External Quality Assessment Program for Next-Generation Sequencing-Based HIV Drug Resistance Testing: Logistical Considerations

被引:7
作者
Ji, Hezhao [1 ,2 ]
Parkin, Neil [3 ]
Gao, Feng [4 ,5 ]
Denny, Thomas [4 ,5 ]
Jennings, Cheryl [6 ]
Sandstrom, Paul [1 ,2 ]
Kantor, Rami [7 ]
机构
[1] Publ Hlth Agcy Canada, JC Wilt Infect Dis Res Ctr, Natl HIV & Retrovirol Labs, Winnipeg, MB R3E 3R2, Canada
[2] Univ Manitoba, Dept Med Microbiol & Infect Dis, Winnipeg, MB R3E 0J9, Canada
[3] Data First Consulting Inc, Sebastopol, CA 95472 USA
[4] Duke Univ, Duke Human Vaccine Inst, Med Ctr, Durham, NC 27710 USA
[5] Duke Univ, Med Ctr, Dept Med, Durham, NC 27710 USA
[6] Rush Univ, Dept Mol Pathogens & Immun, Chicago, IL 60612 USA
[7] Brown Univ, Div Infect Dis, Alpert Med Sch, Providence, RI 02906 USA
来源
VIRUSES-BASEL | 2020年 / 12卷 / 05期
关键词
HIV; drug resistance; next generation sequencing; external quality assessment; PROFICIENCY; ORGANIZATION; STANDARDIZE;
D O I
10.3390/v12050556
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
Next-generation sequencing (NGS) is likely to become the new standard method for HIV drug resistance (HIVDR) genotyping. Despite the significant advances in the development of wet-lab protocols and bioinformatic data processing pipelines, one often-missing critical component of an NGS HIVDR assay for clinical use is external quality assessment (EQA). EQA is essential for ensuring assay consistency and laboratory competency in performing routine biomedical assays, and the rollout of NGS HIVDR tests in clinical practice will require an EQA. In September 2019, the 2(nd) International Symposium on NGS HIVDR was held in Winnipeg, Canada. It convened a multidisciplinary panel of experts, including research scientists, clinicians, bioinformaticians, laboratory biologists, biostatisticians, and EQA experts. A themed discussion was conducted on EQA strategies towards such assays during the symposium. This article describes the logistical challenges identified and summarizes the opinions and recommendations derived from these discussions, which may inform the development of an inaugural EQA program for NGS HIVDR in the near future.
引用
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页数:18
相关论文
共 29 条
[1]  
[Anonymous], ISO IEC GUID 43 1 1
[2]  
CLSI, 2019, HARM TERM DAT
[3]   HIV-1 drug resistance and resistance testing [J].
Clutter, Dana S. ;
Jordan, Michael R. ;
Bertagnolio, Silvia ;
Shafer, Robert W. .
INFECTION GENETICS AND EVOLUTION, 2016, 46 :292-307
[4]   Model for assessment of proficiency of human immunodeficiency virus type 1 sequencing-based genotypic antiretroviral assays [J].
Huang, DD ;
Bremer, JW ;
Brambilla, DJ ;
Palumbo, PE .
JOURNAL OF CLINICAL MICROBIOLOGY, 2005, 43 (08) :3963-3970
[5]  
Inzaule Seth C, 2016, Lancet Infect Dis, V16, pe267, DOI 10.1016/S1473-3099(16)30118-9
[6]   Bioinformatic data processing pipelines in support of next-generation sequencing-based HIV drug resistance testing: the Winnipeg Consensus [J].
Ji, Hezhao ;
Enns, Eric ;
Brumme, Chanson J. ;
Parkin, Neil ;
Howison, Mark ;
Lee, Emma R. ;
Capina, Rupert ;
Marinier, Eric ;
Avila-Rios, Santiago ;
Sandstrom, Paul ;
Van Domselaar, Gary ;
Harrigan, Richard ;
Paredes, Roger ;
Kantor, Rami ;
Noguera-Julian, Marc .
JOURNAL OF THE INTERNATIONAL AIDS SOCIETY, 2018, 21 (10)
[7]   Next-generation sequencing of dried blood spot specimens: a novel approach to HIV drug-resistance surveillance [J].
Ji, Hezhao ;
Li, Yang ;
Graham, Morag ;
Liang, Ben Binhua ;
Pilon, Richard ;
Tyson, Shari ;
Peters, Geoff ;
Tyler, Shaun ;
Merks, Harriet ;
Bertagnolio, Silvia ;
Soto-Ramirez, Luis ;
Sandstrom, Paul ;
Brooks, James .
ANTIVIRAL THERAPY, 2011, 16 (06) :871-878
[8]   Minority HIV-1 drug resistance mutations are present in antiretroviral treatment-naive populations and associate with reduced treatment efficacy [J].
Johnson, Jeffrey A. ;
Li, Jin-Fen ;
Wei, Xierong ;
Lipscomb, Jonathan ;
Irlbeck, David ;
Craig, Charles ;
Smith, Amanda ;
Bennett, Diane E. ;
Monsour, Michael ;
Sandstrom, Paul ;
Lanier, E. Randall ;
Heneine, Walid .
PLOS MEDICINE, 2008, 5 (07) :1112-1122
[9]   Quality control trial for human immunodeficiency virus type 1 drug resistance testing using clinical samples reveals problems with detecting minority species and interpretation of test results [J].
Korn, K ;
Reil, H ;
Walter, H ;
Schmidt, B .
JOURNAL OF CLINICAL MICROBIOLOGY, 2003, 41 (08) :3559-3565
[10]   TREAT Asia Quality Assessment Scheme (TAQAS) to standardize the outcome of HIV genotypic resistance testing in a group of Asian laboratories [J].
Land, Sally ;
Cunningham, Philip ;
Zhou, Jialun ;
Frost, Kevin ;
Katzenstein, David ;
Kantor, Rami ;
Chen, Yi-Ming Arthur ;
Oka, Shinichi ;
DeLong, Allison ;
Sayer, David ;
Smith, Jeffery ;
Dax, Elizabeth M. ;
Law, Matthew .
JOURNAL OF VIROLOGICAL METHODS, 2009, 159 (02) :185-193