| Autor: |
Angela M. Early, Rachel F. Daniels, Timothy M. Farrell, Jonna Grimsby, Sarah K. Volkman, Dyann F. Wirth, Bronwyn L. MacInnis, Daniel E. Neafsey |
| Jazyk: |
angličtina |
| Rok vydání: |
2019 |
| Předmět: |
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| Zdroj: |
Malaria Journal, Vol 18, Iss 1, Pp 1-13 (2019) |
| Druh dokumentu: |
article |
| ISSN: |
1475-2875 |
| DOI: |
10.1186/s12936-019-2856-1 |
| Popis: |
Abstract Background Deep sequencing of targeted genomic regions is becoming a common tool for understanding the dynamics and complexity of Plasmodium infections, but its lower limit of detection is currently unknown. Here, a new amplicon analysis tool, the Parallel Amplicon Sequencing Error Correction (PASEC) pipeline, is used to evaluate the performance of amplicon sequencing on low-density Plasmodium DNA samples. Illumina-based sequencing of two Plasmodium falciparum genomic regions (CSP and SERA2) was performed on two types of samples: in vitro DNA mixtures mimicking low-density infections (1–200 genomes/μl) and extracted blood spots from a combination of symptomatic and asymptomatic individuals (44–653,080 parasites/μl). Three additional analysis tools—DADA2, HaplotypR, and SeekDeep—were applied to both datasets and the precision and sensitivity of each tool were evaluated. Results Amplicon sequencing can contend with low-density samples, showing reasonable detection accuracy down to a concentration of 5 Plasmodium genomes/μl. Due to increased stochasticity and background noise, however, all four tools showed reduced sensitivity and precision on samples with very low parasitaemia ( |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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