A*02:01+ patients with advanced solid tumors received weekly IV doses from 0.3-320 mcg. The primary objective was to identify the maximum tolerated dose (MTD) or recommended phase 2 dose (RP2D); additional objectives included pharmacokinetics, pharmacodynamics, and preliminary anti-tumor activity. Brenetafusp demonstrated manageable safety and preliminary efficacy in PRAME+ tumors. A phase 3 trial in metastatic cutaneous melanoma is ongoing

  Study EGAS50000001976

• RNA-seq for "A preinvasive regulatory T cell axis for lung cancer interception" paper

  Bulk RNA sequencing data generated from primary resected non-small cell lung cancer (NSCLC) tumour tissue collected through the ASCENT study (Analysis of Screen-Detected Lung Cancers’ Genomic Traits; NCT04204499). The dataset comprises tumour RNA-seq from 89 patients with CT screen-detected NSCLC, predominantly early-stage disease, including lung adenocarcinoma and lung squamous cell carcinoma. The RNA-seq data were used to characterise tumour-immune transcriptional programmes and were analysed alongside matched peripheral blood immune profiling and clinical follow-up data.

  Dataset EGAD50000002852

• LUAD RNAseq – LORD

  RNA-seq data from paired normal and adenocarcinoma lung samples obtained from 515 patients that underwent lung cancer surgery.

  Study EGAS50000001705

• LUAD RNAseq - LORD

  The Lung Oncology Research and Discovery (LORD) program is a multi-omics translational initiative aimed at advancing precision medicine in lung cancer. It builds on a lung tissue biobank and leverages biological samples collected from patients who underwent lung cancer surgery at the IUCPQ-UL (Quebec City, Canada). LORD is therefore a single-site, retrospective, case-only study. Genomic profiling of biobanked samples is ongoing, with samples being analyzed sequentially in phases defined by sample type and omic modality. For this dataset, we provide RNA-seq data from paired normal and adenocarcinoma lung samples obtained from 515 patients.

  Dataset EGAD50000002450

• MOSAIC Window Glioblastoma Data

  This dataset will include Spatial Transcriptomics, Single-Cell RNA-Seq, Bulk RNA-Seq, Clinical data, WES, and H&E data from 10 Glioblastoma (GBM) Cancer patients. Researchers from private or public institutions outside the MOSAIC Consortium will be able to apply to access this data and, pending approval, use the data for their research.

  Dataset EGAD50000001352

• Non-invasive anal (pre)cancer dataset

  Molecular analysis of DNA from human anal swabs offers a non-invasive method for anal cancer screening. Current guidelines recommend anal swab-based screening and highlight the need for objective biomarkers to improve risk stratification. We performed genome-wide methylation profiling on DNA from 86 anal swab samples, including 40 HSIL-AIN3 cases (high-grade squamous intraepithelial lesions), 39 controls (<=LSIL), and 7 anal cancer patients, using the 850K Infinium MethylationEPIC BeadChip (Illumina). From this analysis, we identified a three-gene methylation classifier that showed strong discriminatory performance in distinguishing HSIL-AIN3 and anal cancer from <=LSIL lesions and successfully identified all anal cancer cases when applied to an independent validation cohort.

  Dataset EGAD00010002832