UV radiation may lead to melanoma and nonmelanoma skin cancers by causing helix-distorting DNA damage such as cyclobutane pyrimidine dimers (CPDs). These DNA lesions, if located in important genes and not repaired promptly, are mutagenic and may eventually result in carcinogenesis. Examining CPD formation and repair processes across the genome can shed light on the mutagenesis mechanisms associated with UV damage in relevant cancers. We recently developed CPD-Seq, a high-throughput and single-nucleotide resolution sequencing technique that can specifically capture UV-induced CPD lesions across the genome. This novel technique has been increasingly used in studies of UV damage and can be adapted to sequence other clinically relevant DNA lesions. Although the library preparation protocol has been established, a systematic protocol to analyze CPD-Seq data has not been described yet. To streamline the various general or specific analysis steps, we developed a protocol named CPDSeqer to assist researchers with CPD-Seq data processing. CPDSeqer can accommodate both a single- and multiple-sample experimental design, and it allows both genome-wide analyses and regional scrutiny (such as of suspected UV damage hotspots). The runtime of CPDSeqer scales with raw data size and takes roughly 4 h per sample with the possibility of acceleration by parallel computing. Various guiding graphics are generated to help diagnose the performance of the experiment and inform regional enrichment of CPD formation. UV damage comparison analyses are set forth in three analysis scenarios, and the resulting HTML pages report damage directional trends and statistical significance. CPDSeqer can be accessed at https://github.com/shengqh/cpdseqer.

紫外线辐射可能通过引起螺旋扭曲的 DNA 损伤（如环丁烷嘧啶二聚体 (CPD)）而导致黑色素瘤和非黑色素瘤皮肤癌。这些 DNA 损伤，如果位于重要基因中且不及时修复，就会产生诱变，最终可能导致致癌。检查整个基因组的 CPD 形成和修复过程可以揭示与相关癌症中的紫外线损伤相关的诱变机制。我们最近开发了 CPD-Seq，这是一种高通量和单核苷酸分辨率的测序技术，可以特异性地捕获整个基因组中紫外线诱导的 CPD 病变。这种新技术已越来越多地用于紫外线损伤的研究，并可用于对其他临床相关的 DNA 病变进行测序。虽然已经建立了文库制备协议，尚未描述分析 CPD-Seq 数据的系统方案。为了简化各种一般或特定分析步骤，我们开发了一个名为 CPDSeqer 的协议来帮助研究人员进行 CPD-Seq 数据处理。CPDSeqer 可以适应单样本和多样本实验设计，它允许进行全基因组分析和区域审查（例如可疑的紫外线损伤热点）。CPDSeqer 的运行时间随原始数据大小而变化，每个样本大约需要 4 小时，并有可能通过并行计算加速。生成各种指导图形以帮助诊断实验的性能并告知 CPD 形成的区域富集。紫外线损伤比较分析在三个分析场景中进行，生成的 HTML 页面报告损伤方向趋势和统计意义。