8432 results for "canc*"

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• BioKey: T cell Trafficking and Expansion as Early Indicators of Sustained Clinical Response to Immune Checkpoint Blockade

  BioKey (NCT03197389) is a single-center, open-label, non-randomized window-of-opportunity study conducted at University Hospitals Leuven in female patients with non-metastatic, newly diagnosed primary invasive breast cancer (ER−/PR− or ER+). Patients in cohort A (n=27) were treatment-naïve and received a single dose of pembrolizumab (anti-PD1) 9±2 days before surgery. Patients in cohort B (n=11) received neoadjuvant chemotherapy for 20–24 weeks followed by a pembrolizumab boost before surgery. In both cohorts, a tumor biopsy and a paired peripheral blood sample were collected before anti-PD1 (baseline) and again at the time of surgery (after-boost), yielding paired samples from 38 patients in total. Single-cell data were generated to investigate T cell and B cell trafficking between tumor and blood during anti-PD1 treatment in early-stage breast cancer and complement the previously deposited BioKey tumor scRNA-seq and scTCR-seq dataset (EGAS00001004809).

  Study EGAS50000002113

• PBMCs Bellini TNBC anti-PD1 monotherapy

  Immune checkpoint blockade (ICB) combined with chemotherapy (CT) has improved outcome in high-risk early-stage triple-negative breast cancer (TNBC); yet it is unclear which patients benefit from the addition of ICB beyond chemotherapy alone. We profiled 67 serial tumor and 175 blood samples obtained before and during anti-PD1 treatment across 3 breast cancer trials using single-cell transcriptomic and T cell receptor (TCR) sequencing. Early intratumoral T cell expansion emerged as a consistent hallmark of clinical benefit. This expansion was reflected in increased TCR sharing between tumor and blood after treatment initiation, with shared blood T cells displaying immune-activated programs and their tumor counterparts enriched for expanding clonotypes, suggesting blood-to-tumor trafficking of activated T cells. In TNBC treated with anti-PD1+CT, T cell expansion distinguished an immune-driven response from a chemotherapy-dominant route to pathological complete response (pCR). To enable baseline patient stratification, we derived a 15-gene tumor signature predictive of T cell expansion, which associated with response in independent breast cancer cohorts and with improved survival across ICB-treated cancer types. Our data establish T cell expansion as an early marker of sustained ICB response and could allow stratification of patients likely to benefit from the addition of ICB to chemotherapy.

  Study EGAS50000002067

• Multi-omics datasets (WES, RNA-seq) of mesothelioma MIST3 study, a phase IIA AXL/PD1 inhibition clinical trial

  This study comprises 26 mesothelioma patients with whole exome and RNA sequencing, aimed to reveal tumour intrinsic and extrinsic features that confer responsiveness.

  Study EGAS50000001704

• Spatial Profiling Uncovers a High-Risk Stromal-Fibrotic Subtype in Hormone Receptor-Positive, HER2-Negative Breast Cancer

  This study characterizes the spatial transcriptomic landscape of treatment-naive hormone receptor-positive, HER2-negative invasive breast carcinomas of no special type. Spatial transcriptomic profiling was performed on 86 tumors from 85 patients and integrated with histopathological annotation and cell-type deconvolution. The analyses were used to identify spatially defined molecular and microenvironmental patterns and to derive the Spatial4HR+ subtypes. These subtypes were subsequently evaluated for biological characteristics and clinical outcome associations.

  Study EGAS50000002228

• Genomic variants in 121 genes associated with ovarian cancer in cancer tissue and derived organoids

  High-grade serous ovarian cancer (HGSOC) likely originates from the fallopian tube (FT) epithelium, but advanced stages are mostly found outside the FT. We used ex-vivo cultures of HGSOC and knock-out of tumor suppressors in FT organoids to study changes in epithelial cells and niche requirements for normal and transformed FT cells. We found that transformed cells require BMP signaling and are growth arrested in Wnt rich medium. A SureSelectXT Automation Custom Capture Library (Agilent) target enrichment panel was designed. The enrichment panel comprised all coding exons of 121 genes associated with ovarian cancer. Capture was performed according to the manufacturer’s instructions using an NGS Workstation Option B (Agilent) for automated library preparation starting with 3 μg DNA per sample. Sequencing was performed on a Illumina Hiseq 2500 system gnerating 2x100bp paired end reads and a target coverage of >200 per sample. Sequence reads were mapped to the haploid human reference genome (hg19) using BWA. Variants where called with FreeBayes v1.1.

  Dataset EGAD00001005279

• Deep multi-region WGS of lung cancer tumours

  Deep WGS (germline and 2-5 tumour regions) was performed on 20 patients: 13 lung adenocarcinoma, 5 squamous cell carcinoma, 2 small-cell lung cancers. A total of 68 BAM files are provided, where tumours were sequenced to 60x or 150x depth.

  Dataset EGAD00001005287

• LINE luminal breast cancer Neoadjuvant Chemotherapy Study (2019-08-28)

  A targeted gene screen of 365 known cancer genes in luminal breast cancer samples pre-chemotherapy and at resection post-chemotherapy to evalaute clonal expansion of chemotherapy cancer cells. . This dataset contains all the data available for this study on 2019-08-28.

  Dataset EGAD00001005297

• Patient-derived lung cancer organoids

  Patient-derived lung cancer organoids cram files : targeted seq 13 samples, whole exome seq 12 samples mutation profiles of PDO and matched tissue : aggregated vcf 1 file details : https://www.nature.com/articles/s41467-019-11867-6

  Dataset EGAD00001005317

• Exome and Transcriptome for gynecologic cancer gene-drug analysis

  Total of 180 gynecologic tumor specimens were subjected for targeted-exome and/or whole-transcriptome sequencing.

  Dataset EGAD00001005331

• August 2019 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  August 2019 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001005335