{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"technology_type":["ILLUMINA, Illumina HiSeq 2500, NextSeq 500, Nanostring"],"study_type":["Other"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001002839"],"host":["EGA"],"description":["EGA study EGAS00001002839"],"dataset_title":["Deep amplicon sequencing to infer malignant clonal populations for The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer","Whole-genome sequence data for The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer","TCR- and BCR-sequencing data for The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer","Nanostring"],"category":["restricted"],"repository":["EGA"],"description_synonyms":["B Cells, determination, Bursa-Dependent Lymphocytes, B cell, T-Lymphocyte, Tumor, Technic, Transcript Expression Analysis, dmTAF[[II]]230, Techniques, diseases, Immunogold-Silver Techniques, T Lymphocyte, Immunogold-Silver Technique, responsivity, Gene Expression Monitorings, diseases and disorders, Analysis, Profilings, immature T cell, treatment, human disease, TFIID TAF250, Genomes, Analyses, cel, T-Cells, T, crosscutting, Gene Expression Analysis, T Cells, Immunogold-Silver Technic, B lymphocyte, malignant neoplasm, Immunolabeling Technique, disease management, Therapies, Homo sapiens disease, Malignancies, Lymphoid, Immunogold Technics, Thymus Dependent Lymphocytes, intersecting, Tumors, Therapy, dTAF[[II]]230, B Lymphocytes, Immunogold Technique, Monitorings, TAF200, TAFII-250, TAF250/230, Immunogold, Gene Expression, Immunogold Techniques, TAFII250, Benign, Immunolabeling Technic, epithelial, T-Cell, Diseases, Immunolabeling Technics, Lymphoid Cell, Technics, oligonucleotide random primer, T-cell, Transcriptome Profilings, p32, Thymus-Dependent, Benign Neoplasms, Immunogold Silver Techniques, whole genome, T-lymphocyte, CG17603, TAF[[II]], Treatments, Thymus-Dependent Lymphocyte, Malignant Neoplasms, disease, metastatic, T cell, Gene Expression Analyses, Patient, Taf250, B-Lymphocyte, SR3-5, Cells, medical condition., Expression Analysis, T Cell, other neoplasm, TAF230, other disease, Immunogold-Silver, d230, Thymus-Dependent Lymphocytes, Neoplasms, Benign Neoplasm, number, IMAGE, Gene, dTAFII250, Malignant, EfW1, presence, Gene Expression Profilings, mRNA Differential Displays, Gene Expression Pattern Analysis, relational shape quality, dmTAF1, Taf230, disease or disorder, MAL, Technique, Immunogold Silver Technics, TAF250, reactivity, Taf200, B-cell, dTAF[[II]]250, pattern, Malignancy, cell, distribution, Transcriptomics, Taf1p, Transcript Expression, Transcriptome Analysis, Monitoring, non-neoplastic, Neoplasias, dTAF250, RANDOM, Clients, mature T cell, heterogeneity, disorder, malignant ovarian serous tumour, serous ovarian cancer, Expression Analyses, TAF, T Lymphocytes, Lymphocyte, Cancer, Profiling, TAF[[II]]250, Transcriptome, Malignant Neoplasm, Immunogold Technic, disorders, Leu2, Immunohistocytochemistry, l(3)84Ab, medical condition, BG:DS00004.13, Client, Cell, dTAF230, Differential Display, transcription profiling, count in organism, Transcript Expression Analyses, MT, p230, chemical analysis, Neoplasm, TAF[[II]]250/230, condition, TFIID, mRNA Differential Display, T lymphocyte, gene expression profiling, Lymphoid Cells, epitheliocyte, Random selection by shearing, Immunolabeling, Taf[[II]]250, Gene Expression Monitoring, primary cancer, Immunocytochemistry, TAF[[II]]230, Transcriptome Profiling, mRNA, intercrossing, INV, Bursa-Equivalent Lymphocyte, Lymphocytes, TAF[II]250, Cancers, Differential Displays, malignant tumor, Transcriptome Analyses, DmelCG17603, Therapeutic, Immunogold-Silver Technics, Immunolabeling Techniques, Treatment, assay, response, CD8, B-lymphocyte, Neoplasia, TAF1"],"name_synonyms":["malignant ovarian serous tumour, serous ovarian cancer."],"additional_accession":[]},"is_claimable":false,"name":"The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer","description":"High-grade serous ovarian cancer exhibits extensive intratumoral heterogeneity coupled with widespread intraperitoneal disease. Despite this, metastatic spread of tumor clones is non-random, implying the existence of local microenvironmental factors that shape tumor progression. We interrogated the molecular interface between tumorinfiltrating lymphocytes (TIL) and cancer cells in 143 samples from 21 patients using whole-genome sequencing, immunohistochemistry, histologic image analysis, gene expression profiling, and T- and B-cell receptor sequencing. We identify 3 immunologic response categories, which frequently co-exist within individual patients. Furthermore, epithelial CD8+ TIL were inversely associated with malignant cell diversity, evidenced by subclonal neoepitope elimination and spatial tracking between tumor and T-cell clones. Intersecting mutational signatures and immune analysis showed that foldback inversion genomic aberrations lead to worse outcomes even in the presence of cytotoxic TIL (n=433). Thus, regional variation in immune contexture mirrors the pattern of intraperitoneal malignant spread, provoking new perspectives for treatment of this challenging disease.","dates":{"updated":"2022-11-22 12:10:03"},"accession":"EGAS00001002839","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAD00010001515","EGAD00001003985","EGAD00001003984","EGAD00001003986","EGAC00001000122","EGAC00000000011"]}}