{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"study_type":["Cancer Genomics"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001004396"],"host":["EGA"],"description":["EGA study EGAS00001004396"],"dataset_title":["Whole Exome Sequencing of 5 FFPE prostate samples (normal and tumour pairs) to identify mutations","smMIP-seq of 18 FFPE prostate samples (normal and tumour pairs) to identify mutations","RNA-seq of 27 FFPE prostate samples (tumour only) to identify gene fusions"],"category":["restricted"],"repository":["EGA"],"name_synonyms":["hereditary prostate cancer, cancer of the prostate, Prostatic Neoplasm, Cancer of the Prostate, Prostate Neoplasms, Neoplasms, Prostatic Cancer, Neoplasm, Prostatic Cancers, Prostatic, familial, prostate cancer, PC, NOS, Cancers, Cancer of Prostate, Prostate Cancer, cancer of prostate, Prostate, Prostate Neoplasm, Cancer, Prostate Cancers."],"description_synonyms":["AI317206, IPP2A2, Health Problem, Materials, Adaptive Immune, p160, RNA Sequence Determination, determination, Sequence Determination, RNA Sequence, Adoptive Immunity, Tumor, CG11482, Repair, limitations, 5730420M11Rik, Mutations, Techniques, Acquired Immunity, Method, Associations, symptoms, Problems, Whole Transcriptome, Transcriptome Sequencing, Analysis, study limitations, Work Flow, Health Problems, SET, me75, Analyses, Genomes, Determination, TAF-I, Complete Exome Sequencing, C1, Whole Transcriptome Sequencing, PMNC, procedures, Sequence Determinations, HSAP, D17Mit170, T1, DmelCG4299, IGAAD, set, Prostatic Neoplasm, Cancer of the Prostate, Methodological Studies, DmelCG10574, ATMSH6, malignant neoplasm, International Health, Lymphoid, Malignancies, Mismatch, COCA2, Tumors, Diagnostic Findings, phapii, SIGNS SYMPTOMS, MUTS HOMOLOG 6-1, screening, MUTS homolog 6, cancer of the prostate, Immunity, Global, DESC, Exome, familial, StF-IT-1, Adaptive, PMN cell, Procedure, Tl3, Tl2, Determinations, immune memory response, Workflows, Benign, count, Adoptive, Genetic Materials, NOS, Lymphoid Cell, dmlh1, Problem, Genetic Material, region, long patch mismatch repair system, Complete Transcriptome, Acquired, HNPCC2, HNPCC5, HLA-DR-associated protein II, mismatch repair, DI-2, I-2Dm, AU044881, Mismatch Repair, signs, Benign Neoplasms, ATMLH1, INSDC_feature:gene, CG4299, whole genome, Methodological, PMS3, PMS2, cancer of prostate, Methodological Study, International, Malignant Neoplasms, Atlases, I-2PP1, International Health Problems, white blood cell, Health, TAF-IBETA, Patient, Material, MLH1, hMLH1, Cells, Whole Exome Sequencing, Cistron, TAF-Ibeta, DNA, other neoplasm, Transcriptome Sequencings, Clinical Finding, i2pp2a, AI561766, AI325952, Work Flows, Prostate, polymorphonuclear cell, dmlh-1, Procedures, Prostate Neoplasms, Complete Exome, Neoplasms, infiltrating, Benign Neoplasm, p55, IMAGE, Gene, Malignant, Symptoms and Signs, PHAPII, Worldwide, DmelCG11482, Prostatic Cancers, Studies, Worldwide Health, Low, Finding, Cancer of Prostate, Technique, MUTL-homologue 1, Prostate Cancers, GTMBP, study, WES, erg-3, Complete, Exome Sequencings, Genetic, MutS/MutL/MutH pathway, Malignancy, 1110035C23Rik, Hybrid Immunity, Direction, ipp2a2, Gtmbp, DNA Mismatch, study., 2pp2a, CG7003, erg_A, ARABIDOPSIS THALIANA MUTL-HOMOLOGUE 1, erg, Sequencing, CG10574, Neoplasias, Study, Whole Exome, Immune Response, AW550279, 2PP2A, RNA Sequence Analyses, acquired immune response, taf-ibeta, Clients, Whole, D030036I24Rik, dSET, dSet, Prostatic, RNA Sequencing, site, Lymphocyte, Cancer, Sequence Analyses, hereditary prostate cancer, RNA, findings, immune cell, Complete Exome Sequencings, Malignant Neoplasm, cou, World, RNA Sequence Determinations, igaad, T10M13.8, World Health, Hybrid Immunities, Cistrons, Client, Cell, group, MSH6-1, International Healths, Exome Sequencing, Signs and Symptoms, T10M13_8, Lr, MT, Hybrid, I-2PP2A, F23J3_170, Prostatic Cancer, chemical analysis, Dm I-2, I2PP2A, Neoplasm, sequence, techniques, Lymphoid Cells, primary cancer, leucocyte, Complete Transcriptome Sequencing, ensemble, Healths, patient, MutL-like pathway, Cancers, International Health Problem, GTBP, malignant tumor, primary structure of sequence macromolecule, Prostate Neoplasm, Adaptive Immune Response, dSET/TAF-Ibeta, DmelCG7003, 2610030F17Rik, FCC2, RNA Sequence Analysis, ARABIDOPSIS THALIANA MUTS HOMOLOG 6, Bra, Response, HNPCC, prostate cancer, PC, assay, F23J3.170, AA407739, Prostate Cancer, Neoplasia, methodology"],"additional_accession":[]},"is_claimable":false,"name":"Detailed molecular and immune marker profiling of archival prostate cancer samples","description":"Prostate cancer is a significant global health issue, and limitations to current patient management pathways often result in overtreatment or undertreatment. New ways to stratify patients are urgently needed. We conducted a feasibility study of such novel assessments, looking for associations between genomic changes and lymphocyte infiltration. An innovative workflow using an in-house targeted sequencing panel, immune cell profiling using an image analysis pipeline, RNA sequencing, and exome sequencing in select cases was tested. Gene fusions were profiled by RNA sequencing in 27 of 27 cases, and a significantly higher tumor-infiltrating lymphocyte (TIL) count was noted in tumors without a TMPRSS2:ERG fusion compared with those with the fusion (P = 0.01). Although this finding was not replicated in a larger validation set (n = 436) of The Cancer Genome Atlas images, there was a trend in the same direction. Differential expression analysis of TIL-high and TIL-low tumors revealed the enrichment of both innate and adaptive immune response pathways. Mutations in mismatch repair genes (MLH1 and MSH6 mutations in 1 of 27 cases) were identified. We describe a potential immune escape mechanism in TMPRSS2:ERG fusion-positive tumors. Detailed profiling, as shown herein, can provide novel insights into tumor biology. Likely differences with findings with other cohorts are related to methods used to define region of interest, but this warrants further study in a larger cohort.","dates":{"updated":"2020-06-18 16:51:49"},"accession":"EGAS00001004396","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAD00001006108","EGAD00001006107","EGAD00001006109","EGAC00001001566"]}}