Separating the signal from the noise in metagenomic cell-free DNA sequencing
Separating the signal from the noise in metagenomic cell-free DNA sequencing
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DOI：
10.1186/s40168-020-0793-4
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发表时间：
2020-02-11
期刊：
影响因子：
15.5
通讯作者：
De Vlaminck, Iwijn
中科院分区：
文献类型：
--
作者：
Burnham, Philip;Gomez-Lopez, Nardhy;De Vlaminck, Iwijn
血液、尿液和其他生物流体中的无细胞DNA（cfDNA）为了解人类健康提供了一个独特的窗口。一部分cfDNA来源于细菌和病毒，为通过宏基因组测序诊断感染创造了机会。临床分离株中微生物来源的cfDNA的总生物量低，这使得宏基因组cfDNA测序易受污染和比对噪声的影响。结果在这里，我们报告了低生物量背景校正（LBBC），这是一种生物信息学噪音过滤工具，根据微生物基因组覆盖的均匀性和微生物cfDNA绝对丰度的批次差异来提供信息。我们证明，LBBC导致假阳性率显著降低，同时对cfDNA测试筛查尿路感染的真阳性率影响最小。接下来，我们对羊水中的cfDNA进行了高通量测序，所述羊水收集自足月无并发症妊娠或并发有和无羊膜内感染的临床绒毛膜炎的妊娠。结论该数据提供了对羊水中胎儿和母体cfDNA性质的独特见解，证明了cfDNA筛查羊水内感染的实用性，支持正常妊娠期间羊水是无菌的观点，并揭示了足月时无感染的羊水内炎症病例。
Background Cell-free DNA (cfDNA) in blood, urine, and other biofluids provides a unique window into human health. A proportion of cfDNA is derived from bacteria and viruses, creating opportunities for the diagnosis of infection via metagenomic sequencing. The total biomass of microbial-derived cfDNA in clinical isolates is low, which makes metagenomic cfDNA sequencing susceptible to contamination and alignment noise. Results Here, we report low biomass background correction (LBBC), a bioinformatics noise filtering tool informed by the uniformity of the coverage of microbial genomes and the batch variation in the absolute abundance of microbial cfDNA. We demonstrate that LBBC leads to a dramatic reduction in false positive rate while minimally affecting the true positive rate for a cfDNA test to screen for urinary tract infection. We next performed high-throughput sequencing of cfDNA in amniotic fluid collected from term uncomplicated pregnancies or those complicated with clinical chorioamnionitis with and without intra-amniotic infection. Conclusions The data provide unique insight into the properties of fetal and maternal cfDNA in amniotic fluid, demonstrate the utility of cfDNA to screen for intra-amniotic infection, support the view that the amniotic fluid is sterile during normal pregnancy, and reveal cases of intra-amniotic inflammation without infection at term.