Background: Cell-free DNA (cfDNA) isolated from plasma consists of DNA fragments surviving clearance of dying cells and bloodstream trafficking. In cancer, these fragments carry the footprint of tumor somatic variation as well as its microenvironment. Since genomic distribution of cell free DNA fragments was shown to reflect nucleosomal occupancy in hematopoietic cells, we hypothesized that (a) heterogeneous patterns of cfDNA positioning would be associated with distinct mutations in patient tumors and (b) integration of fragmentation patterns into analysis would allow increased sensitivity and specificity of somatic mutation detection.

Methods: cfDNA fragment length and position distributions as well as associated somatic genomic profiles of over 15,000 patients with advanced-stage clinical cancer were determined by a highly accurate, deep-coverage (15,000x) ctDNA NGS test targeting 70 genes (Guardant360). An integrative data analysis of variant-free fragmentomics domain across different driver mutations was performed to identify patterns associated with detected somatic alterations.

Results: We discovered distinct classes of fragmentomics subtypes significantly enriched in samples with different genomic subtypes. An independent cohort of samples with known HER2 immunohistochemistry status was interrogated to confirm discovered association between fragmentation patterns and HER2 status. Integrating fragmentomics amplification signature with ERBB2 copy number analysis has resulted in 42% increase in the sensitivity and 7% increase in specificity of detection. Observed lung adenocarcinoma fragmentomics subtypes co-occured with mutually exclusive genomic alterations and previously described intrinsic molecular subtypes of lung cancer.

Conclusions: Fragmentomics classification of cancer cfDNA provides independent evidence for observed somatic variation and underlying tumor microenviroment, leading to higher sensitivity and accuracy of variant detection.

Citation Format: Diana Abdueva, Helmy Eltoukhy, Darya Chudova, AmirAli Talasaz. Cell-free DNA fragmentation patterns analyzed in over 15000 cancer patients reveal changes associated with tumor somatic mutations and result in improved sensitivity and specificity of somatic variant detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3350. doi:10.1158/1538-7445.AM2017-3350