Identification of Somatic Structural Variants in Solid Tumors by Optical Genome Mapping

Genomic structural variants comprise a significant fraction of somatic mutations driving cancer onset and progression. However, such variants are not readily revealed by standard next-generation sequencing. Optical genome mapping (OGM) surpasses short-read sequencing in detecting large (>500 bp) and complex structural variants (SVs) but requires isolation of ultra-high-molecular-weight DNA from the tissue of interest. We have successfully applied a protocol involving a paramagnetic nanobind disc to a wide range of solid tumors. Using as little as 6.5 mg of input tumor tissue, we show successful extraction of high-molecular-weight genomic DNA that provides a high genomic map rate and effective coverage by optical mapping. We demonstrate the system’s utility in identifying somatic SVs affecting functional and cancer-related genes for each sample. Duplicate/triplicate analysis of select samples shows intra-sample reliability but also intra-sample heterogeneity. We also demonstrate that simply filtering SVs based on a GRCh38 human control database provides high positive and negative predictive values for true somatic variants. Our results indicate that the solid tissue DNA extraction protocol, OGM and SV analysis can be applied to a wide variety of solid tumors to capture SVs across the entire genome with functional importance in cancer prognosis and treatment.

基因组结构变异（genomic structural variants）是驱动癌症发生与进展的体细胞突变的重要组成部分。然而，这类变异无法通过标准的下一代测序（next-generation sequencing, NGS）轻易检出。光学基因组图谱（Optical Genome Mapping, OGM）在检测大型（>500碱基对）且复杂的结构变异（structural variants, SVs）方面优于短读长测序，但该技术需要从目标组织中提取超高分子量DNA。我们已将一种基于顺磁性纳米结合盘的实验方案成功应用于多种实体瘤样本，仅需6.5毫克的起始肿瘤组织，即可成功提取高分子量基因组DNA，该DNA可实现较高的基因组图谱绘制效率与光学图谱有效覆盖度。我们验证了该系统在各样本中识别影响功能基因与癌症相关基因的体细胞结构变异的实用性。对选定样本进行重复/三次重复分析的结果显示，样本内部既具备检测可靠性，也存在异质性。我们还证实，仅通过基于GRCh38人类参考基因组数据库的结构变异过滤流程，即可为真实体细胞变异提供较高的阳性与阴性预测值。本研究结果表明，这套实体瘤组织DNA提取方案、光学基因组图谱技术与结构变异分析流程可应用于多种实体瘤，从而捕获全基因组范围内与癌症预后及治疗具有重要功能关联的结构变异。