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dc.contributor.authorLiu, W-C
dc.contributor.authorLin, C-P
dc.contributor.authorCheng, C-P
dc.contributor.authorHo, C-H
dc.contributor.authorLan, K-L
dc.contributor.authorCheng, J-H
dc.contributor.authorYen, C-J
dc.contributor.authorCheng, P-N
dc.contributor.authorWu, I-C
dc.contributor.authorLi, I-C
dc.contributor.authorChang, BC-H
dc.contributor.authorTseng, VS
dc.contributor.authorChiu, Y-C
dc.contributor.authorChang, T-T
dc.date.accessioned2020-12-17T03:49:06Z
dc.date.available2020-12-17T03:49:06Z
dc.date.issued2016-01
dc.identifierpii: 10.1007/s12072-015-9645-x
dc.identifier.citationLiu, 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.
dc.identifier.issn1936-0533
dc.identifier.urihttp://hdl.handle.net/11343/255044
dc.description.abstractBACKGROUND: 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.
dc.languageeng
dc.publisherSpringer Science and Business Media LLC
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.titleAligning to the sample-specific reference sequence to optimize the accuracy of next-generation sequencing analysis for hepatitis B virus.
dc.typeJournal Article
dc.identifier.doi10.1007/s12072-015-9645-x
melbourne.affiliation.departmentVeterinary Biosciences
melbourne.source.titleHepatology International
melbourne.source.volume10
melbourne.source.issue1
melbourne.source.pages147-157
dc.rights.licenseCC BY
melbourne.elementsid1328096
melbourne.openaccess.pmchttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722079
melbourne.contributor.authorChang, Bill
dc.identifier.eissn1936-0541
melbourne.accessrightsOpen Access


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