5498 results for "*oma"

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• microRNA and isomiR profiling of Stage 1 epithelial ovarian carcinoma

  Study EGAS00001006617

• 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

• 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

• Cell-free DNA methylation profiling in classic Hodgkin lymphoma using cfEM-seq

  Genome-wide DNA methylation profiling using cfEM-seq and Ultima Genomics sequencing in classic Hodgkin lymphoma. The study includes plasma-derived cell-free DNA from patients with classic Hodgkin lymphoma together with classic Hodgkin lymphoma and anaplastic large cell lymphoma cell lines. The deposited data comprise original sequencing CRAM files and associated sequencing-provider QC metadata.

  Study EGAS50000002038

• Integrative_Oncogenomics_of_Multiple_Myeloma

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from Multiple Myeloma patient DNA and matched normal DNA from the same patients. Two lanes of Illumina GA sequencing will be performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00001000036

• Chondrosarcoma_Exome_

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from Chondrosarcoma cancer and matched normal DNA from the same patients. Next Generation sequencing will be performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes

  Study EGAS00001000038

• Whole genome sequencing, SNP array and RNA-seq of uveal melanomas

  We conducted whole genome sequencing and DNA SNP array of 12 uveal melanoma genomes and their matched DNA from blood. We also conducted RNA-seq of the 12 tumour samples.

  Study EGAS00001000472

• Angiosarcoma_whole_exome

  Extension of angiosarcoma whole genome sequencing study

  Study EGAS00001000588

• RNAseq_of_patients_with_Ewings_sarcoma

  Cancer is driven my mutations in the genome. We will uncover the mutations that give rise to Ewing’s sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewings’ sarcoma tumours.

  Study EGAS00001000267