nplnv: accurate detection and genotyping of inversions using long read sub-alignment

作者：Shao Haojing; Ganesamoorthy Devika; Duarte Tania; Minh Duc Cao; Hoggart Clive J^*; Coin Lachlan J M^*

来源：BMC Bioinformatics, 2018, 19(1): 261.

DOI：10.1186/s12859-018-2252-9

• Inversion
• Non allelic homologous recombination (NAHR)
• Inverted repeat (IR)
• Split read
• Long read sequencing
• NA12878

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 nplnv, a novel tool specifically for detecting and genotyping NAHR inversion using long read sub-alignment of long read sequencing data. We benchmark nplnv with other tools in both simulation and real data. We use nplnv 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 nplnv shows high accuracy in both simulation and real data. The results give deeper insight into understanding inversion.

• 出版日期2018-7-13