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タイトル: | IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis |
著者: | Shigemizu, Daichi Miya, Fuyuki Akiyama, Shintaro Okuda, Shujiro Boroevich, Keith A Fujimoto, Akihiro Nakagawa, Hidewaki Ozaki, Kouichi Niida, Shumpei Kanemura, Yonehiro Okamoto, Nobuhiko Saitoh, Shinji Kato, Mitsuhiro Yamasaki, Mami Matsunaga, Tatsuo Mutai, Hideki Kosaki, Kenjiro Tsunoda, Tatsuhiko |
著者名の別形: | 藤本, 明洋 |
発行日: | 4-Apr-2018 |
出版者: | Springer Nature |
誌名: | Scientific Reports |
巻: | 8 |
論文番号: | 5608 |
抄録: | Insertions and deletions (indels) have been implicated in dozens of human diseases through the radical alteration of gene function by short frameshift indels as well as long indels. However, the accurate detection of these indels from next-generation sequencing data is still challenging. This is particularly true for intermediate-size indels (≥50 bp), due to the short DNA sequencing reads. Here, we developed a new method that predicts intermediate-size indels using BWA soft-clipped fragments (unmatched fragments in partially mapped reads) and unmapped reads. We report the performance comparison of our method, GATK, PINDEL and ScanIndel, using whole exome sequencing data from the same samples. False positive and false negative counts were determined through Sanger sequencing of all predicted indels across these four methods. The harmonic mean of the recall and precision, F-measure, was used to measure the performance of each method. Our method achieved the highest F-measure of 0.84 in one sample, compared to 0.56 for GATK, 0.52 for PINDEL and 0.46 for ScanIndel. Similar results were obtained in additional samples, demonstrating that our method was superior to the other methods for detecting intermediate-size indels. We believe that this methodology will contribute to the discovery of intermediate-size indels associated with human disease. |
記述: | A Publisher Correction to this article was published on 04 July 2018. This article has been updated. |
著作権等: | © The Author(s) 2018. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
URI: | http://hdl.handle.net/2433/236111 |
DOI(出版社版): | 10.1038/s41598-018-23978-z |
PubMed ID: | 29618752 |
関連リンク: | https://doi.org/10.1038/s41598-018-28698-y |
出現コレクション: | 学術雑誌掲載論文等 |
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