npInv：使用长读子比对进行准确的倒置检测和基因分型。
npInv: accurate detection and genotyping of inversions using long read sub-alignment.
机构信息
Genomics of Development and Disease Division, Institute for Molecular Bioscience, University of Queensland, 306 Carmody Rd, St Lucia, Brisbane, 4067, Australia.
Department of Medicine, Imperial College London, Level 2, Faculty Building South Kensington Campus, London, SW7 2AZ, United Kingdom.
出版信息
BMC Bioinformatics. 2018 Jul 13;19(1):261. doi: 10.1186/s12859-018-2252-9.
BACKGROUND
Detection of genomic inversions remains challenging. Many existing methods primarily target inzversions with a non repetitive breakpoint, leaving inverted repeat (IR) mediated non-allelic homologous recombination (NAHR) inversions largely unexplored.
RESULT
We present npInv, a novel tool specifically for detecting and genotyping NAHR inversion using long read sub-alignment of long read sequencing data. We benchmark npInv with other tools in both simulation and real data. We use npInv to generate a whole-genome inversion map for NA12878 consisting of 30 NAHR inversions (of which 15 are novel), including all previously known NAHR mediated inversions in NA12878 with flanking IR less than 7kb. Our genotyping accuracy on this dataset was 94%. We used PCR to confirm the presence of two of these novel inversions. We show that there is a near linear relationship between the length of flanking IR and the minimum inversion size, without inverted repeats.
CONCLUSION
The application of npInv shows high accuracy in both simulation and real data. The results give deeper insight into understanding inversion.
背景
基因组倒位的检测仍然具有挑战性。许多现有的方法主要针对非重复断点的倒位，而对反向重复（IR）介导的非等位基因同源重组（NAHR）倒位的研究则相对较少。
结果
我们提出了 npInv，这是一种专门用于使用长读测序数据的长读子比对来检测和分型 NAHR 倒位的新工具。我们在模拟和真实数据中用其他工具对 npInv 进行了基准测试。我们使用 npInv 为 NA12878 生成了一个全基因组倒位图谱，其中包括 30 个 NAHR 倒位（其中 15 个是新的），包括 NA12878 中所有以前已知的侧翼 IR 小于 7kb 的 NAHR 介导的倒位。我们在这个数据集上的基因分型准确率为 94%。我们使用 PCR 来确认这两个新倒位的存在。我们表明，在没有反向重复的情况下，侧翼 IR 的长度与最小倒位大小之间存在近乎线性的关系。
结论
npInv 在模拟和真实数据中的应用都具有很高的准确性。结果深入了解了对倒位的理解。
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