Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling

Bioinformatics

Volumn 31, Issue 5, 2015, Pages 682-690

  Skums, Pavel ^a   Artyomenko, Alexander ^b   Glebova, Olga ^b   Ramachandran, Sumathi ^a   Mandoiu, Ion ^c   Campo, David S ^a   Dimitrova, Zoya ^a   Zelikovsky, Alex ^b   Khudyakov, Yury ^a  

^a CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^b GEORGIA STATE UNIVERSITY   (United States)

^c University of Connecticut   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HEPATITIS C VIRUS;

VIRUS DNA;

ALGORITHM; BIOLOGY; CLASSIFICATION; DNA SEQUENCE; GENETIC VARIATION; GENETICS; HEPACIVIRUS; HIGH THROUGHPUT SEQUENCING; HUMAN; PROCEDURES; VIRUS; VIRUS GENOME;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DNA, VIRAL; GENETIC VARIATION; GENOME, VIRAL; HEPACIVIRUS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SEQUENCE ANALYSIS, DNA; VIRUSES;

EID: 84929001549     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu726     Document Type: Article

References (32)

1. Alon, S. et al. (2011) Barcoding bias in high-throughput multiplex sequencing of mirna. Genome Res, 21, 1506-1511.
2. Bansal, V. (2010) A statistical method for detection of variants from next-generation resequencing of dna pools. Bioinformatics, 26, i318-i324.
3. Berman, P. et al. (2004) Tight approximability results for test set problems in bioinformatics. Lect. Notes Comput. Sci., 3111, 39-50.
4. Bull, R. et al. (2011) Sequential bottlenecks drive viral evolution in early acute hepatitis c virus infection. PLoS Pathog, 7, e1002243.
5. Campo, D. et al. (2014a) Drug-resistance of a viral population and its individual intra-host variants during the first 48 hours of therapy. Clin. Pharmacol. Ther., 95, 627-635.
6. Campo, D. et al. (2014b) Next-generation sequencing reveals large connected networks of intra-host hcv variants. BMC Genomics, 15(Suppl 5), S4.
7. Caraballo Cortes, K. et al. (2013) Ultradeep pyrosequencing of hepatitis c virus hypervariable region 1 in quasispecies analysis. Biomed. Res. Int., 2013, 626083.
8. Culasso, A. et al. (2014) Intra-host evolution of multiple genotypes of hepatitis c virus in a chronically infected patient with HIV along a 13-year follow-up period. Virology, 449, 317-327.
9. Deakin, C.T. et al. (2014) Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence. Nucleic Acids Res., 42, e129.
10. Dierynck, I. et al. (2014) Deep sequencing analysis of the hcv ns3-4a region confirms low prevalence of telaprevir-resistant variants at baseline and end of the realize study. J Infect Dis., pii, jiu340.
11. Dimitrova, Z. et al. (2012) Assessments of intra-and inter-host diversity of hepatitis c virus using next generation sequencing and mass spectrometry. In Silico Biol., 11, 183-192.
12. Du, D.-Z. et al. (2006) Pooling Design and Nonadaptive Group Testing: Important Tools for DNA Sequencing, volume 18. World Scientific Publishing Company. Series on Applied Mathematics.
13. Duma, D. et al. (2013) Accurate decoding of pooled sequenced data using compressed sensing. Lect. Notes Comp. Sci., 8126, 70-84.
14. Edgar, R. (2004) Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
15. Erlich, Y. et al. (2009) Dna sudoku-harnessing high-throughput sequencing for multiplexing specimen analysis. Genome Res, 19, 1243-1253.
16. Golan, D. et al. (2012) Weighted pooling-practical and cost-effective techniques for pooled high-throughput sequencing. Bioinformatics, 28, i197-i206.
17. Gregori, J. et al. (2013) Ultra-deep pyrosequencing (udps) data treatment to study amplicon hcv minor variants. PLoS One, 8, e83361.
18. He, D. et al. (2011) Genotyping common and rare variation using overlapping pool sequencing. BMC Bioinformatics, 12(Suppl. 6), S2.
19. Holodniy, M. et al. (2012) Results from a large-scale epidemiologic look-back investigation of improperly reprocessed endoscopy equipment. Infect Control Hosp. Epidemiol., 33, 649-656.
20. Khuller, S. et al. (2007) Greedy methods. In: T.F., Gonzalez (ed.) Chapter Handbook of Approximation Algorithms and Metaheuristics. Chapman and Hall/CRC, Boca Raton.
21. Lara, J. et al. (2012) Coordinated evolution among hepatitis c virus genomic sites is coupled to host factors and resistance to interferon. In Silico Biol., 11, 213-224.
22. Lonardi, S. et al. (2013) Combinatorial pooling enables selective sequencing of the barley gene space. PLoS Comput. Biol., 9, e1003010.
23. Metzner, K.J. et al. (2009) Minority quasispecies of drug-resistant hiv-1 that lead to early therapy failure in treatment-naive and-adherent patients. Clin. Infect Dis., 48, 239-247.
24. Palmer, B.A. et al. (2012) Insertion and recombination events at hypervariable region 1 over 9.6 years of hepatitis c virus chronic infection. J. Gen. Virol., 93, 2614-2624.
25. Prabhu, S. et al. (2009) Overlapping pools for high-throughput targeted resequencing. Genome Res., 19, 1254-1261.
26. Ramachandran, S. et al. (2011) Temporal variations in the hepatitis c virus intrahost population during chronic infection. J. Virol., 85, 6369-6380.
27. Shental, N. et al. (2010) Identification of rare alleles and their carriers using compressed se(que)nsing. Nucleic Acids Res., 38, 1-22.
28. Skums, P. et al. (2012a) Efficient error correction for next-generation sequencing of viral amplicons. BMC Bioinformatics, 13(Suppl 10), S6.
29. Skums, P. et al. (2012b) Numerical detection, measuring and analysis of differential interferon resistance for individual hcv intra-host variants and its influence on the therapy response. In Silico Biol., 11, 263-269.
30. Wang, W. et al. (2014) High-resolution quantification of hepatitis c virus genome-wide mutation load and its correlation with the outcome of peginterferon-alpha2a and ribavirin combination therapy. PLoS One, 9, e100131.
31. Wertheim, J. et al. (2014) The global transmission network of HIV-1. J Infect Dis, 209, 304-313.
32. Wu, W. et al. (2006) On error-tolerant dna screening. Discrete Appl. Math., 154, 1753-1758.