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Full article title A polyglot approach to bioinformatics data integration: A phylogenetic analysis of HIV-1
Journal Evolutionary Bioinformatics
Author(s) Reisman, S.; Hatzopoulos, T.; Läufer, K.; Thiruvathukal, G.K.; Putonti, C.
Author affiliation(s) Loyola University Chicago
Primary contact Email: cputonti@luc.edu
Year published 2016
Volume and issue 12
Page(s) 23–27
DOI 10.4137/EBO.S32757
ISSN 1176-9343
Distribution license Creative Commons Attribution-NonCommercial 3.0 Unported
Website http://www.la-press.com/
Download http://www.la-press.com/ (PDF)
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Abstract

As sequencing technologies continue to drop in price and increase in throughput, new challenges emerge for the management and accessibility of genomic sequence data. We have developed a pipeline for facilitating the storage, retrieval, and subsequent analysis of molecular data, integrating both sequence and metadata. Taking a polyglot approach involving multiple languages, libraries, and persistence mechanisms, sequence data can be aggregated from publicly available and local repositories. Data are exposed in the form of a RESTful web service, formatted for easy querying, and retrieved for downstream analyses. As a proof of concept, we have developed a resource for annotated HIV-1 sequences. Phylogenetic analyses were conducted for >6,000 HIV-1 sequences revealing spatial and temporal factors influence the evolution of the individual genes uniquely. Nevertheless, signatures of origin can be extrapolated even despite increased globalization. The approach developed here can easily be customized for any species of interest.

Keywords: polyglot programming, RESTful web service, phylogenetics

Introduction

The increased throughput, coupled with reduced cost and time, of contemporary sequencing technologies has led to a surge in the number of publicly available, complete, annotated genomic sequences. For smaller viral species, it is now feasible to not only produce a single genome for a species but also capture the diversity present in an ecological niche, the focus of numerous metagenomic studies[1][2][3] as well as more targeted investigations.[4] Furthermore, next-generation sequencing technologies have tremendous potential for the future of diagnostics and subsequent treatment choices, particularly for viral infections.[5] The sensitivity of deep sequencing can capture even rare variants in mixed infections as well as quasispecies.[6][7][8][9][10][11] Investigation of the viable variations within a viral species not only provides insight into the evolutionary history of a species but also unveils putative avenues for targeted therapies, such as small interfering RNAs[12][13][14][15] and control strategies.

References

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  2. ↑ Holmfeldt, K.; Solonenko, N.; Shah, M. et al. (2013). "Twelve previously unknown phage genera are ubiquitous in global oceans". Proceedings of the National Academy of Sciences of the United States of America 110 (31): 12798-803. doi:10.1073/pnas.1305956110. PMC PMC3732932. PMID 23858439. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3732932. 
  3. ↑ Hurwitz, B.L.; Sullivan, M.B. (2013). "The Pacific Ocean Virome (POV): A marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology". PLoS One 8 (2): e57355. doi:10.1371/journal.pone.0057355. PMC PMC3585363. PMID 23468974. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3585363. 
  4. ↑ Deng, L.; Ignacio-Espinoza, J.C.; Gregory, A.C. (2014). "Viral tagging reveals discrete populations in Synechococcus viral genome sequence space". Nature 513 (7517): 242-5. doi:10.1038/nature13459. PMID 25043051. 
  5. ↑ Barzon, L.; Lavezzo, E.; Militello, V. et al. (2011). "Applications of next-generation sequencing technologies to diagnostic virology". International Journal of Medical Sciences 12 (11): 7861-84. doi:10.3390/ijms12117861. PMC PMC3233444. PMID 22174638. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3233444. 
  6. ↑ Wang, C.; Mitsuya, Y.; Gharizadeh, B. et al. (2007). "Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance". Genome Research 17 (8): 1195-201. doi:10.1101/gr.6468307. PMC PMC1933516. PMID 17600086. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933516. 
  7. ↑ Ramakrishnan, M.A.; Tu, Z.J.; Singh, S. et al. (2009). "The feasibility of using high resolution genome sequencing of influenza A viruses to detect mixed infections and quasispecies". PLoS One 4 (9): e7105. doi:10.1371/journal.pone.0007105. PMC PMC2740821. PMID 19771155. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2740821. 
  8. ↑ Solmone, M.; Vincenti, D.; Prosperi, M.C. et al. (2009). "Use of massively parallel ultradeep pyrosequencing to characterize the genetic diversity of hepatitis B virus in drug-resistant and drug-naive patients and to detect minor variants in reverse transcriptase and hepatitis B S antigen". Journal of Virology 83 (4): 1718-26. doi:10.1128/JVI.02011-08. PMC PMC2643754. PMID 19073746. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643754. 
  9. ↑ Abdelrahman, T.; Hughes, J.; Main, J. et al. (2015). "Next-generation sequencing sheds light on the natural history of hepatitis C infection in patients who fail treatment". Hepatology 61 (1): 88–97. doi:10.1002/hep.27192. PMC PMC4303934. PMID 24797101. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4303934. 
  10. ↑ Verheyen, J.; Litau, E.; Sing, T. et al. (2006). "Compensatory mutations at the HIV cleavage sites p7/p1 and p1/p6-gag in therapy-naive and therapy-experienced patients". Antiviral Therapy 11 (7): 879-87. PMID 17302250. 
  11. ↑ Quiñones-Mateu, M.E.; Avila, S.; Reyes-Teran, G.; Martinez, M.A. (2015). "Deep sequencing: becoming a critical tool in clinical virology". Journal of Clinical Virology 61 (1): 9–19. doi:10.1016/j.jcv.2014.06.013. PMC PMC4119849. PMID 24998424. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119849. 
  12. ↑ Lares, M.R.; Rossi, J.J.; Ouellet, D.L. (2010). "RNAi and small interfering RNAs in human disease therapeutic applications". Trends in Biotechnology 28 (11): 570-9. doi:10.1016/j.tibtech.2010.07.009. PMC PMC2955826. PMID 20833440. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2955826. 
  13. ↑ Truong, N.P.; Gu, W.; Prasadam, I. et al. (2013). "An influenza virus-inspired polymer system for the timed release of siRNA". Nature Communications 4: 1902. doi:10.1038/ncomms2905. PMID 23695696. 
  14. ↑ Paul, A.M.; Shi, Y.; Acharya, D. et al. (2014). "Delivery of antiviral small interfering RNA with gold nanoparticles inhibits dengue virus infection in vitro". Journal of General Virology 95 (Pt 8): 1712-22. doi:10.1099/vir.0.066084-0. PMC PMC4103068. PMID 24828333. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103068. 
  15. ↑ Jin, F.; Li, S.; Zheng, K. et al. (2014). "Silencing herpes simplex virus type 1 capsid protein encoding genes by siRNA: a promising antiviral therapeutic approach". PLoS One 9 (5): e96623. doi:10.1371/journal.pone.0096623. PMC PMC4008601. PMID 24794394. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4008601. 

Notes

This presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added.

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