Evaluation of GS Junior and MiSeq next-generation sequencing technologies as an alternative to Trugene population sequencing in the clinical HIV laboratory

Journal of Virological Methods

Volumn 212, Issue , 2015, Pages 12-16

  Ram, Daniela ^a   Leshkowitz, Dena ^b   Gonzalez, Dimitri ^c   Forer, Relly ^d   Levy, Itzchak ^e   Chowers, Michal ^f   Lorber, Margalit ^g   Hindiyeh, Musa ^a,h   Mendelson, Ella ^a,h   Mor, Orna ^a  

^a MINISTRY OF HEALTH   (Israel)

^b WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^c ABL TherapyEdge Spain SL ^*  (Spain)

^d DYN LABS Ltd   (Israel)

^e SHEBA MEDICAL CENTER   (Israel)

^f MEIR MEDICAL CENTER   (Israel)

^g RAMBAM MEDICAL CENTER   (Israel)

^h TEL AVIV UNIVERSITY   (Israel)

Author keywords

DeepChek HIV TherapyEdge; GS junior; HIV 1 mutations; MiSeq; Next generation sequencing (NGS); Trugene

Indexed keywords

AMINO ACID; ANTIRETROVIRUS AGENT; ATAZANAVIR; EMTRICITABINE PLUS TENOFOVIR DISOPROXIL; NONNUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITOR; PROTEINASE; RNA DIRECTED DNA POLYMERASE; RNA DIRECTED DNA POLYMERASE INHIBITOR; HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE;

ADULT; AMINO ACID SUBSTITUTION; ARTICLE; CLINICAL ARTICLE; CLINICAL LABORATORY; CONSENSUS; CONTROLLED STUDY; FEMALE; GENE SEQUENCE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; ISRAEL; MALE; PREVALENCE; SEQUENCE ANALYSIS; VIRUS CARRIER; CLASSIFICATION; COMPARATIVE STUDY; COMPUTER PROGRAM; DIAGNOSTIC PROCEDURE; EVALUATION STUDY; GENETICS; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; MICROBIAL SENSITIVITY TEST; MISSENSE MUTATION; PROCEDURES; SENSITIVITY AND SPECIFICITY; VIROLOGY;

HUMAN IMMUNODEFICIENCY VIRUS 1;

AMINO ACID SUBSTITUTION; CLINICAL LABORATORY TECHNIQUES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HIV; HIV INFECTIONS; HIV PROTEASE; HIV REVERSE TRANSCRIPTASE; ISRAEL; MICROBIAL SENSITIVITY TESTS; MUTATION, MISSENSE; SENSITIVITY AND SPECIFICITY; SOFTWARE;

EID: 84913534915     PISSN: 01660934     EISSN: 18790984     Source Type: Journal    
DOI: 10.1016/j.jviromet.2014.11.003     Document Type: Article

References (36)

1. Archer J., Baillie G., Watson S.J., Kellam P., Rambaut A., Robertson D.L. Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II. BMC Bioinform. 2012, 13:47.
2. Archer J., Weber J., Henry K., Winner D., Gibson R., Lee L., Paxinos E., Arts E.J., Robertson D.L., Mimms L., Quinones-Mateu M.E. Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism. PLoS ONE 2012, 7:e49602.
3. Armenia D., Vandenbroucke I., Fabeni L., Van Marck H., Cento V., D'Arrigo R., Van Wesenbeeck L., Scopelliti F., Micheli V., Bruzzone B., Lo Caputo S., Aerssens J., Rizzardini G., Tozzi V., Narciso P., Antinori A., Stuyver L., Perno C.F., Ceccherini-Silberstein F. Study of genotypic and phenotypic HIV-1 dynamics of integrase mutations during raltegravir treatment: a refined analysis by ultra-deep 454 pyrosequencing. J. Infect. Dis. 2012, 205:557-567.
4. Avidor B., Girshengorn S., Matus N., Talio H., Achsanov S., Zeldis I., Fratty I.S., Katchman E., Brosh-Nissimov T., Hassin D., Alon D., Bentwich Z., Yust I., Amit S., Forer R., Vulih Shultsman I., Turner D. Evaluation of a benchtop HIV ultradeep pyrosequencing drug resistance assay in the clinical laboratory. J. Clin. Microbiol. 2013, 51:880-886.
5. Beerenwinkel N., Gunthard H.F., Roth V., Metzner K.J. Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data. Front. Microbiol. 2012, 3:329.
6. Buzon M.J., Codoner F.M., Frost S.D., Pou C., Puertas M.C., Massanella M., Dalmau J., Llibre J.M., Stevenson M., Blanco J., Clotet B., Paredes R., Martinez-Picado J. Deep molecular characterization of HIV-1 dynamics under suppressive HAART. PLoS Pathog. 2011, 7:e1002314.
7. Codoner F.M., Pou C., Thielen A., Garcia F., Delgado R., Dalmau D., Alvarez-Tejado M., Ruiz L., Clotet B., Paredes R. Added value of deep sequencing relative to population sequencing in heavily pre-treated HIV-1-infected subjects. PLoS ONE 2011, 6:e19461.
8. D'Aquila R.T., Geretti A.M., Horton J.H., Rouse E., Kheshti A., Raffanti S., Oie K., Pappa K., Ross L.L. Tenofovir (TDF)-selected or abacavir (ABC)-selected low-frequency HIV type 1 subpopulations during failure with persistent viremia as detected by ultradeep pyrosequencing. AIDS Res. Hum. Retroviruses 2011, 27:201-209.
9. Dudley D.M., Chin E.N., Bimber B.N., Sanabani S.S., Tarosso L.F., Costa P.R., Sauer M.M., Kallas E.G., O'Connor D.H. Low-cost ultra-wide genotyping using Roche/454 pyrosequencing for surveillance of HIV drug resistance. PLoS ONE 2012, 7:e36494.
10. Dundas N., Leos N.K., Mitui M., Revell P., Rogers B.B. Comparison of automated nucleic acid extraction methods with manual extraction. J. Mol. Diagn. 2008, 10:311-316.
11. Fisher R., van Zyl G.U., Travers S.A., Kosakovsky Pond S.L., Engelbrech S., Murrell B., Scheffler K., Smith D. Deep sequencing reveals minor protease resistance mutations in patients failing a protease inhibitor regimen. J. Virol. 2012, 86:6231-6237.
12. Gall A., Ferns B., Morris C., Watson S., Cotten M., Robinson M., Berry N., Pillay D., Kellam P. Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes. J. Clin. Microbiol. 2012, 50:3838-3844.
13. Gianella S., Richman D.D. Minority variants of drug-resistant HIV. J. Infect. Dis. 2010, 202:657-666.
14. Glenn T.C. Field guide to next-generation DNA sequencers. Mol. Ecol. Resour. 2011, 11:759-769. 10.1111/j.1755-0998.2011.03024.x.
15. Halvas E.K., Aldrovandi G.M., Balfe P., Beck I.A., Boltz V.F., Coffin J.M., Frenkel L.M., Hazelwood J.D., Johnson V.A., Kearney M., Kovacs A., Kuritzkes D.R., Metzner K.J., Nissley D.V., Nowicki M., Palmer S., Ziermann R., Zhao R.Y., Jennings C.L., Bremer J., Brambilla D., Mellors J.W. Blinded, multicenter comparison of methods to detect a drug-resistant mutant of human immunodeficiency virus type 1 at low frequency. J. Clin. Microbiol. 2006, 44:2612-2614.
16. Hedskog C., Mild M., Jernberg J., Sherwood E., Bratt G., Leitner T., Lundeberg J., Andersson B., Albert J. Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing. PLoS ONE 2010, 5:e11345.
17. Jiang Q., Turner T., Sosa M.X., Rakha A., Arnold S., Chakravarti A. Rapid and efficient human mutation detection using a bench-top next-generation DNA sequencer. Hum. Mutat. 2012, 33:281-289.
18. Joshi N.A., Fass J.N. Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33) [Software] 2011, Available at https://github.com/najoshi/sickle.
19. Kivioja T., Vähärautio A., Karlsson K., Bonke M., Enge M., Linnarsson S., Taipale J. Counting absolute numbers of molecules using unique molecular identifiers. Nat. Methods 2011, 9:72-74.
20. Le T., Chiarella J., Simen B.B., Hanczaruk B., Egholm M., Landry M.L., Dieckhaus K., Rosen M.I., Kozal M.J. Low-abundance HIV drug-resistant viral variants in treatment-experienced persons correlate with historical antiretroviral use. PLoS ONE 2009, 4:e6079.
21. Li H., Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010, 26:589-595.
22. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25:2078-2079.
23. Li J.Z., Chapman B., Charlebois P., Hofmann O., Weiner B., Porter A.J., Samuel R., Vardhanabhuti S., Zheng L., Eron J., Taiwo B., Zody M.C., Henn M.R., Kuritzkes D.R., Hide W., Wilson C.C., Berzins B.I., Acosta E.P., Bastow B., Kim P.S., Read S.W., Janik J., Meres D.S., Lederman M.M., Mong-Kryspin L., Shaw K.E., Zimmerman L.G., Leavitt R., De La Rosa G., Jennings A. Comparison of illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy. PLoS ONE 2014, 9:e90485.
24. Messiaen P., Verhofstede C., Vandenbroucke I., Dinakis S., Van Eygen V., Thys K., Winters B., Aerssens J., Vogelaers D., Stuyver L.J., Vandekerckhove L. Ultra-deep sequencing of HIV-1 reverse transcriptase before start of an NNRTI-based regimen in treatment-naive patients. Virology 2012, 426:7-11.
25. Paredes R., Boulme R., Gonzalez D., Noyuegra-Julian M., Delgado R., Dalmau D., Alvarez-Tejado M., Saaya C., Gracia F. Use of DeepChek-HIV system in the PRIUS study: validation of a new reliable genotyping solution to streamline the 454 sequencing analysis of HIV drug resistance in routine diagnosis and research applications. Antivir. Ther. 2012, 17:A151.
26. Pou C., Noguera-Julian M., Perez-Alvarez S., Garcia F., Delgado R., Dalmau D., Alvarez-Tejado M., Gonzalez D., Sayada C., Chueca N., Pulido F., Ibanez L., Rodriguez C., Casadella M., Santos J.R., Ruiz L., Clotet B., Paredes R. Improved prediction of salvage antiretroviral therapy outcomes using ultrasensitive HIV-1 drug resistance testing. Clin. Infect. Dis. 2014.
27. Schuurman R., Brambilla D., de Groot T., Huang D., Land S., Bremer J., Benders I., Boucher C.A. Underestimation of HIV type 1 drug resistance mutations: results from the ENVA-2 genotyping proficiency program. AIDS Res. Hum. Retroviruses 2002, 18:243-248.
28. Shafer R.W. Rationale and uses of a public HIV drug-resistance database. J. Infect. Dis. 2006, 194(Suppl. 1):S51L 8.
29. Shendure J., Lieberman Aiden E. The expanding scope of DNA sequencing. Nat. Biotechnol. 2012, 30:1084-1094.
30. Shulman L.M., Hindiyeh M., Muhsen K., Cohen D., Mendelson E., Sofer D. Evaluation of four different systems for extraction of RNA from stool suspensions using MS-2 coliphage as an exogenous control for RT-PCR inhibition. PLoS ONE 2012, 7:e39455.
31. Simen B.B., Braverman M.S., Abbate I., Aerssens J., Bidet Y., Bouchez O., Gabriel C., Izopet J., Kessler H.H., Stelzl E., Di Giallonardo F., Schlapbach R., Radonic A., Paredes R., Recordon-Pinson P., Sakwa J., St John E.P., Schmitz-Agheguian G.G., Metzner K.J., Daumer M.P. An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing. J. Virol. Methods 2014, 204:31-37.
32. Simen B.B., Simons J.F., Hullsiek K.H., Novak R.M., Macarthur R.D., Baxter J.D., Huang C., Lubeski C., Turenchalk G.S., Braverman M.S., Desany B., Rothberg J.M., Egholm M., Kozal M.J. Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J. Infect. Dis. 2009, 199:693-701.
33. Snoeck J., Riva C., Steegen K., Schrooten Y., Maes B., Vergne L., Van Laethem K., Peeters M., Vandamme A.M. Optimization of a genotypic assay applicable to all human immunodeficiency virus type 1 protease and reverse transcriptase subtypes. J. Virol. Methods 2005, 128:47-53.
34. Stelzl E., Proll J., Bizon B., Niklas N., Danzer M., Hackl C., Stabentheiner S., Gabriel C., Kessler H.H. Human immunodeficiency virus type 1 drug resistance testing: evaluation of a new ultra-deep sequencing-based protocol and comparison with the TRUGENE HIV-1 Genotyping Kit. J. Virol. Methods 2011, 178:94-97.
35. Zagordi O., Klein R., Daumer M., Beerenwinkel N. Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. Nucleic Acids Res. 2010, 38:7400-7409.
36. Zhou Z., Wagar N., DeVos J.R., Rottinghaus E., Diallo K., Nguyen D.B., Bassey O., Ugbena R., Wadonda-Kabondo N., McConnell M.S., Zulu I., Chilima B., Nkengasong J., Yang C. Optimization of a low cost and broadly sensitive genotyping assay for HIV-1 drug resistance surveillance and monitoring in resource-limited settings. PLoS ONE 2011, 6:e28184.