bistro: An R package for vector bloodmeal identification by short tandem repeat overlap.
bistro: An R package for vector bloodmeal identification by short tandem repeat overlap.
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bistro：一个 R 包，用于通过短串联重复重叠来识别载体血粉。
DOI：
10.1101/2023.09.14.23295566
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Markwalter,ChristineF
中科院分区：
文献类型：
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作者：
Lapp,Zena;Abel,Lucy;Mangeni,Judith;Obala,AndrewA;O'Meara,Wendy;Taylor,SteveM;Markwalter,ChristineF
在自然环境中测量媒介与人类的接触可以为精确确定干预措施的目标提供信息，以阻断媒介传播疾病的传播。一种方法是使用歧视性短串联重复序列(STR)的基因型面板将媒介血粉中的人类DNA与被叮咬的个体直接匹配。现有的方法将血粉中的STR图谱与被咬人进行匹配，无法匹配大多数不完整的图谱和多来源血粉以匹配被咬人。我们开发了BISTRO，一个R包，它实现了三种先前存在的STR匹配方法，以及该包的同名算法BISTRO，这里介绍了一种新的算法。Bistro使用法医分析方法来计算似然比，并使用动态阈值将血餐中的人类STR图谱与人进行匹配。我们评估了算法的准确性，并将其与现有的匹配方法进行了比较，使用了一个公开可用的小组，该小组由188个单源样本和100个多源样本组成，其中包含来自50个已知人类来源的DNA。然后将其应用于现场采集的777份蚊血与645人的数据库进行匹配，R包以用户友好的功能实现了4种STR匹配算法，文档清晰。BISTRO在单源样本中正确匹配99%(187/188)的轮廓，在多源样本中正确匹配62%(224/359)的轮廓，导致灵敏度为0.75(而其他算法为0.51)。BISTRO的特异度为0.9998(其他算法为1)。此外，Bistro在所有可能的野外蚊子匹配中识别了79%(720/906)，比现有算法多1.4倍。Bistro识别出比现有方法更正确的血粉-人类匹配，从而能够更准确和可靠地分析自然环境中媒介-人类接触。Bistro R包和相应的文档允许其他人直接理解该算法。
Measuring vector–human contact in a natural setting can inform precise targeting of interventions to interrupt transmission of vector‐borne diseases. One approach is to directly match human DNA in vector bloodmeals to the individuals who were bitten using genotype panels of discriminative short tandem repeats (STRs). Existing methods for matching STR profiles in bloodmeals to the people bitten preclude the ability to match most incomplete profiles and multisource bloodmeals to bitten individuals.We developed bistro, an R package that implements three pre‐existing STR matching methods as well as the package's namesake, bistro, a new algorithm described here. bistro employs forensic analysis methods to calculate likelihood ratios and match human STR profiles in bloodmeals to people using a dynamic threshold. We evaluated the algorithm's accuracy and compared it to existing matching approaches using a publicly available panel of 188 single‐source and 100 multisource samples containing DNA from 50 known human sources. Then, we applied it to match 777 newly field‐collected mosquito bloodmeals to a database of 645 people.The R package implements four STR matching algorithms in user‐friendly functions with clear documentation. bistro correctly matched 99% (187/188) of profiles in single‐source samples, and 62% (224/359) of profiles from multisource samples, resulting in a sensitivity of 0.75 (vs. <0.51 for other algorithms). The specificity of bistro was 0.9998 (vs. 1 for other algorithms). Furthermore, bistro identified 79% (720/906) of all possible matches for field‐derived mosquitoes, yielding 1.4× more matches than existing algorithms.bistro identifies more correct bloodmeal–human matches than existing approaches, enabling more accurate and robust analyses of vector–human contact in natural settings. The bistro R package and corresponding documentation allow for straightforward uptake of this algorithm by others.