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SmartGene in Science

Recent journal articles and posters citing the use of SmartGene's technology are listed below. Please use the links to the left to access archived publications, organized by year. Or, click on the images immediately following this text to access publications grouped by the area of study.

      Bacteria       Fungi       HIV


Recent Publications

2019

Microbiota shifts and histopathology of the turkey ceca during early Histomonas meleagridis infection. E. Chadwick, F. Edens, D. Ellis, and R. Beckstead. Poster presented by NC State University, Prestage Department of Poultry Science at the 2019 Poultry Science Association’s Annual Meeting held in Montreal, Canada, July 15-19. The poster’s primary author, Elle Chadwick, received a Certificate of Excellence for her work. (Click here to request additional information.)

Citation: “… Microbiota sequencing data was analyzed in the SmartGene® 16s Microbiome Pipeline and populations identified via the SmartGene® 16S Centroid reference database ...”


Same meat, different gravy: ignore the new names of mycobacteria. E. Tortoli, B. Brown-Elliott, J. Chalmers, D.  Cirillo, C.  Daley, S.  Emler, RA Floto, M. Garcia, W. Hoefsloot, W-J Koh, C. Lange, M. Loebinger, F. Maurer, K. Morimoto, S. Niemann, E. Richter, C. Turenne, R. Vasireddy, S. Vasireddy, D. Wagner, R. Wallace Jr., N. Wengenack, and J. van Ingen. European Respiratory Journal 2019 Vol 54 Issue 1 1900795. Published 11 July 2019. (Click here to access the article.)

Citation: "...We are confident that microbiologists and clinicians will clearly support the possibility, offered by the Code, to wilfully ignore renaming of clinically important organisms such as nontuberculous mycobacteria."


First evaluation of the Next-Generation Sequencing platform for the detection of HIV-1 drug resistance mutations in Belgium. G. Dessilly, L. Goeminne, A. Vandenbroucke, FE Dufrasne, A. Martin, B. Kabamba-Mukabi. PLOS One 13(12):e0209561. Published December 31, 2018; corrected January 25, 2019. (Click here to request additional information.)

Citation: "... Sequences were proofread using the SmartGene HIV module ... and sequences were analysed with IDNS-HIV1 SmartGene module … . DRMs (as well as reads, coverage) and drug resistance reports were compared by exporting raw FASTQ sequences ... and analysing them with the ... HIV SmartGene module, IDNS-ASP (Lausanne, Switzerland)."


2018

Rare occurrence of doravirine resistance-associated mutations in HIV-1-infected, treatment-naive patients. C. Soulie, MM Santoro, C. Charpentier, A. Storto, D. Paraskevis, D. Di Carlo, W. Gennari, G. Sterrantino, M. Zazzi, CF Perno, V. Calvez, D. Descamps, F. Ceccherini-Silberstein, and AG Marcelin. Journal of Antimicrobial Chemotherapy doi:10.1093/jac/dky464. Accepted 13 October 2018, 4 pages. (Click here to request additional information.)

Citation: “… Resistance interpretation was made using the SmartGene Integrated Database Network System (SmartGene, Switzerland; http://www.smartgene.com) according to the Stanford algorithm … or the ANRS algorithm ... HIV-1 subtype was determined based on the RT and protease coding regions by the SmartGene algorithm (SmartGene, Switzerland) or by phylogenetic analyses, using reference sequences of HIV-1 subtypes and circulating recombinant forms (CRFs) from the Los Alamos Database ...”


Evaluation of different analysis pipelines for the detection of HIV-1 minority resistant variants. M. Perrier, N. Désiré, A. Storto, E. Todesco, C. Rodriguez, M. Bertine, Q. Le Hingrat, B. Visseaux, V. Calvez, D. Descamps, A. Marcelin, and C. Charpentier. PLOS One: Detection of HIV-1 minority variants by different software, published online 1 June 2018, 13 pages. (Click here to request additional information.)

Citation: "… The SmartGene NGS HIV-1 module is based on the proprietary IDNS (Integrated Database Network System). This analysis platform offers a web interface on which sff or fastq files can be uploaded. The analysis pipeline can be chosen by the user. Also appropriate cut-off for ambiguous bases/background (0.5%), minimum coverage of variant (50 reads) and interpretation cut-off have been selected before the analysis. ... HIV drug resistance mutations were interpreted with the embedded ANRS resistance algorithm at the chosen cut-off .... The complete mutation list with their respective frequencies as percentage values was compiled, and lastly a drug resistance profile was generated for each sample. … SmartGene software proved to be more user-friendly, and it provided a time-saving, offering an integrated solution from the raw sequence data, to the results, and finally to the clinical report. All of the tested tools are web-based, thus constituting a portable work-space. The read alignments are viewable and different technical variables are readily available, thus allowing for technical validation of the results. …"


Molecular detection of fungal pathogens in clinical specimens by 18S rDNA high-throughput screening in comparison to ITS PCR and culture. K. Wagner, B. Springer, VP Pires, and PM Keller. Nature.com Scientific Reports, published online 03 May 2018. (Click here to request additional information.)

Citation: "… We used two SmartGene databases, the ITS SmartGene IDNS database ... and the 18S SmartGene IDNS database .... Only sequences of high quality … are accepted in these SmartGene IDNS databases to allow standardized, reproducible, and accurate identification of fungal pathogens. ... We found high concordance between 18S rDNA RT-PCR, ITS PCR, and culture, respectively for the diagnosis of fungal infections. … "


Frequency of occurrence of HIV-1 dual infection in a Belgian MSM population. L. Hebberecht, L. Vancoillie, M. Schauvliege, D. Staelens, K. Dauwe, V. Mortier, and C. Verhofstede. PLOS One: HIV-1 superinfection in MSM, 6 April 2018. (Click here to request additional information.)

Citation: "…Subtyping of the HIV-1 infection at diagnosis was done using the subtyping tool of Smartgene IDNS... and the protease and reverse transcriptase sequences generated for the purpose of baseline resistance analysis. … Proofreading was done using Smartgene IDNS. … Population HIV-1 protease-reverse transcriptase sequences were obtained through routine laboratory activities for the purpose of drug resistance analysis using an in-house Sanger sequencing protocol. … For the sequences generated by clonal or population sequencing, proofreading was done using Smartgene IDNS (Smartgene, Zug, Switzerland). ..."


Phylogenetic analysis of the Belgian HIV-1 epidemic reveals that local transmission is almost exclusively driven by men having sex with men despite presence of large African migrant communities. C. Verhofstede, K. Dauwe, K. Fransen, K. Van Laethem, S. Van den Winjngaert, J. Ruelle, M. Delforge, E. Vancutsem, D. Vaira, K. Stoffels, SG Ribas, G. Dessilly, L. Debaisieux, D. Pierard, M. Van Ranst, M. Hayette, J. Deblonde, A. Sasse, D. Van Beckhoven, V. Mortier. Elsevier: Infection, Genetics and Evolution 61 (2018) 36-44, 4 March 2018. (Click here to request additional information.)

Citation: "...Collection of sequence data was facilitated by the use of a network database (Integrated Database Network System, Smartgene, Zug, Switzerland). ..."