Amplicon测序最小信息(ASqMI):生物防御应用中可操作调用的质量和报告指南。

IF 1.7 4区 农林科学 Q3 CHEMISTRY, ANALYTICAL
Ishi Keenum, Robert Player, Jason Kralj, Stephanie Servetas, Michael D Sussman, Joe Russell, Jennifer Stone, Sailaja Chandrapati, Shanmuga Sozhamannan
{"title":"Amplicon测序最小信息(ASqMI):生物防御应用中可操作调用的质量和报告指南。","authors":"Ishi Keenum,&nbsp;Robert Player,&nbsp;Jason Kralj,&nbsp;Stephanie Servetas,&nbsp;Michael D Sussman,&nbsp;Joe Russell,&nbsp;Jennifer Stone,&nbsp;Sailaja Chandrapati,&nbsp;Shanmuga Sozhamannan","doi":"10.1093/jaoacint/qsad047","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>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.</p><p><strong>Objectives: </strong>Data reporting standards are critical to data trustworthiness. The standards presented herein aim to provide a framework for method quality assessment in biodetection.</p><p><strong>Methods: </strong>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.</p><p><strong>Results: </strong>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.</p><p><strong>Conclusion: </strong>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.</p><p><strong>Highlights: </strong>Standardized reporting guidance for actionable calls is critical to ensuring trustworthy data.</p>","PeriodicalId":15003,"journal":{"name":"Journal of AOAC International","volume":null,"pages":null},"PeriodicalIF":1.7000,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10472743/pdf/","citationCount":"0","resultStr":"{\"title\":\"Amplicon Sequencing Minimal Information (ASqMI): Quality and Reporting Guidelines for Actionable Calls in Biodefense Applications.\",\"authors\":\"Ishi Keenum,&nbsp;Robert Player,&nbsp;Jason Kralj,&nbsp;Stephanie Servetas,&nbsp;Michael D Sussman,&nbsp;Joe Russell,&nbsp;Jennifer Stone,&nbsp;Sailaja Chandrapati,&nbsp;Shanmuga Sozhamannan\",\"doi\":\"10.1093/jaoacint/qsad047\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>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.</p><p><strong>Objectives: </strong>Data reporting standards are critical to data trustworthiness. The standards presented herein aim to provide a framework for method quality assessment in biodetection.</p><p><strong>Methods: </strong>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.</p><p><strong>Results: </strong>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.</p><p><strong>Conclusion: </strong>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.</p><p><strong>Highlights: </strong>Standardized reporting guidance for actionable calls is critical to ensuring trustworthy data.</p>\",\"PeriodicalId\":15003,\"journal\":{\"name\":\"Journal of AOAC International\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":1.7000,\"publicationDate\":\"2023-09-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10472743/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of AOAC International\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://doi.org/10.1093/jaoacint/qsad047\",\"RegionNum\":4,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"CHEMISTRY, ANALYTICAL\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of AOAC International","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1093/jaoacint/qsad047","RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"CHEMISTRY, ANALYTICAL","Score":null,"Total":0}
引用次数: 0

摘要

背景:准确、高置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停工或死亡,分别付出高昂的金钱和心理代价。感兴趣的试剂的定量PCR测定已成功用于常规生物监测。最近,扩增子测序(AS)用于生物监测的动力越来越大,因为它能够区分真阳性和近邻假阳性,以及以高通量方案广泛、同时检测许多病原体中的许多靶标。然而,AS的高灵敏度可能导致假阳性。适当的控制和工作流程报告可以帮助解决这些挑战。目标:数据报告标准对数据可信度至关重要。本文提出的标准旨在为生物探测中的方法质量评估提供一个框架。方法:我们提出了一套标准,即Amplicon测序最小信息(ASqMI),该标准是在AOAC国际利益相关者项目的支持下开发的,用于在生物监测应用中进行可操作的调用。除了AS的第一个最低信息指南外,我们还提供了控制清单和评分方案,以确保AS运行质量并评估潜在的样本污染。结果:采用ASqMI指南将提高数据质量,有助于跟踪工作流性能,并最终为决策者提供信心,让他们相信这项新的强大技术的结果。结论:AS工作流程可以为生物探测提供强有力、自信的呼吁;然而,需要在报告和控制方面进行尽职调查。ASqMI指南是第一份AS最低报告指导文件,它还为最终用户提供了评估其工作流程以提高信心的方法。亮点:可操作电话的标准化报告指南对于确保可靠的数据至关重要。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

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

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

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

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.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Journal of AOAC International
Journal of AOAC International 医学-分析化学
CiteScore
3.10
自引率
12.50%
发文量
144
审稿时长
2.7 months
期刊介绍: The Journal of AOAC INTERNATIONAL publishes the latest in basic and applied research in analytical sciences related to foods, drugs, agriculture, the environment, and more. The Journal is the method researchers'' forum for exchanging information and keeping informed of new technology and techniques pertinent to regulatory agencies and regulated industries.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信