Targeted Sequencing of Genomic Repeat Regions Detects Circulating Cell-free Echinococcus DNA

PLoS Neglected Tropical Diseases
Zhengqing WanZhuohua Zhang

Abstract

Echinococcosis is a chronic zoonosis caused by tapeworms of the genus Echinococcus. Treatment of the disease is often expensive and complicated, sometimes requiring extensive surgery. Ultrasonographic imaging is currently the main technique for diagnosis, while immunological analysis provides additional information. Confirmation still needs pathological analysis. However, these diagnostic techniques generally detect infection in late stages of the disease. An accurate, early and non-invasive molecular diagnostic method is still unavailable. We sequenced the cell-free DNA (cfDNA) from plasma of echinococcosis patients and confirmed the presence of Echinococcus DNA. To improve detection sensitivity, we developed a method based on targeted next-generation sequencing of repeat regions. Simulation experiments demonstrate that the targeted sequencing is sensitive enough to detect as little as 0.1% of an Echinococcus genome in 1 mL of plasma. Results obtained using patient plasma shows that the Area Under the Curve (AUC) of the method is 0.862, with a detection sensitivity of 62.50% and specificity of 100%, corresponding to a Youden-index of 0.625. This study provides evidence that hydatid cysts release cfDNA fragments into patient pl...Continue Reading

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Datasets Mentioned

BETA
ERR065034

Methods Mentioned

BETA
imaging techniques
biopsy
PCR
blood collection
nucleic acid extraction
PCRs

Software Mentioned

bowtie2
BLAST
RepeatExplorer
SPSS
RepeatExplore
SAMtools
trim
BLAST ( Basic Local Alignment Search Tool
FastUniq
Galaxy

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