扩增子测序最低信息 (ASqMI)：生物防御应用中可操作调用的质量和报告指南。

Amplicon Sequencing Minimal Information (ASqMI): Quality and Reporting Guidelines for Actionable Calls in Biodefense Applications.

机构信息

National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD 20899, USA.

The Johns Hopkins University, Applied Physics Laboratory, Laurel, MD 20723, USA.

出版信息

J AOAC Int. 2023 Sep 1;106(5):1424-1430. doi: 10.1093/jaoacint/qsad047.

DOI:10.1093/jaoacint/qsad047

PMID:37067472

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10472743/

Abstract

BACKGROUND

Accurate, high-confidence data is critical for assessing potential biothreat incidents. In a biothreat event, false-negative and -positive results have serious consequences. Worst case scenarios can result in unnecessary shutdowns or fatalities at an exorbitant monetary and psychological cost, respectively. Quantitative PCR assays for agents of interest have been successfully used for routine biosurveillance. Recently, there has been increased impetus for adoption of amplicon sequencing (AS) for biosurveillance because it enables discrimination of true positives from near-neighbor false positives, as well as broad, simultaneous detection of many targets in many pathogens in a high-throughput scheme. However, the high sensitivity of AS can lead to false positives. Appropriate controls and workflow reporting can help address these challenges.

OBJECTIVES

Data reporting standards are critical to data trustworthiness. The standards presented herein aim to provide a framework for method quality assessment in biodetection.

METHODS

We present a set of standards, Amplicon Sequencing Minimal Information (ASqMI), developed under the auspices of the AOAC INTERNATIONAL Stakeholder Program on Agent Detection Assays for making actionable calls in biosurveillance applications. In addition to the first minimum information guidelines for AS, we provide a controls checklist and scoring scheme to assure AS run quality and assess potential sample contamination.

RESULTS

Adoption of the ASqMI guidelines will improve data quality, help track workflow performance, and ultimately provide decision makers confidence to trust the results of this new and powerful technology.

CONCLUSION

AS workflows can provide robust, confident calls for biodetection; however, due diligence in reporting and controls are needed. The ASqMI guideline is the first AS minimum reporting guidance document that also provides the means for end users to evaluate their workflows to improve confidence.

HIGHLIGHTS

Standardized reporting guidance for actionable calls is critical to ensuring trustworthy data.

摘要

背景

准确、高可信度的数据对于评估潜在的生物威胁事件至关重要。在生物威胁事件中，假阴性和假阳性结果会产生严重后果。最坏的情况可能会导致不必要的关闭或致命，分别造成高昂的经济和心理代价。针对感兴趣的病原体，定量 PCR 检测已成功用于常规生物监测。最近，由于扩增子测序 (AS) 能够区分真正的阳性和邻近的假阳性，以及在高通量方案中同时广泛检测许多病原体中的许多目标，因此采用扩增子测序进行生物监测的动力有所增加。然而，AS 的高灵敏度可能会导致假阳性。适当的对照和工作流程报告可以帮助解决这些挑战。

目的

数据报告标准对于数据可信度至关重要。本文提出的标准旨在为生物检测中的方法质量评估提供框架。

方法

我们提出了一组标准，即扩增子测序最小信息 (ASqMI)，该标准是在 AOAC INTERNATIONAL 检测试剂检测利益相关者计划的支持下制定的，用于在生物监测应用中做出可操作的检测。除了第一个 AS 的最低信息指南外，我们还提供了一个对照检查表和评分方案，以确保 AS 运行质量并评估潜在的样本污染。