Inferring gene expression from cell-free DNA fragmentation profiles

Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for non-invasive cancer detection and classification. While chromatin fragmentation features in cell-free DNA (cfDNA) have previously been explored, current fragmentomic methods require high concentrations of tumor-derived DNA and are limited by insufficient resolution to infer individual gene expression. Here, we describe promoter fragmentation entropy (PFE) at transcription start sites (TSS) as a novel epigenomic cfDNA feature strongly correlated with RNA expression levels. We also show that residual fragmentation entropy within first exons can be measured by whole exome cfDNA profiling in lung cancers, enabling noninvasive identification of gene expression matching corresponding tissue specimens. PFE is complementary to other fragmentomic features in predicting gene-specific transcription levels and has advantages over them. We leverage these insights within EPIC-Seq, a method for high-resolution cancer detection and tissue-of-origin classification from cfDNA that extracts features of chromatin fragmentation using targeted sequencing from promoters of genes of interest.