{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T18:50:47Z","timestamp":1773687047291,"version":"3.50.1"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T00:00:00Z","timestamp":1773619200000},"content-version":"vor","delay-in-days":15,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Chalmers Area of Advance Health Engineering","award":["AoAH2022"],"award-info":[{"award-number":["AoAH2022"]}]},{"name":"Gender Initiative for Excellence"},{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["VR2024-04145"],"award-info":[{"award-number":["VR2024-04145"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Liquid biopsies, coupled with analysis of copy number alterations (CNAs), have emerged as a promising tool for non-invasive monitoring of cancer progression and tumor composition. However, methods utilizing CNA data from liquid biopsies are limited by the low signal in the samples, caused by a low percentage of cancer DNA in the blood, and inherent noise introduced in the sequencing. To address this challenge, we developed BayesCNA, a method designed to improve signal extraction from low-pass liquid biopsy sequencing data, by utilizing a Bayesian changepoint detection algorithm. We use information of the posterior changepoint probabilities to identify likely changepoints, where a changepoint indicates a shift in the copy number state. The signal is then reconstructed using the identified partition. We show the effectiveness of the method on synthetically generated datasets and compare the method with state-of-the-art bioinformatics tools under noisy conditions. Our results show that this novel approach increases sensitivity in detecting CNAs, particularly in low-quality cases.<\/jats:p>","DOI":"10.1093\/bib\/bbag111","type":"journal-article","created":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T12:39:21Z","timestamp":1771591161000},"source":"Crossref","is-referenced-by-count":0,"title":["Sensitive detection of copy number alterations in low-pass liquid biopsy sequencing data"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-4847-3660","authenticated-orcid":false,"given":"Lotta","family":"Eriksson","sequence":"first","affiliation":[{"name":"Department of Mathematical Sciences, Chalmers University of Technology , Chalmers Tv\u00e4rgata 3, 412 58 Gothenburg,","place":["Sweden"]},{"name":"Department of Mathematical Sciences, University of Gothenburg , Chalmers Tv\u00e4rgata 3, 412 58 Gothenburg,","place":["Sweden"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7221-6850","authenticated-orcid":false,"given":"Eszter","family":"Lakatos","sequence":"additional","affiliation":[{"name":"Department of Mathematical Sciences, Chalmers University of Technology , Chalmers Tv\u00e4rgata 3, 412 58 Gothenburg,","place":["Sweden"]},{"name":"Department of Mathematical Sciences, University of Gothenburg , Chalmers Tv\u00e4rgata 3, 412 58 Gothenburg,","place":["Sweden"]}]}],"member":"286","published-online":{"date-parts":[[2026,3,16]]},"reference":[{"key":"2026031613534515800_ref1","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1186\/s12943-022-01543-7","article-title":"Liquid biopsy: a step closer to transform diagnosis, prognosis and future of cancer treatments","volume":"21","author":"Lone","year":"2022","journal-title":"Mol Cancer"},{"key":"2026031613534515800_ref2","doi-asserted-by":"publisher","first-page":"103166","DOI":"10.1016\/j.critrevonc.2020.103166","article-title":"The main sources of circulating cell-free DNA: apoptosis, necrosis and active secretion","volume":"157","author":"Zijian","year":"2021","journal-title":"Crit Rev Oncol Hematol"},{"key":"2026031613534515800_ref3","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.3007094","article-title":"Detection of circulating tumor DNA in early- and late-stage human malignancies","volume":"6","author":"Bettegowda","year":"2014","journal-title":"Sci Transl Med"},{"key":"2026031613534515800_ref4","doi-asserted-by":"publisher","first-page":"548","DOI":"10.1038\/nm.3519","article-title":"An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage","volume":"20","author":"Newman","year":"2014","journal-title":"Nat Med"},{"key":"2026031613534515800_ref5","doi-asserted-by":"publisher","first-page":"5416","DOI":"10.1158\/1078-0432.CCR-16-3155","article-title":"Early evaluation of circulating tumor DNA as marker of therapeutic efficacy in metastatic colorectal cancer patients (PLACOL study)","volume":"23","author":"Garlan","year":"2017","journal-title":"Clin Cancer Res"},{"key":"2026031613534515800_ref6","doi-asserted-by":"publisher","first-page":"1859","DOI":"10.1038\/s41591-020-1063-5","article-title":"Clinical utility of circulating tumor DNA sequencing in advanced gastrointestinal cancer: SCRUM-Japan GI-SCREEN and GOZILA studies","volume":"26","author":"Nakamura","year":"2020","journal-title":"Nat Med"},{"key":"2026031613534515800_ref7","doi-asserted-by":"publisher","first-page":"2549","DOI":"10.1158\/1078-0432.CCR-20-3345","article-title":"Genome-wide copy-number alterations in circulating tumor DNA as a novel biomarker for patients with high-grade serous ovarian cancer","volume":"27","author":"Paracchini","year":"2021","journal-title":"Clin Cancer Res"},{"key":"2026031613534515800_ref8","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1158\/1078-0432.CCR-22-1696","article-title":"Clara Montagut, and Spanish cooperative Group for the Treatment of digestive tumours (TTD). 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