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

Wen Chun Liu, Chih Peng Lin, Chun Pei Cheng, Cheng Hsun Ho, Kuo Lun Lan, Ji Hong Cheng, Chia Jui Yen, Pin Nan Cheng, I. Chin Wu, I. Chen Li, Bill Chia Han Chang, Vincent S. Tseng, Yen Cheng Chiu, Ting Tsung Chang

研究成果: Article

4 引文 斯高帕斯(Scopus)

摘要

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.

原文English
頁(從 - 到)147-157
頁數11
期刊Hepatology International
10
發行號1
DOIs
出版狀態Published - 2016 一月 1

All Science Journal Classification (ASJC) codes

  • Hepatology

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