{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Scandino R"],"funding":["Ministero della Salute (Ministry of Health, Italy)"],"pagination":["25"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11890748"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["11(1)"],"pubmed_abstract":["Cell-free DNA (cfDNA) extracted from peripheral blood has emerged as a crucial biomarker source in oncology research. To enhance the detection of somatic copy number alterations (SCNAs) and circulating tumor DNA (ctDNA), we developed eSENSES, a 2 Mb breast cancer-targeted NGS panel. It includes 15,000 genome-wide SNPs, 500 focal SNPs in breast cancer driver regions, and exons from 81 commonly altered genes, alongside a custom computational approach. We assessed the performance of eSENSES using both synthetic and clinical samples showing that eSENSES can detect ctDNA levels below 1%, exhibiting high sensitivity and specificity at 2-3% ctDNA levels. In patients with metastatic breast cancer, ctDNA estimations correlated with disease progression. When compared with other technologies and stat"],"journal":["NPJ breast cancer"],"pubmed_title":["Enabling sensitive and precise detection of ctDNA through somatic copy number aberrations in breast cancer."],"pmcid":["PMC11890748"],"funding_grant_id":["GR-2018-12365195"],"pubmed_authors":["Biagioni C","Pestrin M","Casiraghi N","Nardone A","Galardi F","Moretti E","Romagnoli D","Tonina A","Malorni L","Paoli M","Scandino R","Biganzoli L","Genovese M","Benelli M","Migliaccio I","Romanel A"],"additional_accession":[]},"is_claimable":false,"name":"Enabling sensitive and precise detection of ctDNA through somatic copy number aberrations in breast cancer.","description":"Cell-free DNA (cfDNA) extracted from peripheral blood has emerged as a crucial biomarker source in oncology research. To enhance the detection of somatic copy number alterations (SCNAs) and circulating tumor DNA (ctDNA), we developed eSENSES, a 2 Mb breast cancer-targeted NGS panel. It includes 15,000 genome-wide SNPs, 500 focal SNPs in breast cancer driver regions, and exons from 81 commonly altered genes, alongside a custom computational approach. We assessed the performance of eSENSES using both synthetic and clinical samples showing that eSENSES can detect ctDNA levels below 1%, exhibiting high sensitivity and specificity at 2-3% ctDNA levels. In patients with metastatic breast cancer, ctDNA estimations correlated with disease progression. When compared with other technologies and stat","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Mar","modification":"2025-04-04T08:23:08.344Z","creation":"2025-04-04T08:23:08.344Z"},"accession":"S-EPMC11890748","cross_references":{"pubmed":["40057527"],"doi":["10.1038/s41523-025-00739-6"]}}