{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Felsheim BM"],"funding":["Breast Cancer Research Foundation (BCRF)","U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)","Susan G. Komen (Susan G. Komen Breast Cancer Foundation)","NCI NIH HHS","NIGMS NIH HHS"],"pagination":["24"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11890565"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["11(1)"],"pubmed_abstract":["Triple-negative breast cancer (TNBC) is an aggressive and heterogeneous disease that remains challenging to target with traditional therapies and to predict risk. We provide a comprehensive characterization of 238 stage II-III TNBC tumors with paired RNA and DNA sequencing data from the CALGB 40603 (Alliance) clinical trial, along with 448 stage II-III TNBC tumors with paired RNA and DNA data from three additional datasets. We identify DNA mutations associated with RNA-based subtypes, specific TP53 missense mutations compatible with potential neoantigen activity, and a consistently highly altered copy number landscape. We train exploratory multi-modal elastic net models of TNBC patient overall survival to determine the added impact of DNA-based features to RNA and clinical features. We fin"],"journal":["NPJ breast cancer"],"pubmed_title":["Prognostic and molecular multi-platform analysis of CALGB 40603 (Alliance) and public triple-negative breast cancer datasets."],"pmcid":["PMC11890565"],"funding_grant_id":["U10CA180882","T32 GM135123","R01-CA14876","U10 CA180882","P50 CA058223","UG1 CA233180","BCRF-23-127","U24 CA196171","SAC-160074","P50-CA058223","U10 CA180821","U10 CA180888","U10CA180821","U24CA176171"],"pubmed_authors":["Sikov WM","Tolaney SM","Felsheim BM","Hoadley KA","Carey LA","Pfefferle AD","Somlo G","Perou CM","Fernandez-Martinez A","Fan C","Hayward MC","Rashid NU"],"additional_accession":[]},"is_claimable":false,"name":"Prognostic and molecular multi-platform analysis of CALGB 40603 (Alliance) and public triple-negative breast cancer datasets.","description":"Triple-negative breast cancer (TNBC) is an aggressive and heterogeneous disease that remains challenging to target with traditional therapies and to predict risk. We provide a comprehensive characterization of 238 stage II-III TNBC tumors with paired RNA and DNA sequencing data from the CALGB 40603 (Alliance) clinical trial, along with 448 stage II-III TNBC tumors with paired RNA and DNA data from three additional datasets. We identify DNA mutations associated with RNA-based subtypes, specific TP53 missense mutations compatible with potential neoantigen activity, and a consistently highly altered copy number landscape. We train exploratory multi-modal elastic net models of TNBC patient overall survival to determine the added impact of DNA-based features to RNA and clinical features. We fin","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Mar","modification":"2026-06-01T20:12:19.749Z","creation":"2025-04-06T08:35:06.193Z"},"accession":"S-EPMC11890565","cross_references":{"pubmed":["40057511"],"doi":["10.1038/s41523-025-00740-z"]}}