{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina HiSeq 4000;ILLUMINA"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001004113"],"sample_count":["1281"],"description":["EGA dataset EGAD00001004113"],"repository":["EGA"],"title":["Clinical sequencing in multiple myeloma"],"pubmed_abstract":["The purpose of this study is to identify prognostic markers and treatment targets using a clinically certified sequencing panel in multiple myeloma. We performed targeted sequencing of 578 individuals with plasma cell neoplasms using the FoundationOne Heme panel and identified clinically relevant abnormalities and novel prognostic markers. Mutational burden was associated with maf and proliferation gene expression groups, and a high-mutational burden was associated with a poor prognosis. We identified homozygous deletions that were present in multiple myeloma within key genes, including CDKN2C, RB1, TRAF3, BIRC3 and TP53, and that bi-allelic inactivation was significantly enriched at relapse. Alterations in CDKN2C, TP53, RB1 and the t(4;14) were associated with poor prognosis. Alterations in RB1 were predominantly homozygous deletions and were associated with relapse and a poor prognosis which was independent of other genetic markers, including t(4;14), after multivariate analysis. Bi-allelic inactivation of key tumor suppressor genes in myeloma was enriched at relapse, especially in RB1, CDKN2C and TP53 where they have prognostic significance."],"pubmed_title":["Bi-allelic inactivation is more prevalent at relapse in multiple myeloma, identifying RB1 as an independent prognostic marker."],"pubmed_authors":["Chavan S S SS, He J J, Tytarenko R R, Deshpande S S, Patel P P, Bailey M M, Stein C K CK, Stephens O O, Weinhold N N, Petty N N, Steward D D, Rasche L L, Bauer M M, Ashby C C, Peterson E E, Ali S S, Ross J J, Miller V A VA, Stephens P P, Thanendrarajan S S, Schinke C C, Zangari M M, van Rhee F F, Barlogie B B, Mughal T I TI, Davies F E FE, Morgan G J GJ, Walker B A BA"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-UAMS-09-05-2018-19:35:00:131-1808 - samples","description":"DNA (n=1281) and RNA (n=767) were extracted from bone marrow aspirates where CD138+ selection had been performed to enrich plasma cells from patients with monoclonal gammopathy of undetermined significance (MGUS), smoldering multiple myeloma (SMM), or multiple myeloma (MM).  DNA and/or RNA were sent to Foundation Medicine where targeted sequencing was performed using their Foundation 1 Heme panel.  Resulting BAM files were returned along with annotations for somatic events including single nucleotide mutations, indels and structural rearrangements.","dates":{"updated":"2018-05-17 14:50:59"},"accession":"EGAD00001004113","cross_references":{"TAXONOMY":["9606"],"pubmed":["28234347"],"EGA":["EGAC00001000845","EGAS00001002874"]}}