부산대학교 도서관

Simple Summary: Mutations are present in healthy skin long before clinical signs of skin cancer arise. Many studies have shown that mutations in healthy tissue and cancer cluster at specific areas in the genome, often referred to as mutation hotspots. Next-generation sequencing has become the gold standard for studying cancer genomics. However, it is not economically feasible to sequence large genomic regions at the depth necessary to study mutations in healthy tissues. We have created an algorithm that formats mutation data into a targetable panel of genomic segments that can be used to design sequencing experiments. The efficacy of our algorithm was tested using three publicly available datasets. Compared to the original genomic regions used for these studies, the regions identified by our algorithm improved mutation capture efficacy ranging from 9.6 to 12.1-fold. Our web application hotSPOT provides a publicly available resource for researchers to design next-generation sequencing experiments to effectively study mutations in healthy tissues and cancer. Mutations found in skin are acquired in specific patterns, clustering around mutation-prone genomic locations. The most mutation-prone genomic areas, mutation hotspots, first induce the growth of small cell clones in healthy skin. Mutations accumulate over time, and clones with driver mutations may give rise to skin cancer. Early mutation accumulation is a crucial first step in photocarcinogenesis. Therefore, a sufficient understanding of the process may help predict disease onset and identify avenues for skin cancer prevention. Early epidermal mutation profiles are typically established using high-depth targeted next-generation sequencing. However, there is currently a lack of tools for designing custom panels to capture mutation-enriched genomic regions efficiently. To address this issue, we created a computational algorithm that implements a pseudo-exhaustive approach to identify the best genomic areas to target. We benchmarked the current algorithm in three independent mutation datasets of human epidermal samples. Compared to the sequencing panel designs originally used in these publications, the mutation capture efficacy (number of mutations/base pairs sequenced) of our designed panel improved 9.6–12.1-fold. Mutation burden in the chronically sun-exposed and intermittently sun-exposed normal epidermis was measured within genomic regions identified by hotSPOT based on cutaneous squamous cell carcinoma (cSCC) mutation patterns. We found a significant increase in mutation capture efficacy and mutation burden in cSCC hotspots in chronically sun-exposed vs. intermittently sun-exposed epidermis (p < 0.0001). Our results show that our hotSPOT web application provides a publicly available resource for researchers to design custom panels, enabling efficient detection of somatic mutations in clinically normal tissues and other similar targeted sequencing studies. Moreover, hotSPOT also enables the comparison of mutation burden between normal tissues and cancer. [ABSTRACT FROM AUTHOR]