دورية أكاديمية
Evaluating the accuracy and sensitivity of detecting minority HIV-1 populations by Illumina next-generation sequencing.
| العنوان: | Evaluating the accuracy and sensitivity of detecting minority HIV-1 populations by Illumina next-generation sequencing. |
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| المؤلفون: | Kireev DE; Central Research Institute of Epidemiology, Moscow, Russia. Electronic address: dmitkireev@gmail.com., Lopatukhin AE; Central Research Institute of Epidemiology, Moscow, Russia., Murzakova AV; Central Research Institute of Epidemiology, Moscow, Russia., Pimkina EV; Central Research Institute of Epidemiology, Moscow, Russia., Speranskaya AS; Central Research Institute of Epidemiology, Moscow, Russia., Neverov AD; Central Research Institute of Epidemiology, Moscow, Russia., Fedonin GG; Central Research Institute of Epidemiology, Moscow, Russia., Fantin YS; Central Research Institute of Epidemiology, Moscow, Russia., Shipulin GA; Central Research Institute of Epidemiology, Moscow, Russia. |
| المصدر: | Journal of virological methods [J Virol Methods] 2018 Nov; Vol. 261, pp. 40-45. Date of Electronic Publication: 2018 Aug 04. |
| نوع المنشور: | Evaluation Study; Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Elsevier/North-Holland Biomedical Press Country of Publication: Netherlands NLM ID: 8005839 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1879-0984 (Electronic) Linking ISSN: 01660934 NLM ISO Abbreviation: J Virol Methods Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: [Amsterdam] : Elsevier/North-Holland Biomedical Press, 1980- |
| مواضيع طبية MeSH: | Genetic Variation*, HIV Infections/*virology , HIV-1/*classification , HIV-1/*isolation & purification , High-Throughput Nucleotide Sequencing/*methods, Humans ; Sensitivity and Specificity |
| مستخلص: | The accuracy and sensitivity of deep sequencing were assessed using viral standards (pNL4-3 and pLAI.2) of both DNA and RNA. The sequencing accuracy did not depend on the type of nucleic acid, but critically depended on the number of reads and threshold of sensitivity to minor viral populations. With coverage of more than 236 reads, the accuracy of viral RNA sequencing was equal to or exceeded 99.9%, with a sensitivity threshold to minor nucleotides of 20%. When the sensitivity threshold was below 1%, reduced accuracy dynamics were clearly visible even when the coverage was massive (more than 9.000 reads). It was found that the floating sensitivity threshold allowed the sequencing accuracy to be maintained at an acceptable level in cases of low coverage (less than 1.500-2.000) of reads. These results indicate the quality that can be expected with a specific number of reads and sensitivity threshold. Deep sequencing is a very powerful tool that can significantly improve the value of study results, but despite its superior performance, it should be used with caution regarding its sensitivity to minor populations below 1%. (Copyright © 2018 Elsevier B.V. All rights reserved.) |
| فهرسة مساهمة: | Keywords: Accuracy; Deep sequencing; HIV-1; Minor viral population; Sensitivity |
| تواريخ الأحداث: | Date Created: 20180808 Date Completed: 20181211 Latest Revision: 20191210 |
| رمز التحديث: | 20231215 |
| DOI: | 10.1016/j.jviromet.2018.08.001 |
| PMID: | 30086382 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1879-0984 |
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| DOI: | 10.1016/j.jviromet.2018.08.001 |