دورية أكاديمية
Characterization and mitigation of artifacts derived from NGS library preparation due to structure-specific sequences in the human genome
| العنوان: | Characterization and mitigation of artifacts derived from NGS library preparation due to structure-specific sequences in the human genome |
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| المؤلفون: | HuiJuan Chen, YiRan Zhang, Bing Wang, Rui Liao, XiaoHong Duan, ChunYan Yang, Jing Chen, YanTong Hao, YingShuang Shu, LiLi Cai, Xue Leng, Nian-Song Qian, DaWei Sun, Beifang Niu, Qiming Zhou |
| المصدر: | BMC Genomics, Vol 25, Iss 1, Pp 1-13 (2024) |
| بيانات النشر: | BMC, 2024. |
| سنة النشر: | 2024 |
| المجموعة: | LCC:Biotechnology LCC:Genetics |
| مصطلحات موضوعية: | Next generation sequencing, Hybridization capture-based target NGS, Sonication fragmentation, Enzymatic fragmentation, Sequencing errors, Biotechnology, TP248.13-248.65, Genetics, QH426-470 |
| الوصف: | Abstract Background Hybridization capture-based targeted next generation sequencing (NGS) is gaining importance in routine cancer clinical practice. DNA library preparation is a fundamental step to produce high-quality sequencing data. Numerous unexpected, low variant allele frequency calls were observed in libraries using sonication fragmentation and enzymatic fragmentation. In this study, we investigated the characteristics of the artifact reads induced by sonication and enzymatic fragmentation. We also developed a bioinformatic algorithm to filter these sequencing errors. Results We used pairwise comparisons of somatic single nucleotide variants (SNVs) and insertions and deletions (indels) of the same tumor DNA samples prepared using both ultrasonic and enzymatic fragmentation protocols. Our analysis revealed that the number of artifact variants was significantly greater in the samples generated using enzymatic fragmentation than using sonication. Most of the artifacts derived from the sonication-treated libraries were chimeric artifact reads containing both cis- and trans-inverted repeat sequences of the genomic DNA. In contrast, chimeric artifact reads of endonuclease-treated libraries contained palindromic sequences with mismatched bases. Based on these distinctive features, we proposed a mechanistic hypothesis model, PDSM (pairing of partial single strands derived from a similar molecule), by which these sequencing errors derive from ultrasonication and enzymatic fragmentation library preparation. We developed a bioinformatic algorithm to generate a custom mutation “blacklist” in the BED region to reduce errors in downstream analyses. Conclusions We first proposed a mechanistic hypothesis model (PDSM) of sequencing errors caused by specific structures of inverted repeat sequences and palindromic sequences in the natural genome. This new hypothesis predicts the existence of chimeric reads that could not be explained by previous models, and provides a new direction for further improving NGS analysis accuracy. A bioinformatic algorithm, ArtifactsFinder, was developed and used to reduce the sequencing errors in libraries produced using sonication and enzymatic fragmentation. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 1471-2164 |
| Relation: | https://doaj.org/toc/1471-2164 |
| DOI: | 10.1186/s12864-024-10157-w |
| URL الوصول: | https://doaj.org/article/6558761bb9a6419d8414053d9422471a |
| رقم الأكسشن: | edsdoj.6558761bb9a6419d8414053d9422471a |
| قاعدة البيانات: | Directory of Open Access Journals |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 14712164 |
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| DOI: | 10.1186/s12864-024-10157-w |