Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany;
Experimental and Clinical Research Center of the Max Delbrück Center and Charité Berlin, 13125 Berlin, Germany.
Genome Res. 2024 Oct 11;34(9):1355-1364. doi: 10.1101/gr.279123.124.
Circular extrachromosomal DNA (ecDNA) is a form of oncogene amplification found across cancer types and associated with poor outcome in patients. ecDNA can be structurally complex and can contain rearranged DNA sequences derived from multiple chromosome locations. As the structure of ecDNA can impact oncogene regulation and may indicate mechanisms of its formation, disentangling it at high resolution from sequencing data is essential. Even though methods have been developed to identify and reconstruct ecDNA in cancer genome sequencing, it remains challenging to resolve complex ecDNA structures, in particular amplicons with shared genomic footprints. We here introduce Decoil, a computational method that combines a breakpoint-graph approach with regression to reconstruct complex ecDNA and deconvolve co-occurring ecDNA elements with overlapping genomic footprints from long-read nanopore sequencing. Decoil outperforms de novo assembly and alignment-based methods in simulated long-read sequencing data for both simple and complex ecDNAs. Applying Decoil on whole-genome sequencing data uncovered different ecDNA topologies and explored ecDNA structure heterogeneity in neuroblastoma tumors and cell lines, indicating that this method may improve ecDNA structural analyses in cancer.
环状染色体外 DNA（ecDNA）是一种在多种癌症类型中发现的致癌基因扩增形式，与患者的不良预后相关。ecDNA 结构复杂，可能包含来自多个染色体位置的重排 DNA 序列。由于 ecDNA 的结构会影响致癌基因的调控，并可能表明其形成的机制，因此从测序数据中以高分辨率解析它是至关重要的。尽管已经开发了用于在癌症基因组测序中识别和重建 ecDNA 的方法，但解析复杂的 ecDNA 结构仍然具有挑战性，特别是具有共享基因组足迹的扩增子。我们在这里介绍了 Decoil，这是一种计算方法，它结合了断点图方法和回归来重建复杂的 ecDNA，并从长读长纳米孔测序中解卷积具有重叠基因组足迹的同时发生的 ecDNA 元件。在模拟的长读测序数据中，Decoil 在简单和复杂的 ecDNA 上的表现均优于从头组装和基于比对的方法。在全基因组测序数据上应用 Decoil 揭示了不同的 ecDNA 拓扑结构，并探索了神经母细胞瘤肿瘤和细胞系中的 ecDNA 结构异质性，表明该方法可能会改善癌症中的 ecDNA 结构分析。
