{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T21:15:35Z","timestamp":1783372535595,"version":"3.54.6"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T00:00:00Z","timestamp":1783296000000},"content-version":"vor","delay-in-days":5,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Per-base quality scores are widely treated as technical metadata in next-generation sequencing. Here, we show that in rigorously controlled whole-genome sequencing of cell-free DNA, quality profiles may carry fragmentomic-associated signal that enables classification of cancer samples against matched controls. Analyzing four independent batches (23 cancer samples: pancreatic and breast; 22 matched controls) sequenced in a within-lane regime and further normalized per flow-cell tile to reduce technical confounders, we demonstrate through unsupervised analysis that boundary-enriched dynamics captured in these quality scores consistently separate cancer from control samples. A leave-one-batch-out classifier trained on quality-derived scores achieved a pooled area under the curve of 0.81. Furthermore, we show that the quality-derived metric correlates with short-fragment enrichment and tumor-associated 5\u2032-end motifs, performing comparably to established, motif-based orthogonal methods. These results provide initial evidence that quality scores could serve as a low-cost, alignment-free surrogate signal for cfDNA-based cancer detection.<\/jats:p>","DOI":"10.1093\/bib\/bbag359","type":"journal-article","created":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T20:43:20Z","timestamp":1783370600000},"source":"Crossref","is-referenced-by-count":0,"title":["Exploring per-base quality scores as a surrogate marker of cell-free DNA fragmentome"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-1749-405X","authenticated-orcid":false,"given":"Hadas","family":"Volkov","sequence":"first","affiliation":[{"name":"Gray Faculty of Medical and Health Sciences , Tel Aviv University, P.O. Box 39040, Ramat Aviv, Tel Aviv 6997801,","place":["Israel"]},{"name":"Edmond J. Safra Center for Bioinformatics, Tel Aviv University , P.O. Box 39040, Ramat Aviv, Tel Aviv 6997801,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Raitses-Gurevich","sequence":"additional","affiliation":[{"name":"The Jusidman Cancer Center, Sheba Medical Center , P.O. Box 12, Tel HaShomer, Ramat Gan 52621,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meitar","family":"Grad","sequence":"additional","affiliation":[{"name":"Gray Faculty of Medical and Health Sciences , Tel Aviv University, P.O. Box 39040, Ramat Aviv, Tel Aviv 6997801,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rani","family":"Shlayem","sequence":"additional","affiliation":[{"name":"Gray Faculty of Medical and Health Sciences , Tel Aviv University, P.O. Box 39040, Ramat Aviv, Tel Aviv 6997801,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dev","family":"Leibowitz","sequence":"additional","affiliation":[{"name":"Gray Faculty of Medical and Health Sciences , Tel Aviv University, P.O. Box 39040, Ramat Aviv, Tel Aviv 6997801,","place":["Israel"]},{"name":"Edmond J. Safra Center for Bioinformatics, Tel Aviv University , P.O. Box 39040, Ramat Aviv, Tel Aviv 6997801,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tami","family":"Rubinek","sequence":"additional","affiliation":[{"name":"Gray Faculty of Medical and Health Sciences , Tel Aviv University, P.O. Box 39040, Ramat Aviv, Tel Aviv 6997801,","place":["Israel"]},{"name":"Department of Oncology, Tel Aviv Sourasky Medical Center , 6 Weizmann Street, Tel Aviv 6423906,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Talia","family":"Golan","sequence":"additional","affiliation":[{"name":"Gray Faculty of Medical and Health Sciences , Tel Aviv University, P.O. Box 39040, Ramat Aviv, Tel Aviv 6997801,","place":["Israel"]},{"name":"The Jusidman Cancer Center, Sheba Medical Center , P.O. Box 12, Tel HaShomer, Ramat Gan 52621,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noam","family":"Shomron","sequence":"additional","affiliation":[{"name":"Gray Faculty of Medical and Health Sciences , Tel Aviv University, P.O. Box 39040, Ramat Aviv, Tel Aviv 6997801,","place":["Israel"]},{"name":"Edmond J. Safra Center for Bioinformatics, Tel Aviv University , P.O. 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