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基于模拟瘤样本的瘤含量估计方法的比较分析确定了它们对癌症全基因组测序中的体变异检测的影响

Takeshi Nagashima^1,2, Kenichi Urakami¹, Yuji Shimoda¹

¹Cancer Diagnostic Research Division, Shizuoka Cancer Center Research Institute.

Biomedical research (Tokyo, Japan)

|August 6, 2023

概括

准确的瘤含量估计对于癌症全基因组测序 (WGS) 分析至关重要. 这项研究强调了低瘤含量样本的显著变异性,影响体质变异检测,并需要谨慎解释WGS结果.

科学领域:

癌症基因组学癌症基因组学
生物信息学是一种生物信息学.
计算生物学计算生物学

背景情况:

全基因组测序 (WGS) 越来越多地被用于癌症基因组学,产生大量数据.
对WGS结果的准确解释对于临床应用至关重要,特别是关于瘤含量.
瘤含量估计直接影响体质变异检测的可靠性.

研究的目的:

在癌症基因组学中评估瘤含量估计方法的准确性.
用WGS数据评估瘤含量对检测各种体质变化的影响.
为可靠的变种检测建立最低瘤含量值,并为WGS解释提供指导方针.

主要方法:

从细胞系测序数据中构建100个模拟瘤样本,瘤含量不同 (10-100%).
评估用于瘤含量估计的多种计算分析方法.
分析瘤含量对检测全基因组倍增,单核酸变异,插入/删除,结构变异和副本数量变化的影响.

主要成果:

在不同的计算方法中观察到瘤含量估计的显著差异,特别是在瘤含量低 (≤30%).
变异检测的可复制性随着正常细胞的染色体尺度拷贝数量变化而降低.
检测体质改变所需的最小瘤含量在10-30%之间,在最低值确定了全基因组翻倍,其次是SNV/indels,SV和CNV.

结论:

瘤含量显著影响虚假阴性比虚假阳性在WGS数据的变异调用.
来自WGS分析的结果需要在含有不确定的或低瘤含量的样本中谨慎解释.
结果为制定评估癌症WGS数据的指导方针提供了基础,提高了临床实用性.

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