三种人全外显子组捕获探针的性能比较

Performance comparison of three human exome capture systems

目的比较不同平台3个全外显子组探针的性能,为以后建立标准流程提供数据支撑。方法提取人EDTA全血或FFPE组织gDNA,通过酶切方法将gDNA片段化,并为每一个样本的片段化后的DNA加上特异序列的接头,利用IDT、Human Exome和MedExomed三种不同的液相探针的方法将目标基因捕获出来,用Illumina的NextSeq 500二代测序仪进行测序;分析测序数据,比较不同捕获探针的靶向覆盖率、捕获特异性、变异检出能力等。结果本研究所选入组的3种探针,IDT和MedExome展示了对CCDS和Refseq数据库很好的覆盖率(均> 95%);都表现了对靶区域很高的覆盖率(均> 99%);IDT探针对血样gDNA捕获特异性(76.96%±0.75%,n=6),明显高于Human Exome (67.63%±1.62%,n=6)(P <0.001);IDT对FFPE标准品捕获特异性为84.48%±0.64%(n=3),明显高于MedExome的71.07%±0.91%(n=3)(P <0.01)。变异输出数量上,Human Exome最高。结论 IDT探针的捕获特异性明显高于其它2种,而在变异输出数量上,Human Exome探针最高。

Objective To establish the standard operating procedure for whole exome sequencing(WES),we present a comparison of three probes of different commercial exome capture platforms.Methods Genome DNA were extracted from human blood or FFPE slices,then fragmentation by enzyme.Fragments from each sample were ligated with dual-indexed adapters,and target genes were captured by liquid phase probe.Target genes were sequencing by NextSeq 500,and raw data was analyzed by bioinformatics for target region coverage,capture specificity and variations detection.Results In our investigation,IDT and MedExome showed great coverage of CCDS and Refseq.All the three systems showed great coverage of target region.IDT showed the best capture specificity.Human Exome showed the best capability of variations detection.Conclusion Each of the three human exome capture probes have their advantages.