{"entity":{"id":"paper-santonja-tumour-informed-vs-naive-breast-embo-mol-med-2023","kind":"paper","name":"Comparison of tumor-informed and tumor-naïve sequencing assays for ctDNA detection in breast cancer","aka":[],"tldr":"In breast cancer, blood tests built from each patient's tumour mutations found the smallest amounts of tumour DNA, down to a few parts per million when thousands of mutations were tracked.","summary":"Serial plasma from patients with breast cancer was analysed with tumour-informed and tumour-naive assays for structural variants, single-nucleotide variants and copy-number changes, by multiplex PCR, hybrid capture and whole-genome sequencing at different depths. ctDNA dynamics and allele fractions were highly concordant between assays, and tumour-informed assays were the most sensitive at low concentrations. Hybrid capture targeting 1,347 to 7,491 tumour-identified mutations detected ctDNA down to an allele fraction of 0.00024 per cent (2.4 parts per million); multiplex PCR targeting 21 to 47 structural variants detected it down to 0.00047 per cent (4.7 parts per million).","asOf":"2026-11-04","links":[{"label":"Santonja et al., EMBO Mol Med 2023","url":"https://doi.org/10.15252/emmm.202216505"},{"label":"PubMed","url":"https://pubmed.ncbi.nlm.nih.gov/37161793/"}],"tags":[],"related":[],"cancers":["breast-cancer"],"sections":["diagnostics"],"technologies":["mrd-testing"],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["mrd","ctdna","tumour-informed-assay"],"trials":[],"people":[],"bottlenecks":[],"keyPapers":[],"journals":[],"dependsOn":[],"notes":[],"journal":"EMBO Molecular Medicine","year":2023,"doi":"10.15252/emmm.202216505","pmid":"37161793","authors":"Santonja A, Cooper WN, Eldridge MD, et al.","paperType":"methods","findings":["Hybrid capture of 1,347 to 7,491 mutations: detection down to 2.4 ppm.","Multiplex PCR of 21 to 47 structural variants: detection down to 4.7 ppm."],"whatItMeans":"Parts-per-million detection in breast cancer needs thousands of tracked mutations or a smaller set of structural variants; detection still pools them all, so it does not say which clone is present.","caveats":["Lowest detected values, not 95 per cent limits of detection."]},"route":"/key-papers/paper-santonja-tumour-informed-vs-naive-breast-embo-mol-med-2023/","neighbours":{"cancer":[{"id":"breast-cancer","kind":"cancer","name":"Breast cancer (all types)","route":"/cancers/breast-cancer/"}],"section":[{"id":"diagnostics","kind":"section","name":"Diagnostics & Biomarkers","route":"/fronts/diagnostics/"}],"technology":[{"id":"mrd-testing","kind":"technology","name":"MRD / molecular residual disease testing","route":"/technologies/mrd-testing/"}],"term":[{"id":"ctdna","kind":"term","name":"Circulating tumour DNA (ctDNA)","route":"/terms/ctdna/"},{"id":"mrd","kind":"term","name":"Minimal / molecular residual disease (MRD)","route":"/terms/mrd/"},{"id":"tumour-informed-assay","kind":"term","name":"Tumour-informed versus tumour-naive ctDNA assays","route":"/terms/tumour-informed-assay/"}]}}