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在临床环境中优化下一代测序效率:阅读长度对成本和性能影响的分析

Pedro Milet Meirelles^1,2, Pablo Alessandro B Viana^3,4, Diogo Antonio Tschoeke^5,6

¹Institute of Biology, Federal University of Bahia (UFBA), Salvador, Bahia, 41745-715, Brazil. pmeirelles@ufba.br.

|September 12, 2024

概括

较短的读取长度 (75 bp) 对病原体 (元基因组) 监测具有成本效益,特别是对病毒标. 虽然较长的读数为细菌病原体提供了稍微更高的灵敏度,但75bp的读数为快速爆发反应提供了可靠和资源高效的选择.

科学领域:

基因组学就是基因组学.
传染病监测传染病监测传染病
生物信息学是一种生物信息学.

背景情况:

基因组监测在COVID-19大流行期间扩大,需要成本优化.
评估不同的测序读取长度对于有效的病原体识别至关重要.

研究的目的:

评估各种读取长度 (75,150,300bp) 的成本效益和性能,以在元基因组样本中识别病原体.
为了确定最佳的读取长度,在基因组监测中平衡成本,时间和准确性.

主要方法:

对测序成本,时间和病原体检测指标 (灵敏度,精度) 的比较分析.
对病毒和细菌病原体的不同读数长度 (75,150,300bp) 的评估.
评估不同种群的表现在不同种群的丰度水平.

主要成果:

从75bp增加阅读长度到150bp或300bp,大约分别是成本和测序时间的两倍或三倍.
病毒病原体检测灵敏度在所有读数长度 (99-100%) 中都很高,而细菌检测在较长的读数 (87%至97%) 中得到改善.
对于大多数病毒和细菌种群,病原体检测精度在测试的读取长度中是可比的.

结论:

优先考虑75bp的读取长度,以便在疫情爆发期间快速识别病原体,特别是病毒目标,以优化资源利用.
较短的读数可以通过简化工作流程对更多样本进行测序,从而保持可靠的响应能力.
75bp读数为例行基因组监测提供了一个实用且具有成本效益的解决方案,平衡速度和准确性.

关键词:

成本效率成本效率.进行健康监测.转基因组学是指转基因组学.病原体检测检测病原体检测

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