8215 results for "canc*"

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• Colossus Project Single-nuclei RNA sequencing

  Single-nuclei RNA sequencing of human colorectal cancer samples. Nuclei were isolated on ice, followed by single-nuclei RNA-sequencing library preparation using the Chromium Single Cell 3’ reagent kit v3.1 (10x Genomics, Pleasanton, CA) Fastq files, N=18

  Dataset EGAD50000003002

• Colossus Project Whole exome sequencing

  Whole exome sequencing of colorectal cancer samples from stage 2/3 human patients. Whole-genome DNA libraries were prepared with the KAPA HyperPlus kit (Roche, Cape Town, South Africa), and exome fragments were captured using the SureSelect Human All Exon V7 kit (Agilent, Hangzhou, China) Fastq files, N=88

  Dataset EGAD50000003003

• Colossus Project Bulk Tumor RNA sequencing

  Bulk RNA sequencing of colorectal cancer samples from stage 2/3 human patients. RNA extraction using Qiagen RNeasy FFPE Extraction kit (Qiagen, UK), followed by RNA sequencing library generation with the QuantSeq 3' mRNA-Seq Library Prep Kit (FWD) (Illumina, USA). Fastq files, N=295

  Dataset EGAD50000003004

• Colossus Project Whole Genome Sequencing

  Low-coverage whole genome sequencing of colorectal cancer samples from stage 2/3 human patients. Tumor DNA from biopsies was extracted using the QIAamp circulating nucleic acid kit (Qiagen, UK), followed by generation of shot-gun whole genome libraries using the KAPA library preparation kit (KAPA Biosystems). Fastq files, N=295

  Dataset EGAD50000003005

• Expansion and cytotoxicity of mucosal T cells in enterocolitis associated with BCMA CAR-T cell therapy

  This study investigates immune effector cell enterocolitis (IEC-EC) associated with ciltacabtagene autoleucel (cilta-cel), a B-cell maturation antigen (BCMA)-targeting chimeric antigen receptor (CAR) T-cell therapy for relapsed or refractory multiple myeloma. IEC-EC was characterized by infiltration and expansion of clonal CAR-positive cytotoxic T-cell populations within the gastrointestinal tract. Molecular analyses were performed to characterize CAR T-cell clonality, persistence, vector integration, and genomic alterations associated with this complication. This dataset contains whole-genome sequencing (WGS) and whole-exome sequencing (WES) FASTQ files generated as part of the study and associated with the corresponding manuscript.

  Study EGAS50000002146

• Circulating tumour DNA in oligoprogressing metastatic castration-resistant prostate cancer treated with stereotactic body radiotherapy in the TRAP trial

  The TRAP trial (NCT03644303) reported that stereotactic body radiotherapy (SBRT) of up to two imaging-visible metastases in prostate cancer patients showing disease progression whilst continuing an androgen receptor pathway inhibitor (ARPI) improved outcomes. It is possible that the benefit from treatment is heterogeneous and patients with progressing sub-clinical metastases, not detected by imaging, derived no benefit from this intervention. The goal of this study was to determine if ctDNA levels detected before SBRT associates with worse outcome.

  Study EGAS50000002152

• Breast Cancer Atlas Research Consortium (BCARC)

  The Breast Cancer Atlas Research Consortium (BCARC) is an international translational research programme building a multi-modal atlas of breast cancer across subtypes, disease progression states, and treatment phases. Founding investigators span the Swarbrick Laboratory (Garvan Institute of Medical Research, Sydney), the Perou Laboratory (University of North Carolina at Chapel Hill), the Grimmond Laboratory (University of Melbourne Centre for Cancer Research), the Al'Khafaji Laboratory (Broad Institute of MIT and Harvard), and the Lundeberg Laboratory (KTH Royal Institute of Technology, Stockholm). Samples are drawn from primary and metastatic breast tumours together with matched adjacent tissues and where available, blood samples. All samples derive from participants consented under Garvan-approved research protocols. Access is controlled and governed by the BCARC data access agreement; requests are reviewed by the Data Access Committee named in the associated policy record

  Study EGAS00001008520

• Germline whole-genome sequencing (WGS) of colorectal cancer patients

  Whole-genome sequencing (WGS) data generated from matched germline blood DNA samples obtained from patients with primary or metastatic colorectal adenocarcinoma (n=37). These data were generated as part of a multiomic study integrating whole-genome sequencing with single-cell multiome profiling to investigate recurrent epigenetic alterations in colorectal cancer evolution and the tumour microenvironment.

  Dataset EGAD50000002942

• Whole Genome Sequencing (WGS) of Tumour Samples of Primary and Metastatic Colorectal Cancer

  WGS samples of primary (n=33) and metastatic (n=11) colorectal cancer tissues related to Livanova et al. manuscript 'Epigenetic evolution of colorectal cancer and its microenvironment reveals new vulnerabilities'

  Dataset EGAD50000002943

• Single-cell 10x Genomics Multiome ATAC-seq data from primary and metastatic colorectal cancers and normal colon tissues

  This dataset contains single-cell 10x Genomics Multiome ATAC-seq data from 33 primary colorectal cancer, 11 metastatic colorectal cancer, and 7 matched normal colon tissue samples generated as part of the study "Epigenetic evolution of colorectal cancer and its microenvironment reveals novel vulnerabilities."

  Dataset EGAD50000002944

• Single-cell 10x Genomics Multiome RNA-seq data from primary and metastatic colorectal cancers and normal colon tissues

  This dataset contains single-cell 10x Genomics Multiome RNA-seq data from 33 primary colorectal cancer, 11 metastatic colorectal cancer, and 7 matched normal colon tissue samples generated as part of the study "Epigenetic evolution of colorectal cancer and its microenvironment reveals novel vulnerabilities."

  Dataset EGAD50000002945

• 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

• METABRIC

  The elucidation of breast cancer subgroups and their molecular drivers requires integrated views of the genome and transcriptome from representative numbers of patients. We present an integrated analysis of copy number and gene expression in a discovery and validation set of 997 and 995 primary breast tumours, respectively, with long-term clinical follow-up. Inherited variants (CNVs, SNPs) and acquired somatic copy number aberrations (CNAs) were associated with expression in 40% of genes, although the landscape was dominated by cis and trans-acting CNAs. By delineating expression outlier genes driven in cis by CNAs, we identified putative cancer genes, including deletions in PPP2R2A, MTAP, and MAP2K4. Unsupervised analysis of paired DNA/RNA profiles revealed novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort. These include a high-risk, ER-positive 11q13/14 cis-acting subgroup and a favourable prognosis subgroup devoid of CNAs. Trans-acting aberration 0152hotspots were found to modulate subgroup-specific gene networks, including a TCR deletion-mediated adaptive immune response in the 0152CNA-devoid sub-group and a Basal-specific chromosome 5 deletion-driven mitotic network. Our results provide a novel molecular stratification of the breast cancer population, derived from the impact of somatic copy number aberrations on the transcriptome.

  Study EGAS00000000083

• 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 correlates with survival after treatment of oesophageal adenocarcinoma by surgery alone

  A 451 cancer-associated gene panel, described in McCabe et al. 2019, was used to assess genomic alterations associated with survival in a Swedish cohort of 65 oesophageal adenocarcinoma (OAC) patients who underwent surgical resection without perioperative treatment. Primary tumour tissues and matched normal squamous oesophagus tissues were collected from each individual. Laboratory studies were performed at the Centre for Applied Medical Research (AMR) and sequencing was performed at the Kinghorn Cancer Centre. 64 of 65 cancer samples and 61 matched squamous oesophageal mucosa control tissues were successfully sequenced and passed minimal quality metrics.

  Study EGAS50000002190

• 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