病原宏基因组高通量测序医疗机构本地化质量评价联合研究

Benchmarking Study on Quality Evaluation of Localized Pathogen Metagenomic Next-Generation Sequencing in Medical Organizations

目的:开展病原宏基因组高通量测序(mNGS)质量评价联合研究,为医疗机构(医院mNGS本地化建设提供参考经验。方法:参加单位使用本地化建设的mNGS流程,按方案要求检测参考品标本并回报结果。对检测性能及技术选型等因素进行统计分析。结果:来自全国17个省、直辖市的42家医院的47个科室参加本次研究,检测流程包括3种测序平台的10种测序仪。参加单位按研究方案完成质量评价参考品的测试,共回报49组有效数据,其中全部性能指标均为满分的占29%,各性能指标的满分占比分别为阳性符合率(准确性)73%、阴性符合率(特异性)92%、重复性47%、检出限71%,以及稳健性37%。实验流程中标本前处理、病原富集及核酸片段化的技术选型,是显著影响满分率的因素。更大的测序数据量与满分率呈正相关,而不同测序方案则无统计学差异。结论:本次联合研究提示,目前mNGS流程的整体稳定性仍有较大优化空间,实验室在开展本地化建设时应充分考虑影响检测系统稳定的各潜在因素,有助于保证日常运行的稳定可控。

Objective:A benchmarking study on quality evaluation of pathogen metagenomic next-generation sequencing(mNGS)was carried out to provide practical reference for the localization implement of mNGS testing in medical organizations(hospitals).Methods:The mNGS workflows implemented in medical organizations were used to test the reference panel and to report the results as required.This paper presents a statistical analysis of factors such as detection performance and technology selection.Results:The participants came from 47 departments of 42 hospitals in 17 provinces(municipalities),and the workflows included 10 types of sequencers on 3 platforms.Participants completed the tests of reference panel according to the study scheme and a total of 49 sets of valid data were returned.The percentage of full scores for all performance indicators was 29%,and the percentage of perfect scores for each performance indicator was 73%for positive coincidence rate(accuracy),92%for negative coincidence rate(specificity),47%for repeatability,71%for detection limit,and 37%for robustness.The technical characteristic of sample pretreatment,pathogen enrichment and nucleic acid fragmentation were the factors that would significantly affect the full score rate.A larger amount of sequencing data was positively correlated with the full score rate,while different sequencing strategies were not.Conclusion:This study suggests that the overall stability of the current mNGS workflow needs further improvement.The laboratory needs to fully consider the potential factors affecting the stability of the detection system when building a localized mNGS system,which helps ensure the stability and control of daily operation.