University Library
  • Login
A gateway to Melbourne's research publications
Minerva Access is the University's Institutional Repository. It aims to collect, preserve, and showcase the intellectual output of staff and students of the University of Melbourne for a global audience.
View Item 
  • Minerva Access
  • Veterinary and Agricultural Sciences
  • Melbourne Veterinary School
  • Veterinary Biosciences
  • Veterinary Biosciences - Research Publications
  • View Item
  • Minerva Access
  • Veterinary and Agricultural Sciences
  • Melbourne Veterinary School
  • Veterinary Biosciences
  • Veterinary Biosciences - Research Publications
  • View Item
JavaScript is disabled for your browser. Some features of this site may not work without it.

    Aligning to the sample-specific reference sequence to optimize the accuracy of next-generation sequencing analysis for hepatitis B virus.

    Thumbnail
    Download
    Published version (956.4Kb)

    Citations
    Scopus
    Web of Science
    Altmetric
    6
    5
    Author
    Liu, W-C; Lin, C-P; Cheng, C-P; Ho, C-H; Lan, K-L; Cheng, J-H; Yen, C-J; Cheng, P-N; Wu, I-C; Li, I-C; ...
    Date
    2016-01
    Source Title
    Hepatology International
    Publisher
    Springer Science and Business Media LLC
    University of Melbourne Author/s
    Chang, Bill
    Affiliation
    Veterinary Biosciences
    Metadata
    Show full item record
    Document Type
    Journal Article
    Citations
    Liu, W. -C., Lin, C. -P., Cheng, C. -P., Ho, C. -H., Lan, K. -L., Cheng, J. -H., Yen, C. -J., Cheng, P. -N., Wu, I. -C., Li, I. -C., Chang, B. C. -H., Tseng, V. S., Chiu, Y. -C. & Chang, T. -T. (2016). Aligning to the sample-specific reference sequence to optimize the accuracy of next-generation sequencing analysis for hepatitis B virus.. Hepatol Int, 10 (1), pp.147-157. https://doi.org/10.1007/s12072-015-9645-x.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/255044
    DOI
    10.1007/s12072-015-9645-x
    Open Access at PMC
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722079
    Abstract
    BACKGROUND: Hepatitis B virus (HBV) quasispecies are crucial in the pathogenesis of chronic liver disease. Next-generation sequencing (NGS) is powerful for identifying viral quasispecies. To improve mapping quality and single nucleotide variant (SNV) calling accuracy in the NGS analysis of HBV, we compared different mapping references, including the sample-specific reference sequence, same genotype sequences and different genotype sequences, according to the sample. METHODS: Real Illumina HBV datasets from 86 patients, and simulated datasets from 158 HBV strains in the GenBank database, were used to assess mapping quality. SNV calling accuracy was evaluated using different mapping references to align Real Illumina datasets from a single HBV clone. RESULTS: Using the sample-specific reference sequence as a mapping reference produced the largest number of mappable reads and coverages. With a different genotype mapping reference, the consensus sequence derived from the Real Illumina datasets of the single HBV clone showed 21 false SNV callings in polymerase and surface genes, the regions most divergent between the mapping reference and this HBV clone. A ~6 % coverage of most of these false SNVs was yielded even with a same genotype mapping reference, but none with the sample-specific reference sequence. CONCLUSIONS: Using sample-specific reference sequences as a mapping reference in NGS analysis optimized mapping quality and the SNV calling accuracy for HBV quasispecies.

    Export Reference in RIS Format     

    Endnote

    • Click on "Export Reference in RIS Format" and choose "open with... Endnote".

    Refworks

    • Click on "Export Reference in RIS Format". Login to Refworks, go to References => Import References


    Collections
    • Minerva Elements Records [45770]
    • Veterinary Biosciences - Research Publications [441]
    Minerva AccessDepositing Your Work (for University of Melbourne Staff and Students)NewsFAQs

    BrowseCommunities & CollectionsBy Issue DateAuthorsTitlesSubjectsThis CollectionBy Issue DateAuthorsTitlesSubjects
    My AccountLoginRegister
    StatisticsMost Popular ItemsStatistics by CountryMost Popular Authors