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

Abstract

Background 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. Methodology/Principal findings 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. Conclusions/Significance This study provides evidence that hydatid cysts release cfDNA fragments into patient plasma. Using the repeat region targeted sequencing method, highly specific detection of Echinococcus infection was achieved. This study paves a new avenue for potential noninvasive screening and diagnosis of echinococcosis.

Identification of candidate biomarkers of liver hydatid disease via microarray profiling, bioinformatics analysis, and machine learning

“… 36 Typically, physicians depend on standard segmentation systems to evaluate computed tomography images. 37 However, limited medical resources and the difficult diagnosis increase the burden of this disease in the Qinghai region. 38 Hence, identification of reliable biomarkers and practical and useful prediction models for liver hydatid disease in the Qinghai region of China is urgently needed.…”

Cell-free DNA as a diagnostic tool for human echinococcosis

“…However, this conclusion was based on one paper [6]. In recent years there have been several publications on the detection of Echinococcus cfDNA in the samples of echinococcosis patients (Table 1) [7][8][9][10][11][12][13].…”

“…As shown in Table 1 and Figure 1, there is Echinococcus cfDNA in echinococcosis patients' blood, although the concentration is very low [7][8][9][10]12,13]. The difference between the previous review and recent papers is mainly due to the methods used [5,6].…”

Effective Targeted Chemoprophylaxis of Recurrent Liver Echinococcosis with Haplotype CYP1A2F1*A/A: a Clinical Case

“…Однако химиотерапия альбендазолом у реальных пациентов полностью эффективна лишь в 10-58 % случаев и неэффективна у 13-37 % пациентов [10][11][12]. Указанное различие в фармакологической активности в условиях in vitro и клинической эффективности логично обусловлено пациент-ассоциированными факторами [13,14]. Skuhala T. et al (2014) указывали на огромный диапазон значений концентрации альбендазола сульфоксида в крови пациентов (различия между минимумом и максимумом составляли 25-80 раз).…”