8224 results for "canc*"

in 25.37 milliseconds.

• High grade serous ovarian cancer germline exome sequencing

  This cohort includes matched germline samples from the same patient cohort. Germline DNA was isolated from whole blood and normal tissue for whole exome sequencing.

  Study EGAS50000001730

• High grade serous ovarian cancer tumor exome sequencing

  Whole exome sequencing data generated from 25 human high grade serous ovarian cancer (HGSOC) specimens. These data were used to characterize somatic mutations, copy number alterations, and genomic features. Raw sequencing data are provided as BAM files.

  Study EGAS50000001731

• Whole-exome and RNA-seq sequencing of HCC of metastatic and de novo origin

  Multifocal hepatocellular carcinoma (mfHCC) arises via intrahepatic metastasis (IM) or multicentric occurrence (MO), We performed whole-exome and RNA-sequencing of 76 tumor biopsies from 22 HCC patients to determine their evolutionary origins.

  Study EGAS50000002057

• G4SCOPE identifies sequence features and epigenetic contexts of chromatin G-quadruplexes

  Cancer-associated epigenetic remodeling involves both DNA secondary structures and covalent cytosine modifications, yet predicting chromatin-constrained G-quadruplex (G4) folding remains challenging. Here, we develop G4SCOPE, a multi-task deep learning framework that predicts G4 occupancy and quantitative CUT&Tag signal directly from DNA sequence in isogenic human breast epithelial cells. Trained across wild-type, TP53-deficient, TP53/BRCA1-deficient and TP53/BRCA2-deficient backgrounds, the model integrates convolutional motif learning with transformer-based self-attention to capture local motifs and broader contextual sequence features without auxiliary epigenomic inputs. It distinguishes chromatin-associated G4s from GC-matched loci with in vitro G4-forming potential, captures quantitative variation in local CUT&Tag signal, and performs consistently across the four breast epithelial genotypes. Independent application in K562 cells further supports the portability of the framework to a distinct cellular context. Model-derived G4 representations also separate loci with distinct local 5-methylcytosine and 5-hydroxymethylcytosine profiles. Together, these results show that DNA sequence can predict chromatin G4 occupancy and quantitative CUT&Tag signal, and that the learned representations reflect differences in local cytosine-modification state.

  Study EGAS50000002094

• BCAC TIIC Data

  Data on spatially-resolved tissue infiltrating immune cells (TIICs) from 17,265 breast cancer patients of European descent, from studies participating in the Breast Cancer Association Consortium, together with linked clinical data.

  Study EGAS50000001477

• RNA sequencing to characterize ALK

  ALK fusions are present in 3–5% of patients with non-small cell lung cancer (NSCLC). These fusions promote ligand-independent dimerization, resulting in constitutive activation of downstream signaling pathways, including RAS–MAPK and PI3K–AKT3. Here, we report the identification and characterization of the ALK in biopsies from a patient with ALK-positive NSCLC progressing on first-line lorlatinib

  Study EGAS50000001779

• Comprehensive Characterization of Early Relapse and End-Stage Relapsed Refractory Multiple Myeloma (HIPO K08K/H067/H021+nonHIPO)

  Study EGAS00001007469

• H021-Master Umbrella study2 (not to be released)

  Study EGAS00001005145

• Cord blood DNA duplex sequencing libraries using deepDLP

  As part of the DeepClone protocols paper we used three cord blood samples to validate the error rate of deepDLP duplex library preparation method. The FASTQs shared below correspond to these three cord blood samples. With this data we concluded that the error rate of the technology is between 1 and 3x10-8 errors per sequence basepair.

  Study EGAS50000002002

• High Grade Serous Ovarian Cancer Whole Exome Sequencing

  Whole exome sequencing (WES) was performed on genomic DNA (50–200 ng) extracted from high-grade serous ovarian cancer (HGSOC) tumor tissue and matched buffy coat or normal tissue. DNA was sheared using a Covaris E220 system to generate fragments of approximately 150–200 bp. Sequencing libraries were prepared using the Agilent SureSelect XT Low Input Library Preparation Kit with unique dual indices. Tumor libraries were enriched using a custom SureSelect V6 + UTR + OneSeq LowRes capture probe set, while germline libraries were enriched using the Agilent SureSelect Human All Exon V6 capture kit supplemented with custom probes. Libraries underwent initial quality control sequencing on the Illumina MiSeq platform, followed by pooled sequencing on the Illumina NovaSeq 6000 using a 300-cycle kit. Archived here are the BAM files for each sample.

  Dataset EGAD50000002488