Tools for annotation and comparison of structural variation

Abstract

The impact of structural variants (SVs) on a variety of organisms and diseases like cancer has become increasingly evident. Methods for SV detection when studying genomic differences across cells, individuals or populations are being actively developed. Currently, just a few methods are available to compare different SVs callsets, and no specialized methods are available to annotate SVs that account for the unique characteristics of these variant types. Here, we introduce SURVIVOR_ant, a tool that compares types and breakpoints for candidate SVs from different callsets and enables fast comparison of SVs to genomic features such as genes and repetitive regions, as well as to previously established SV datasets such as from the 1000 Genomes Project. As proof of concept we compared 16 SV callsets generated by different SV calling methods on a single genome, the Genome in a Bottle sample HG002 (Ashkenazi son), and annotated the SVs with gene annotations, 1000 Genomes Project SV calls, and four different types of repetitive regions. Computation time to annotate 134,528 SVs with 33,954 of annotations was 22 seconds on a laptop.

Whole-Genome Resequencing and Pan-Transcriptome Reconstruction Highlight the Impact of Genomic Structural Variation on Secondary Metabolite Gene Clusters in the Grapevine Esca Pathogen Phaeoacremonium minimum

“…Forty six percent of the SVs (570 SVs) identified by both programs were also detected by NUCmer ( Figure 3A ). The limited overlap between results of the three programs confirmed previous reports that showed the importance of using multiple callers to reduce the false discovery rate at the cost of reducing sensitivity of SV detection ( Jeffares et al, 2017 ; Sedlazeck et al, 2017 ). All but one of the SVs detected by the three programs were deletions (568 ≥ 50 bp SVs; 1.01 Mb total size; Supplementary Data S7 ).…”

Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements

“…Del: deletion, dup: duplication, inv: inversion, ins: insertion, SV: structural variant, MP: mate-pair, PE: paired-end. The Total row indicates the total number of variants of each type in the three datasets: DGV [19], the HG002 integrated call-set [22] and Conrad et al (2010) [21]. BssSI and BspQI are the two restriction enzymes used in the Bionano optical mapping experiment, Long Ranger: the 10X Genomics mapping-assembly based pipeline, Supernova: the results of a custom pipeline utilizing the Supernova de novo assembler.…”

“…The four WGS technologies performed were utilized in three different settings: i) for solving the derivative chromosome structure of the three CCRs, ii) for a comparison of detection rate of polymorphic CNVs first detected by aCGH in the three cases and iii) for a general assessment of genome wide SV calls from the three cases as compared to calls present in the public datasets [19, 21, 22].…”

Bioinformatics Workflows for Genomic Variant Discovery, Interpretation and Prioritization

“…Chromosomal rearrangements are variations in chromosome structure whose impact on genetic diversity and disease susceptibility has become increasingly evident [82]. Per SO, numerous types of rearrangements exist: duplication, deletion, insertion, mobile element insertion, novel sequence insertion, tandem duplication, inversion, intrachromosomal breakpoint, interchromosomal breakpoint, translocation, and complex SVs.…”