Fragmentation signatures in cancer patients resemble those of patients with vascular or autoimmune diseases

Curtis, SD; Liu, T; Bai, Y; Wang, Y; Panda, S; Li, A; Xu, H; O&#39;Reilly, E; Dobbyn, L; Popoli, M; Ptak, J; Silliman, N; Thoburn, C; Tie, J; Gibbs, P; Ho-Pham, LT; Tran, BNH; Tran, TS; Nguyen, TV; Konig, MF; Petri, M; Rosen, A; Mecoli, CA; Shah, AA; Mulder, F; van Es, N; PLATO-VTE Study Group; Bettegowda, C; Kinzler, KW; Papadopoulos, N; Vogelstein, JT; Vogelstein, B; Douville, C

Author(s): Curtis, SD; Liu, T; Bai, Y; Wang, Y; Panda, S; Li, A; Xu, H; O'Reilly, E; Dobbyn, L; Popoli, M; Ptak, J; Silliman, N; Thoburn, C; Tie, J; Gibbs, P; Ho-Pham, LT; Tran, BNH; Tran, TS; Nguyen, TV; Konig, MF; Petri, M; Rosen, A; Mecoli, CA; Shah, AA; Mulder, F; van Es, N; PLATO-VTE Study Group; Bettegowda, C; Kinzler, KW; Papadopoulos, N; Vogelstein, JT; Vogelstein, B; Douville, C;
Details: Publication Year 2025-08-26,Volume 122,Issue #34,Page e2426890122
Journal Title: Proceedings of the National Academy of Sciences of the United States of America
Publication Type: Research article
Abstract: Multiple case-controlled studies have shown that analyzing fragmentation patterns in plasma cell-free DNA (cfDNA) can distinguish individuals with cancer from healthy controls. However, there have been few studies that investigate various types of cfDNA fragmentomics patterns in individuals with other diseases. We therefore developed a comprehensive statistic, called fragmentation signatures, that integrates the distributions of fragment positioning, fragment length, and fragment end-motifs in cfDNA. We found that individuals with venous thromboembolism, systemic lupus erythematosus, dermatomyositis, or scleroderma have cfDNA fragmentation signatures that closely resemble those found in individuals with advanced cancers. Furthermore, these signatures were highly correlated with increases in inflammatory markers in the blood. We demonstrate that these similarities in fragmentation signatures lead to high rates of false positives in individuals with autoimmune or vascular disease when evaluated using conventional binary classification approaches for multicancer earlier detection (MCED). To address this issue, we introduced a multiclass approach for MCED that integrates fragmentation signatures with protein biomarkers and achieves improved specificity in individuals with autoimmune or vascular disease while maintaining high sensitivity. Though these data put substantial limitations on the specificity of fragmentomics-based tests for cancer diagnostics, they also offer ways to improve the interpretability of such tests. Moreover, we expect these results will lead to a better understanding of the process-most likely inflammatory-from which abnormal fragmentation signatures are derived.
Publisher: National Academy of Sciences
Keywords: Humans; *Neoplasms/blood/genetics/diagnosis; *Autoimmune Diseases/blood/genetics/diagnosis; *Cell-Free Nucleic Acids/blood/genetics; *Vascular Diseases/blood/genetics/diagnosis; Biomarkers/blood; Case-Control Studies; Female; Male; Lupus Erythematosus, Systemic/blood/genetics; autoimmune diseases; cancer screening; cell-free DNA; fragmentomics; rheumatology
Department(s): Medical Oncology
Publisher's Version: https://doi.org/10.1073/pnas.2426890122
Open Access at Publisher's Site: https://doi.org/10.1073/pnas.2426890122
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2025-08-28 05:52:25

Last Modified: 2025-08-28 05:52:35