As EPIC-seq studies epigenetic markers to infer gene expression, one can study epigenetic sequencing methods like ChIP-seq, ATAC-seq, MeDIP-seq, and Bisulfite-Free DNA Methylation sequencing in combination with methods for profiling RNA expression such as RNA-seq and scRNA-seq.
Considering the method is mainly developed for early cancer detection or subgrouping, liquid biopsy methods, such as [https://www.twistbioscience.com/resources/technical-document/twist-cfdna-pan-cancer-reference-standard-variant-list Twist cfDNA Pan-Cancer Reference Standard], can be used as an alternative. Different liquid biopsy methods focus on cell-free tumour markers, tumour methylation markers, exomes, proteins, lipids, carbohydrates, electrolytes, metabolites, RNA, extracellular vesicles, circulating tumour cells, and tumour-educated platelets for early identification of cancer non-invasively. Some of the proposed liquid biopsy methods provide a comprehensive detection of cancer types, such as ATR-FTIR spectroscopy and CancerSEEK, while others, like Dxcover and SelectMdx operate on more specific (even single) cancer targets.
EPIC-seq utilizes fragmentomic features to infer expression levels of genes. Several studies also employ fragmentomic features to infer cancer existence, infer cell death, and detect other clinical conditions such as transplant failure.