Retrotransposons, a type of mobile DNA that spread in the germline via a 'copy-and-paste' mechanism, occupy approximately half of the human genome. They are a major source of innovation in gene regulatory networks, as well as pathogenic mutations. The repetitive nature of retrotransposons has however left them understudied relative to their genomic footprint. My lab has pioneered the application of long-read 'omics approaches to study human retrotransposons. In this talk, I will give a general overview of how retrotransposons can contribute to disease and their potential use in diagnostics. I will then focus on our lung squamous cell carcinoma (LUSC) datasets, where are primarily composed of long-read Oxford Nanopore Technologies (ONT) methylome and Pacific Biosciences (PacBio) transcriptome sequencing. The results obtained from this cohort suggest retrotransposons can be used to discriminate tumour and non-tumour cells, and mined for potential immunotherapy targets.