Shall I trust the report? Variable performance of Sanger sequencing revealed by deep sequencing on HIV drug resistance mutation detection
Background: The clinical utilisation of deep sequencing in HIV treatment has been hindered due to its unknown correlation with standard Sanger genotyping and the undetermined value of minority drug resistance mutation (DRM) detection. Objectives: To compare deep sequencing performance to standard Sa...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2020-04-01
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| Series: | International Journal of Infectious Diseases |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S120197122030062X |
| _version_ | 1818444428814057472 |
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| author | Nan-Yu Chen Shu-Wei Kao Zhuo-Hao Liu Ting-Shu Wu Chia-Lung Tsai Hsi-Hsun Lin Wing-Wai Wong Yea-Yuan Chang Shu-Sheng Chen Stephane Wen-Wei Ku |
| author_facet | Nan-Yu Chen Shu-Wei Kao Zhuo-Hao Liu Ting-Shu Wu Chia-Lung Tsai Hsi-Hsun Lin Wing-Wai Wong Yea-Yuan Chang Shu-Sheng Chen Stephane Wen-Wei Ku |
| author_sort | Nan-Yu Chen |
| collection | DOAJ |
| description | Background: The clinical utilisation of deep sequencing in HIV treatment has been hindered due to its unknown correlation with standard Sanger genotyping and the undetermined value of minority drug resistance mutation (DRM) detection. Objectives: To compare deep sequencing performance to standard Sanger genotyping with clinical samples, in an effort to delineate the correlation between the results from the two methods and to find the optimal deep sequencing threshold for clinical utilisation. Methods: We conducted a retrospective study using stored plasma collected from August 2014 to March 2018 for HIV genotyping with the commercial Sanger genotyping kit. Samples with available Sanger genotyping reports were further deep sequenced. Drug resistance was interpreted according to the Stanford HIV drug resistance database algorithm. Results: At 15–25% minority detection thresholds, 9–15% cases had underestimated DRMs by Sanger sequencing. The concordance between the Sanger and deep sequencing reports was 68–82% in protease-reverse transcriptase region and 88–97% in integrase region at 5–25% thresholds. The undetected drug resistant minority variants by Sanger sequencing contributed to the lower negative predictive value of Sanger genotyping in cases harbouring DRMs. Conclusions: Use of deep sequencing improved detection of antiretroviral resistance mutations especially in cases with virological failure or previous treatment interruption. Deep sequencing with 10–15% detection thresholds may be considered a suitable substitute for Sanger sequencing on antiretroviral DRM detection. Keywords: HIV, Next-generation sequencing, Deep sequencing, Drug resistance, Sanger sequencing |
| first_indexed | 2024-12-14T19:15:47Z |
| format | Article |
| id | doaj.art-ad03902e74dd45f394df6ad4fd28e4a6 |
| institution | Directory Open Access Journal |
| issn | 1201-9712 |
| language | English |
| last_indexed | 2024-12-14T19:15:47Z |
| publishDate | 2020-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | International Journal of Infectious Diseases |
| spelling | doaj.art-ad03902e74dd45f394df6ad4fd28e4a62022-12-21T22:50:37ZengElsevierInternational Journal of Infectious Diseases1201-97122020-04-0193182191Shall I trust the report? Variable performance of Sanger sequencing revealed by deep sequencing on HIV drug resistance mutation detectionNan-Yu Chen0Shu-Wei Kao1Zhuo-Hao Liu2Ting-Shu Wu3Chia-Lung Tsai4Hsi-Hsun Lin5Wing-Wai Wong6Yea-Yuan Chang7Shu-Sheng Chen8Stephane Wen-Wei Ku9Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, TaiwanDivision of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, TaiwanDepartment of Neurosurgery, Chang Gung Memorial Hospital Linkou Branch, TaiwanDivision of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, TaiwanGenomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, TaiwanGeneral Clinical Research Centre, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan; Institute of Public Health, School of Medicine, National Yang-Ming University, Taipei, TaiwanDivision of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, TaiwanDivision of Infectious Diseases, Department of Internal Medicine, National Yang-Ming University Hospital, Yilan, Taiwan; Institute of Clinical Medicine and AIDS Prevention and Research Centre, National Yang-Ming University, Taipei, Taiwan; Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan; Division of Infectious Diseases, Department of Medicine, Taipei City Hospital Ren-Ai Branch, TaiwanDivision of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, TaiwanDivision of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; Division of Infectious Diseases, Department of Medicine, Taipei City Hospital Ren-Ai Branch, Taiwan; Corresponding author at: Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.Background: The clinical utilisation of deep sequencing in HIV treatment has been hindered due to its unknown correlation with standard Sanger genotyping and the undetermined value of minority drug resistance mutation (DRM) detection. Objectives: To compare deep sequencing performance to standard Sanger genotyping with clinical samples, in an effort to delineate the correlation between the results from the two methods and to find the optimal deep sequencing threshold for clinical utilisation. Methods: We conducted a retrospective study using stored plasma collected from August 2014 to March 2018 for HIV genotyping with the commercial Sanger genotyping kit. Samples with available Sanger genotyping reports were further deep sequenced. Drug resistance was interpreted according to the Stanford HIV drug resistance database algorithm. Results: At 15–25% minority detection thresholds, 9–15% cases had underestimated DRMs by Sanger sequencing. The concordance between the Sanger and deep sequencing reports was 68–82% in protease-reverse transcriptase region and 88–97% in integrase region at 5–25% thresholds. The undetected drug resistant minority variants by Sanger sequencing contributed to the lower negative predictive value of Sanger genotyping in cases harbouring DRMs. Conclusions: Use of deep sequencing improved detection of antiretroviral resistance mutations especially in cases with virological failure or previous treatment interruption. Deep sequencing with 10–15% detection thresholds may be considered a suitable substitute for Sanger sequencing on antiretroviral DRM detection. Keywords: HIV, Next-generation sequencing, Deep sequencing, Drug resistance, Sanger sequencinghttp://www.sciencedirect.com/science/article/pii/S120197122030062X |
| spellingShingle | Nan-Yu Chen Shu-Wei Kao Zhuo-Hao Liu Ting-Shu Wu Chia-Lung Tsai Hsi-Hsun Lin Wing-Wai Wong Yea-Yuan Chang Shu-Sheng Chen Stephane Wen-Wei Ku Shall I trust the report? Variable performance of Sanger sequencing revealed by deep sequencing on HIV drug resistance mutation detection International Journal of Infectious Diseases |
| title | Shall I trust the report? Variable performance of Sanger sequencing revealed by deep sequencing on HIV drug resistance mutation detection |
| title_full | Shall I trust the report? Variable performance of Sanger sequencing revealed by deep sequencing on HIV drug resistance mutation detection |
| title_fullStr | Shall I trust the report? Variable performance of Sanger sequencing revealed by deep sequencing on HIV drug resistance mutation detection |
| title_full_unstemmed | Shall I trust the report? Variable performance of Sanger sequencing revealed by deep sequencing on HIV drug resistance mutation detection |
| title_short | Shall I trust the report? Variable performance of Sanger sequencing revealed by deep sequencing on HIV drug resistance mutation detection |
| title_sort | shall i trust the report variable performance of sanger sequencing revealed by deep sequencing on hiv drug resistance mutation detection |
| url | http://www.sciencedirect.com/science/article/pii/S120197122030062X |
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