Abstract LB-024: The effects of chromatin structure on variation in fragment size of cell free DNA

Abstract

Abstract Liquid biopsy using cell-free DNA (cfDNA) has established its clinical utilities in multiple clinical cohorts. However, the exact mechanism by which cell-free DNA (cfDNA) is generated remains undetermined. The fragment size of cfDNA sheds important insights on elucidating the process. Previous studies qualitatively concluded that tumor-derived cfDNA is shorter than cfDNA from healthy cells, but the exact size distribution of tumor-derived cfDNA remains unclear. To better understand the mechanism of cfDNA generation and directly study cfDNA of tumor origins, we analyzed the deep targeted sequencing results of cfDNA from 605 patients with various cancer types, and developed a method that separates tumor cfDNA through identification of somatic variant alleles-containing fragments. We show that tumor-derived cfDNA has an increased proportion of fragments less than 150bp compared to healthy controls, while the most common size is still 166 bp. It has been speculated that differences in nucleosome wrapping may contribute to differing fragment lengths of cfDNA.To better understand the relationship between the magnitude of chromatin packaging and cfDNA length, we quantitatively analyzed the size distribution of cfDNA collected from 5 cancer patients in genomic regions with the varying degree of chromatin openness. We discovered that the fragment size of cfDNA was closely associated with chromatin inaccessibility and chromosome condensation as measured by transcriptional start sites, DNase I hypersensitivity, histone modifications, and Giemsa banding, or as implied by chromosomal sub-nuclear localization. The shortening occurs at both 5' and 3' ends of cfDNA fragments without bias. Taken together, these results collectively established a positive correlation between cfDNA fragment size and chromatin inaccessibility. Citation Format: Hui Xia, Xingya Li, Hua Bao, Xiangyuan Ma, Xue Wu, Yang W. Shao, Feixiang Wu, Shucai Zhang. The effects of chromatin structure on variation in fragment size of cell free DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-024.