Loading…
Shall I trust the report? Variable performance of Sanger sequencing revealed by deep sequencing on HIV drug resistance mutation detection
•For HIV genotyping, the undetected minority populations by standard Sanger sequencing (SS) were not always minor.•9–15% of cases with treatment failure/interruption had underestimated drug resistant variants accounting for ≥15–25% total viral population.•The study suggested that 10-15% threshold de...
Saved in:
Published in: | International journal of infectious diseases 2020-04, Vol.93, p.182-191 |
---|---|
Main Authors: | , , , , , , , , , |
Format: | Article |
Language: | English |
Subjects: | |
Citations: | Items that this one cites Items that cite this one |
Online Access: | Get full text |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
cited_by | cdi_FETCH-LOGICAL-c466t-9350f0ab56c098c7dc9444f9556ed855a95e63b8b99b09cae4380941ed8311c03 |
---|---|
cites | cdi_FETCH-LOGICAL-c466t-9350f0ab56c098c7dc9444f9556ed855a95e63b8b99b09cae4380941ed8311c03 |
container_end_page | 191 |
container_issue | |
container_start_page | 182 |
container_title | International journal of infectious diseases |
container_volume | 93 |
creator | Chen, Nan-Yu Kao, Shu-Wei Liu, Zhuo-Hao Wu, Ting-Shu Tsai, Chia-Lung Lin, Hsi-Hsun Wong, Wing-Wai Chang, Yea-Yuan Chen, Shu-Sheng Ku, Stephane Wen-Wei |
description | •For HIV genotyping, the undetected minority populations by standard Sanger sequencing (SS) were not always minor.•9–15% of cases with treatment failure/interruption had underestimated drug resistant variants accounting for ≥15–25% total viral population.•The study suggested that 10-15% threshold deep sequencing may be considered a suitable substitute for SS on HIV drug resistant mutation detection.
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.
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.
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.
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.
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. |
doi_str_mv | 10.1016/j.ijid.2020.02.004 |
format | article |
fullrecord | <record><control><sourceid>proquest_doaj_</sourceid><recordid>TN_cdi_doaj_primary_oai_doaj_org_article_ad03902e74dd45f394df6ad4fd28e4a6</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><els_id>S120197122030062X</els_id><doaj_id>oai_doaj_org_article_ad03902e74dd45f394df6ad4fd28e4a6</doaj_id><sourcerecordid>2356576361</sourcerecordid><originalsourceid>FETCH-LOGICAL-c466t-9350f0ab56c098c7dc9444f9556ed855a95e63b8b99b09cae4380941ed8311c03</originalsourceid><addsrcrecordid>eNp9Uctu1DAUjRCIPuAHWCAv2ST4nVhCQqiCdqRKLArdWo59M3WUxIPtVOon8Nc4nVKxYuUrn4d9z6mqdwQ3BBP5cWz86F1DMcUNpg3G_EV1Srq2q5kg5GWZKSa1agk9qc5SGnFhSNm9rk4YxZJ0kp5Wv2_uzDShHcpxTRnlO0ARDiHmz-jWRG_6CdAB4hDibBYLKAzoxix7iCjBrxUW65d9UdyDmcCh_gE5gMO_WFjQ1e4WubhuvORTfvSZ12yyL6CDDHab3lSvBjMlePt0nlc_v339cXFVX3-_3F18ua5t-XyuFRN4wKYX0mLV2dZZxTkflBASXCeEUQIk67teqR4ra4CzDitOCsgIsZidV7ujrwtm1IfoZxMfdDBeP16EuNcmZm8n0MZhpjCFljvHxcAUd4M0jg-OdsCNLF4fjl6HGMrGKevZJwvTZBYIa9KUCSlaySQpVHqk2hhSijA8P02w3urUo97q1FudGlNdyiqi90_-az-De5b87a8QPh0JUBK79xB1sr4kD87HEmtZyf_P_w_rBrI8</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2356576361</pqid></control><display><type>article</type><title>Shall I trust the report? Variable performance of Sanger sequencing revealed by deep sequencing on HIV drug resistance mutation detection</title><source>ScienceDirect</source><source>BACON - Elsevier - GLOBAL_SCIENCEDIRECT-OPENACCESS</source><creator>Chen, Nan-Yu ; Kao, Shu-Wei ; Liu, Zhuo-Hao ; Wu, Ting-Shu ; Tsai, Chia-Lung ; Lin, Hsi-Hsun ; Wong, Wing-Wai ; Chang, Yea-Yuan ; Chen, Shu-Sheng ; Ku, Stephane Wen-Wei</creator><creatorcontrib>Chen, Nan-Yu ; Kao, Shu-Wei ; Liu, Zhuo-Hao ; Wu, Ting-Shu ; Tsai, Chia-Lung ; Lin, Hsi-Hsun ; Wong, Wing-Wai ; Chang, Yea-Yuan ; Chen, Shu-Sheng ; Ku, Stephane Wen-Wei</creatorcontrib><description>•For HIV genotyping, the undetected minority populations by standard Sanger sequencing (SS) were not always minor.•9–15% of cases with treatment failure/interruption had underestimated drug resistant variants accounting for ≥15–25% total viral population.•The study suggested that 10-15% threshold deep sequencing may be considered a suitable substitute for SS on HIV drug resistant mutation detection.
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.
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.
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.
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.
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.</description><identifier>ISSN: 1201-9712</identifier><identifier>EISSN: 1878-3511</identifier><identifier>DOI: 10.1016/j.ijid.2020.02.004</identifier><identifier>PMID: 32061862</identifier><language>eng</language><publisher>Canada: Elsevier Ltd</publisher><subject>Deep sequencing ; Drug resistance ; HIV ; Next-generation sequencing ; Sanger sequencing</subject><ispartof>International journal of infectious diseases, 2020-04, Vol.93, p.182-191</ispartof><rights>2020 The Author(s)</rights><rights>Copyright © 2020 The Author(s). Published by Elsevier Ltd.. All rights reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c466t-9350f0ab56c098c7dc9444f9556ed855a95e63b8b99b09cae4380941ed8311c03</citedby><cites>FETCH-LOGICAL-c466t-9350f0ab56c098c7dc9444f9556ed855a95e63b8b99b09cae4380941ed8311c03</cites><orcidid>0000-0002-7073-2325 ; 0000-0003-4079-8697</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S120197122030062X$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>314,780,784,3549,27924,27925,45780</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32061862$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chen, Nan-Yu</creatorcontrib><creatorcontrib>Kao, Shu-Wei</creatorcontrib><creatorcontrib>Liu, Zhuo-Hao</creatorcontrib><creatorcontrib>Wu, Ting-Shu</creatorcontrib><creatorcontrib>Tsai, Chia-Lung</creatorcontrib><creatorcontrib>Lin, Hsi-Hsun</creatorcontrib><creatorcontrib>Wong, Wing-Wai</creatorcontrib><creatorcontrib>Chang, Yea-Yuan</creatorcontrib><creatorcontrib>Chen, Shu-Sheng</creatorcontrib><creatorcontrib>Ku, Stephane Wen-Wei</creatorcontrib><title>Shall I trust the report? Variable performance of Sanger sequencing revealed by deep sequencing on HIV drug resistance mutation detection</title><title>International journal of infectious diseases</title><addtitle>Int J Infect Dis</addtitle><description>•For HIV genotyping, the undetected minority populations by standard Sanger sequencing (SS) were not always minor.•9–15% of cases with treatment failure/interruption had underestimated drug resistant variants accounting for ≥15–25% total viral population.•The study suggested that 10-15% threshold deep sequencing may be considered a suitable substitute for SS on HIV drug resistant mutation detection.
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.
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.
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.
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.
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.</description><subject>Deep sequencing</subject><subject>Drug resistance</subject><subject>HIV</subject><subject>Next-generation sequencing</subject><subject>Sanger sequencing</subject><issn>1201-9712</issn><issn>1878-3511</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>DOA</sourceid><recordid>eNp9Uctu1DAUjRCIPuAHWCAv2ST4nVhCQqiCdqRKLArdWo59M3WUxIPtVOon8Nc4nVKxYuUrn4d9z6mqdwQ3BBP5cWz86F1DMcUNpg3G_EV1Srq2q5kg5GWZKSa1agk9qc5SGnFhSNm9rk4YxZJ0kp5Wv2_uzDShHcpxTRnlO0ARDiHmz-jWRG_6CdAB4hDibBYLKAzoxix7iCjBrxUW65d9UdyDmcCh_gE5gMO_WFjQ1e4WubhuvORTfvSZ12yyL6CDDHab3lSvBjMlePt0nlc_v339cXFVX3-_3F18ua5t-XyuFRN4wKYX0mLV2dZZxTkflBASXCeEUQIk67teqR4ra4CzDitOCsgIsZidV7ujrwtm1IfoZxMfdDBeP16EuNcmZm8n0MZhpjCFljvHxcAUd4M0jg-OdsCNLF4fjl6HGMrGKevZJwvTZBYIa9KUCSlaySQpVHqk2hhSijA8P02w3urUo97q1FudGlNdyiqi90_-az-De5b87a8QPh0JUBK79xB1sr4kD87HEmtZyf_P_w_rBrI8</recordid><startdate>202004</startdate><enddate>202004</enddate><creator>Chen, Nan-Yu</creator><creator>Kao, Shu-Wei</creator><creator>Liu, Zhuo-Hao</creator><creator>Wu, Ting-Shu</creator><creator>Tsai, Chia-Lung</creator><creator>Lin, Hsi-Hsun</creator><creator>Wong, Wing-Wai</creator><creator>Chang, Yea-Yuan</creator><creator>Chen, Shu-Sheng</creator><creator>Ku, Stephane Wen-Wei</creator><general>Elsevier Ltd</general><general>Elsevier</general><scope>6I.</scope><scope>AAFTH</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-7073-2325</orcidid><orcidid>https://orcid.org/0000-0003-4079-8697</orcidid></search><sort><creationdate>202004</creationdate><title>Shall I trust the report? Variable performance of Sanger sequencing revealed by deep sequencing on HIV drug resistance mutation detection</title><author>Chen, Nan-Yu ; Kao, Shu-Wei ; Liu, Zhuo-Hao ; Wu, Ting-Shu ; Tsai, Chia-Lung ; Lin, Hsi-Hsun ; Wong, Wing-Wai ; Chang, Yea-Yuan ; Chen, Shu-Sheng ; Ku, Stephane Wen-Wei</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c466t-9350f0ab56c098c7dc9444f9556ed855a95e63b8b99b09cae4380941ed8311c03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Deep sequencing</topic><topic>Drug resistance</topic><topic>HIV</topic><topic>Next-generation sequencing</topic><topic>Sanger sequencing</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chen, Nan-Yu</creatorcontrib><creatorcontrib>Kao, Shu-Wei</creatorcontrib><creatorcontrib>Liu, Zhuo-Hao</creatorcontrib><creatorcontrib>Wu, Ting-Shu</creatorcontrib><creatorcontrib>Tsai, Chia-Lung</creatorcontrib><creatorcontrib>Lin, Hsi-Hsun</creatorcontrib><creatorcontrib>Wong, Wing-Wai</creatorcontrib><creatorcontrib>Chang, Yea-Yuan</creatorcontrib><creatorcontrib>Chen, Shu-Sheng</creatorcontrib><creatorcontrib>Ku, Stephane Wen-Wei</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Directory of Open Access Journals</collection><jtitle>International journal of infectious diseases</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chen, Nan-Yu</au><au>Kao, Shu-Wei</au><au>Liu, Zhuo-Hao</au><au>Wu, Ting-Shu</au><au>Tsai, Chia-Lung</au><au>Lin, Hsi-Hsun</au><au>Wong, Wing-Wai</au><au>Chang, Yea-Yuan</au><au>Chen, Shu-Sheng</au><au>Ku, Stephane Wen-Wei</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Shall I trust the report? Variable performance of Sanger sequencing revealed by deep sequencing on HIV drug resistance mutation detection</atitle><jtitle>International journal of infectious diseases</jtitle><addtitle>Int J Infect Dis</addtitle><date>2020-04</date><risdate>2020</risdate><volume>93</volume><spage>182</spage><epage>191</epage><pages>182-191</pages><issn>1201-9712</issn><eissn>1878-3511</eissn><abstract>•For HIV genotyping, the undetected minority populations by standard Sanger sequencing (SS) were not always minor.•9–15% of cases with treatment failure/interruption had underestimated drug resistant variants accounting for ≥15–25% total viral population.•The study suggested that 10-15% threshold deep sequencing may be considered a suitable substitute for SS on HIV drug resistant mutation detection.
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.
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.
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.
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.
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.</abstract><cop>Canada</cop><pub>Elsevier Ltd</pub><pmid>32061862</pmid><doi>10.1016/j.ijid.2020.02.004</doi><tpages>10</tpages><orcidid>https://orcid.org/0000-0002-7073-2325</orcidid><orcidid>https://orcid.org/0000-0003-4079-8697</orcidid><oa>free_for_read</oa></addata></record> |
fulltext | fulltext |
identifier | ISSN: 1201-9712 |
ispartof | International journal of infectious diseases, 2020-04, Vol.93, p.182-191 |
issn | 1201-9712 1878-3511 |
language | eng |
recordid | cdi_doaj_primary_oai_doaj_org_article_ad03902e74dd45f394df6ad4fd28e4a6 |
source | ScienceDirect; BACON - Elsevier - GLOBAL_SCIENCEDIRECT-OPENACCESS |
subjects | Deep sequencing Drug resistance HIV Next-generation sequencing Sanger sequencing |
title | Shall I trust the report? Variable performance of Sanger sequencing revealed by deep sequencing on HIV drug resistance mutation detection |
url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-23T10%3A42%3A49IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_doaj_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Shall%20I%20trust%20the%20report?%20Variable%20performance%20of%20Sanger%20sequencing%20revealed%20by%20deep%20sequencing%20on%20HIV%20drug%20resistance%20mutation%20detection&rft.jtitle=International%20journal%20of%20infectious%20diseases&rft.au=Chen,%20Nan-Yu&rft.date=2020-04&rft.volume=93&rft.spage=182&rft.epage=191&rft.pages=182-191&rft.issn=1201-9712&rft.eissn=1878-3511&rft_id=info:doi/10.1016/j.ijid.2020.02.004&rft_dat=%3Cproquest_doaj_%3E2356576361%3C/proquest_doaj_%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c466t-9350f0ab56c098c7dc9444f9556ed855a95e63b8b99b09cae4380941ed8311c03%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2356576361&rft_id=info:pmid/32061862&rfr_iscdi=true |