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在没有匹配的正常样本的情况下,精确识别体和生殖系变异

Hui Li¹, Lu Meng², Hongke Wang²

¹The Medical Oncology Translational Research Laboratory, Jilin Provincial Key Laboratory of Molecular Diagnostics for Lung Cancer, Jilin Cancer Hospital, No. 1066, Jinhu Road, Changchun, 130012, China.

Briefings in bioinformatics

|December 31, 2024

概括

在癌症基因组分析中,OncoTOP是一种新的计算方法,可以在没有正常样本的情况下,准确地区分癌症基因组分析中的体质突变与生殖系变异. 该工具在变异调用和生物标志物估计方面显示出高可靠性,改善了临床基因组测试.

科学领域:

基因组学就是基因组学.
计算生物学计算生物学
癌症研究癌症研究

背景情况:

在没有匹配的正常对照的情况下,在瘤样本中区分体质和生殖系变异是具有挑战性的.
现有的仅针对瘤的基因组分析方法具有性能限制和解释性问题.
对于仅针对瘤的基因组分析,需要一种可靠的计算方法.

研究的目的:

介绍OncoTOP,一种新的计算方法,用于在没有匹配的正常对照的情况下在瘤样本中准确区分体质和生殖系变异.
评估OncoTOP在变异调用,突变起源预测和生物标志物估计方面的表现.
为了证明OncoTOP在预测免疫治疗反应方面的临床实用性.

主要方法:

OncoTOP是作为一种仅使用瘤样本进行基因组分析的计算方法而开发的.
该方法的性能使用参考样本和18种癌症类型的2864个瘤样本的大队伍进行了评估.
评估了包括瘤突变负担 (TMB),微卫星不稳定性 (MSI) 和白细胞抗原 (LA) 亚型在内的关键生物标志物.

主要成果:

在参考样本分析中,OncoTOP实现了0%的错误阳性率和99.7%的可重复性.
在2864个瘤样本中,OncoTOP显示了99.8%的积极百分比一致和99.9%的积极预测值.
对于TMB (vs.瘤正常分析),MSI (97%),LA类I亚型 (99.3%) 和同性 (99.9%) 观察到高一致性.
OncoTOP准确地预测了突变起源 (97.4%的体质,95.7%的生殖系) 并确定了可操作的变体和亚克隆突变.
通过OncoTOP识别的高TMB患者在免疫治疗队列中表现出长期无进展生存 (PFS).

结论:

在瘤基因组分析中,OncoTOP是一种可靠的计算工具,用于区分体质和生殖系变异.
该方法在变异调用,突变起源预测和关键生物标志物估计方面表现出高准确性.
在临床基因组测试方面,OncoTOP提供了实质性的优势,包括用于预测治疗反应的生物标志物评估.

关键词:

在DNA测序过程中,DNA测序在OncoTOP上生物信息学是一种生物信息学.生物标志物生物标志物癌症基因组学癌症基因组学

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