8253 results for "canc*"

in 15.14 milliseconds.

• Human breast cancer epigenetic sequencing data

  Controlled-access sequencing data generated from human breast tumor samples in the study "Epigenetic Heterogeneity in Breast Tumors with Implications for Disease Diagnosis and Monitoring". The dataset includes whole-genome DNA methylation sequencing, enzyme-mediated methylation sequencing of sorted tumor-cell populations, single-nucleus CUT&Tag, and single-cell RNA and chromatin-accessibility multiome sequencing. Raw sequencing data are provided as FASTQ files.

  Dataset EGAD50000002972

• ICGC PanCancer Analysis of Whole Genomes

  The Pancancer Analysis of Whole Genomes (PCAWG) study is an international collaboration to identify common patterns of mutation in more than 2,800 cancer whole genomes from the International Cancer Genome Consortium. Building upon previous work which examined cancer coding regions (Cancer Genome Atlas Research Network, The Cancer Genome Atlas Pan-Cancer analysis project, Nat. Genet. 2013 45:1113), this project is exploring the nature and consequences of somatic and germline variations in both coding and non-coding regions, with specific emphasis on cis-regulatory sites, non-coding RNAs, and large-scale structural alterations.

  Study EGAS00001001692

• CRCbiome: Gut metagenome of Norwegian screening participants using FIT sampling

  The study aims to characterize the gut metagenome of Norwegian screening participants and assess the ability of the gut metagenome to identify those at need for colonoscopy. Background: Colorectal cancer (CRC) screening reduces CRC incidence and mortality. However, current screening methods are either hampered by invasiveness or suboptimal performance, limiting their effectiveness as primary screening methods. To aid in the development of a non-invasive screening test with improved sensitivity and specificity, we have initiated a prospective biomarker study (CRCbiome), nested within a large randomized CRC screening trial in Norway. We aim to develop a microbiome-based classification algorithm to identify advanced colorectal lesions in screening participants testing positive for an immunochemical fecal occult blood test (FIT). We will also examine interactions with host factors, diet, lifestyle and prescription drugs. The prospective nature of the study also enables the analysis of changes in the gut microbiome following the removal of precancerous lesions. Methods: The CRCbiome study recruits participants enrolled in the Bowel Cancer Screening in Norway (BCSN) study, a randomized trial initiated in 2012 comparing once-only sigmoidoscopy to repeated biennial FIT, where women and men aged 50–74 years at study entry are invited to participate. Since 2017, participants randomized to FIT screening with a positive test result have been invited to join the CRCbiome study. Self-reported diet, lifestyle and demographic data are collected prior to colonoscopy after the positive FIT-test (baseline). Screening data, including colonoscopy findings are obtained from the BCSN database. Fecal samples for gut microbiome analyses are collected both before and 2 and 12 months after colonoscopy. Samples are analyzed using metagenome sequencing, with taxonomy profiles, and gene and pathway content as primary measures. CRCbiome data will also be linked to national registries to obtain information on prescription histories and cancer relevant outcomes occurring during the 10 year follow-up period. Discussion: The CRCbiome study will increase our understanding of how the gut microbiome, in combination with lifestyle and environmental factors, influences the early stages of colorectal carcinogenesis. This knowledge will be crucial to develop microbiome-based screening tools for CRC. By evaluating biomarker performance in a screening setting, using samples from the target population, the generalizability of the findings to future screening cohorts is likely to be high.

  Study EGAS50000000170

• Non-small cell lung cancer sequencing

  Study EGAS00001005499

• The evolutionary dynamics of human colorectal cancer using single-gland spatial multi-omic profiling of DNA, RNA and chromatin.

  Study EGAS00001005827

• WES of breast cancer patients and controls

  This study assessed the variant profiles of 408 samples from 126 breast cancer patients with various survival outcomes, including paired uninvolved mammary gland samples collected at proximal distances from primary lesions. As a reference, control samples from 15 mammoplasty individuals without cancer history were studied. Whole exome sequencing was performed to identify post-zygotic and germline variants present in the studied samples. Variant annotation in known databases, interpretation, and statistical analyses followed to discern the clinical relevance of called variants.

  Study EGAS50000000539

• Zanidatamab in Patients with Early Stage HER2-positive Breast Cancer: The NeoZanHER Phase 2 Single-Arm Open-Label Trial

  Strategies are needed to avoid chemotherapy in early stage HER2-positive (HER2+) breast cancer (BC). We conducted a neoadjuvant therapy trial with zanidatamab, a dual HER2-directed bispecific antibody, in patients with 1-3 cm, node-negative HER2+ BC. Primary endpoint was pathologic complete response (pCR). Secondary endpoints were radiographic response by ultrasound and magnetic resonance imaging. US and MRI, pathologic response by residual cancer burden (RCB), rate of adverse events, feasibility of accrual and biomarkers of response. Fifteen patients with HER2 IHC 3+, and 5 with HER2 IHC 2+/ISH+ BC were enrolled. Patients received zanidatamab 20 mg/kg every 2 weeks for 6 (n=11) or 10 doses (n=9). Fourteen patients also received endocrine therapy. At 6 weeks, there was a significant decrease in tumor size and volume. At surgery, six patients (30%) had pCR, meeting the prespecified pCR target, and four had limited RCB (RCB-1; 20%). Treatment was well tolerated. All patients with pCR had HER2 IHC 3+ tumors, ERBB2 amplification on WES, PAM50 HER2-high subtype, and a trend towards higher HER2 mRNA expression (p=0.06). In conclusion, de-escalation to HER2-targeted therapy alone may be feasible. Further research is needed to refine patient selection.

  Study EGAS50000001930

• Oslo University Hospital Data Access Committee for I-BCT study datasets submitted to FEGA Norway

  This is the Data Access Committee appointed by Oslo University Hospital for controlled access to datasets from the Improved Breast Cancer Treatment (I-BCT) study under the Ethical approval reference EU CT 2024-515087-31-00 (Originally approved by REK: 2014/167/REK sør-øst A) .

  Dac EGAC50000001170

• I-BCT-1 (Improved Breast Cancer Therapy) - WXS

  A prospective, randomized neoadjuvant study that evaluates DNA-based biomarkers to identify breast cancer patients most likely to benefit from carboplatin (Cb). While Cb improves outcomes in triple-negative breast cancer (TNBC), responses vary, and its role in aggressive hormone receptor–positive breast cancer (HR+BC) remains uncertain. Patients (N = 187) with early, high-risk, HER2-negative cT2-4 tumors received 12 weekly paclitaxel with or without Cb, followed by four cycles of epirubicin and cyclophosphamide. Whole Exome Sequencing data for normal-tumor pairs from the same subjects is available in the matching study titled I-BCT-1 (Improved Breast Cancer Therapy) - WES

  Study EGAS50000002154

• I-BCT-1 (Improved Breast Cancer Therapy) - WES

  A prospective, randomized neoadjuvant study that evaluates DNA-based biomarkers to identify breast cancer patients most likely to benefit from carboplatin (Cb). While Cb improves outcomes in triple-negative breast cancer (TNBC), responses vary, and its role in aggressive hormone receptor–positive breast cancer (HR+BC) remains uncertain. Patients (N = 187) with early, high-risk, HER2-negative cT2-4 tumors received 12 weekly paclitaxel with or without Cb, followed by four cycles of epirubicin and cyclophosphamide. Transcriptomic analysis data for the tumor samples in this study is available in the matching Study titled I-BCT-1 (Improved Breast Cancer Therapy) - WXS.

  Study EGAS50000002155

• Genomic gain of EBV's LMP-1 in NKTCL

  The study found a high recurrence of genomic gain of LMP1 locus within EBV-associated NKTCL. The pilot data set and extended dataset of 77 WGS NKTCLs found 18/77 tumoral genomes to harbour genomic gain of LMP-1 locus within the EBV viral genomes within NKTCL tumoral sequencing data. The study also found 1/10 NKTCL cell lines to be positive for LMP-1 locus gain within EBV genomes too. This dataset includes solely the confirmatory WGS data of LMP-1 gain from NKYS cell lines using Oxford Nanopore long-read sequencing technology.

  Study EGAS50000000260

• Nanopore whole-genome sequencing of human sarcomas

  We performed single and multi-region nanopore whole-genome sequencing on human sarcoma samples from adult and paediatric patients.

  Study EGAS50000000651

• Bladder cancer subtyping study across 4 atezo clinical trials

  Checkpoint inhibitors targeting the PD-1/PD-L1 interaction have revolutionized cancer therapy across many indications. In urothelial carcinoma (UC), several PD-1/PD-L1 inhibitors have been approved for treatment in localized and metastatic disease. While these agents provide durable clinical benefit in a number of patients, the majority do not respond. A better understanding of the molecular mechanisms underlying response and resistance is needed to tailor existing treatments and develop new therapeutics in UC. We profiled tumors from 2803 patients from four late-stage randomized clinical trials evaluating the PD-L1 inhibitor atezolizumab in metastatic UC and muscle-invasive bladder cancer by RNA-seq, a targeted DNA panel, immunohistochemistry, and digital pathology. A machine learning algorithm identified four UC transcriptional subtypes, representing luminal desert, stromal, immune, and basal tumors. Overall survival benefit from atezolizumab over standard-of-care was observed in immune and basal tumors (45% of patients). Digital pathology showed enrichment of human interpretable features in specific molecular subtypes, and a self-supervised approach could classify molecular subtypes from H&E slides with high accuracy, suggesting that machine-based image interpretation could accelerate tumor molecular profiling. Somatic alterations showed limited capacity to identify responders. Finally, mechanisms of benefit with PD-L1 blockade appeared different in immune and basal tumors, with immune tumors benefiting from B/plasma cell enrichment, while basal tumors benefited from granulocyte enrichment. This study represents the largest integration of UC molecular and curated clinical data in randomized clinical trials to date, paving the way for prospective clinical studies tailoring treatment regimens to specific tumor molecular subtypes in UC and other indications.

  Study EGAS50000000497

• Plasma Nucleosome Profiling Reports on Tumor Burden and Molecular Subtypes in Small Cell Lung Cancer

  Small cell lung cancer (SCLC) is an aggressive malignancy with dismal prognosis and marked transcriptional heterogeneity that drives distinct therapeutic vulnerabilities. The clinical translation of these molecular insights is limited by limited access to tumor biopsies. Here, we apply chromatin immunoprecipitation of cell-free nucleosomes carrying active histone modifications followed by sequencing (cfChIP-seq) to 441 plasma samples from individuals with advanced SCLC, other neuroendocrine carcinomas (NEC), non-SCLC cancers, and healthy controls. cfChIP-seq faithfully captured the epigenetic and transcriptional landscape of tumor-derived cfDNA, including SCLC tissue/cell-of-origin signatures, and yielded a quantitative score of tumor fraction that tracked radiographic burden and prognosis. Integrating plasma cfChIP-seq with matched tumor transcriptomes (n = 73, including 41 time-matched pairs), we show that cfChIP-seq levels at promoters of lineage-defining transcription factors (ASCL1, NEUROD1, POU2F3, and ATOH1) correlate strongly with tumor RNA and support noninvasive inference of SCLC transcriptional subtypes directly from plasma. These findings establish cfChIP-seq as a practical liquid-biopsy platform that reports real-time tumor state and subtype, enabling precision monitoring and laying the groundwork for subtype-informed therapeutic stratification in SCLC.

  Study EGAS50000001916

• Liquid Biopsy-informed Precision Oncology Study to Evaluate the Clinical Utility of Non-invasive Genomic Profiling for Cancer Treatment Selection

  DAC for EGA study: "Liquid Biopsy-informed Precision Oncology Study to Evaluate the Clinical Utility of  Non-invasive Genomic Profiling for Cancer Treatment Selection".

  Dac EGAC50000001165

• Nanopore Amplicon Sequencing data of 33 patient tumor and one primary cell line samples - all uveal melanoma

  Nanopore Amplicon Sequencing data of 4 amplicons in the GNA11, GNAQ, SF3B1 and SRSF2 genes in 33 uveal melanoma patient tumor samples and one primary cell line sample. Sequencing was performed on a MinION platform (Mk1B) using the SQK-RBK114.24 kit multiplexing 24 samples per flow cell. Basecalling was performed using the dna_r10.4.1_e8.2_400bps_sup@v4.3.0 model and dorado v.0.6.2.

  Study EGAS50000002137

• Liquid Biopsy-informed Precision Oncology Study to Evaluate the Clinical Utility of Non-invasive Genomic Profiling for Cancer Treatment Selection

  This dataset pertains to the first planned analysis of an observational trial assessing the clinical utility of serial LB, combined with precision oncology recommendations by a molecular tumor board (MTB). Serial LBs utilized a clinically validated 33-gene panel next-generation sequencing (NGS) assay. Key eligibility criteria included age≥18years, ECOG performance status 0-1, and advanced/metastatic solid tumors with progression on ≥1 lines of therapy. 50 patients were enrolled between March 2023 and July 2024.

  Study EGAS50000002145

• Evolutionary dynamics in the decades preceding acute myeloid leukaemia

  Somatic evolution in ageing tissues underlies many cancers, yet the quantitative rules governing pre-cancerous evolution remain incompletely understood. This study exploits a collection of serial blood serum samples from the UK Collaborative Trial of Ovarian Cancer Screening (UKCTOCS), collected annually from as early as 15 years before a diagnosis of acute myeloid leukaemia (AML), to provide a quantitative description of pre-cancerous evolutionary dynamics. Longitudinal samples from women who subsequently developed AML, alongside timepoint-matched samples from age-matched cancer-free controls, were sequenced using TETRIS-seq, a deep duplex error-corrected sequencing approach covering a custom panel of single-nucleotide variants and indels, mosaic chromosomal alterations, and chromosomal rearrangements associated with clonal haematopoiesis and AML. Combined with evolutionary modelling, these data quantify the acquisition ages and fitness effects of key driver events in AML development, characterise the clonal dynamics that precede diagnosis, and show that pre-leukaemic evolution is consistent with a small set of evolutionary rules balancing chance and determinism. The deposited data comprise raw paired-end FASTQ files for all sequenced samples.

  Study EGAS50000002168

• Alterations of whole genome and extrachromosomal circular cell-free DNA fragmentomes across the cancer care continuum

  The origins and properties of cancer-associated genetic changes in cell-free DNA (cfDNA) are not fully understood. Through genome-wide analyses of 1,807 samples from 1,064 patients across eight common cancer types, we identified extrachromosomal circular DNA (eccDNA) as a source of cfDNA fragments. Characterization of eccDNA-derived cfDNA fragments along with single base substitutions, small insertions and deletions, rearrangements, and phased variants in single cfDNA molecules, revealed differences between tumor tissues and cfDNA, with an increase in tumor-derived cfDNA alterations at epigenetically repressed regions and a decrease at active promoters. Combination of variant characteristics with individual error rates and machine learning analyses enabled tumor-informed and tumor-independent measures of circulating tumor DNA for early detection, detection of minimal residual disease, and for monitoring patients during therapy. The universal nature of eccDNA and other tumor-derived characteristics of cfDNA may be broadly useful for cancer detection.

  Study EGAS50000001331

• Cryptic mRNA Splicing in FLT3 Internal Tandem Duplications

  NGS analyses of genetic material from Acute Myeloid Leukemia cases harboring FLT3 Internal Tandem Duplications to investigate the occurrence of cryptic mRNA splicing.

  Study EGAS50000002156

• Standardized Molecular Detection of RET and Other Gene Fusions in Thyroid Cancer: A Two-Site Validation Study

  This study validated methods for detecting RET gene alterations in thyroid cancer using molecular testing across two institutions. It found that next-generation sequencing (NGS) reliably identified RET fusions, other gene fusions, and key mutations, with confirmation by FISH and RT-PCR. Results showed a high level of agreement between both institutions, demonstrating the accuracy and reproducibility of the testing methods. These findings support the use of standardized NGS-based protocols to identify patients who may benefit from RET-targeted therapies. 60 DNA and 60 RNA has been sequenced by targeted NGS

  Study EGAS50000001977

• VHIR Data Access Committee 2

  VHIR "Data Access CommitteeStandardized Molecular Detection of RET and Other Gene Fusions in Thyroid Cancer: A Two-Site Validation Study" Data Access Committee

  Dac EGAC50000001089

• Trascriptional profile of primary human NK cells after culture with A549 ß2m-/-

  This dataset comprises the transcriptional profiles of human Natural Killer (NK) cells obtained via bulk RNA sequencing approach. The NK cells were isolated from the peripheral blood mononuclear cells (PBMCs) of six healthy donors and subsequently cultured in the presence of A549 ß2m-/- cancer cells for a duration of 9 days. After culture, RNA was extracted using the QiagenRNeasy Plus Mini Kit (250) (Qiagen, 74136) according to manufacturer's instructions and sequencing was performed on two lanes of the Illumina NovaSeq 6000 instrument resulting in 51nt-long paired-end reads.

  Dataset EGAD50000000819

• RNA-seq fastq files

  RNA-seq fastq files for ER+ breast cancer patients before and after neo-adjuvant endocrine therapy

  Dataset EGAD50000001221

• ctDNA detection in preSBRT samples in oligoprogressing metastatic castration-resistant prostate cancer patients

  Targeted sequencing using the PCF-SELECT capture panel and the KAPA Hypercap workflow on DNA extracted from liquid biopsies to test if ctDNA detection in pretreatment samples associates with worse outcome to stereotactic body radiotherapy in oligoprogressing metastatic castration-resistant prostate cancer patients.

  Dataset EGAD50000003089