Academic Journal
Droplet based whole genome amplification for sequencing minute amounts of purified Mycobacterium tuberculosis DNA
| العنوان: | Droplet based whole genome amplification for sequencing minute amounts of purified Mycobacterium tuberculosis DNA |
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| المؤلفون: | Anzaan Dippenaar, Nabila Ismail, Tim H. Heupink, Melanie Grobbelaar, Johannes Loubser, Annelies Van Rie, Robin M. Warren |
| المصدر: | Scientific Reports, Vol 14, Iss 1, Pp 1-9 (2024) |
| بيانات النشر: | Nature Portfolio, 2024. |
| سنة النشر: | 2024 |
| المجموعة: | LCC:Medicine LCC:Science |
| مصطلحات موضوعية: | Tuberculosis, Whole genome amplification, WGS, Sequencing, Droplet generator, Medicine, Science |
| الوصف: | Abstract Implementation of whole genome sequencing (WGS) for patient care is hindered by limited Mycobacterium tuberculosis (Mtb) in clinical specimens and slow Mtb growth. We evaluated droplet multiple displacement amplification (dMDA) for amplification of minute amounts of Mtb DNA to enable WGS as an alternative to other Mtb enrichment methods. Purified genomic Mtb-DNA (0.1, 0.5, 1, and 5 pg) was encapsulated and amplified using the Samplix Xdrop-instrument and sequenced alongside a control sample using standard Illumina protocols followed by MAGMA-analysis. The control and 5 pg input dMDA samples underwent nanopore sequencing followed by Nanoseq and TB-profiler analysis. dMDA generated 105-2400 ng DNA from the 0.1-5 pg input DNA, respectively. Followed by Illumina WGS, dMDA raised mean sequencing depth from 7 × for 0.1 pg input DNA to ≥ 60 × for 5 pg input and the control sample. Bioinformatic analysis revealed a high number of false positive and false negative variants when amplifying ≤ 0.5 pg input DNA. Nanopore sequencing of the 5 pg dMDA sample presented excellent coverage depth, breadth, and accurate strain characterization, albeit elevated false positive and false negative variants compared to Illumina-sequenced dMDA sample with identical Mtb DNA input. dMDA coupled with Illumina WGS for samples with ≥ 5 pg purified Mtb DNA, equating to approximately 1000 copies of the Mtb genome, offers precision for drug resistance, phylogeny, and transmission insights. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 2045-2322 |
| Relation: | https://doaj.org/toc/2045-2322 |
| DOI: | 10.1038/s41598-024-60545-1 |
| URL الوصول: | https://doaj.org/article/bb85ec90990f42c3bc897a1f886ce1b5 |
| رقم الانضمام: | edsdoj.bb85ec90990f42c3bc897a1f886ce1b5 |
| قاعدة البيانات: | Directory of Open Access Journals |
Full Text Finder | تدمد: | 20452322 |
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| DOI: | 10.1038/s41598-024-60545-1 |