ArticleBMC genomics2020
Towards a better understanding of the low recall of insertion variants with short-read based variant callers.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 28 citations in OpenAlex.
- Complementarity of Long-Reads and Optical Mapping in Parkinson's Disease for Structural Variants.Annals of clinical and translational neurology · 2026Article
- Strawberry atlas:PeerJ · 2026Article
- Comprehensive detection of structural variations in long and short reads dataset of French cattle.Scientific reports · 2025Article
- The Landscape of Structural Variation in Aye-Ayes (Daubentonia madagascariensis).Genome biology and evolution · 2025Article
- Pooled, Long-read Sequencing for Structural Variant Characterization in Schistosome Populations.Genome biology and evolution · 2025Article
- The promise and challenges of characterizing genome-wide structural variants: A case study in a critically endangered parrot.Molecular ecology resources · 2025Article
- Using bioinformatics to investigate functional diversity: a case study of MHC diversity in koalas.Immunogenetics · 2024Article
- Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome.Cell reports methods · 2023Article
- MTG-Link: leveraging barcode information from linked-reads to assemble specific loci.BMC bioinformatics · 2023Article
- SVJedi-graph: improving the genotyping of close and overlapping structural variants with long reads using a variation graph.Bioinformatics (Oxford, England) · 2023Article
- Localized assembly for long reads enables genome-wide analysis of repetitive regions at single-base resolution in human genomes.Human genomics · 2023Article
- Slaying (Yet Again) the Brain-Eating Zombie Called the "Isochore Theory": A Segmentation Algorithm Used to "Confirm" the Existence of Isochores Creates "Isochores" Where None Exist.International journal of molecular sciences · 2022Article
- Assessment of linkage disequilibrium patterns between structural variants and single nucleotide polymorphisms in three commercial chicken populations.BMC genomics · 2022Article
- Characterization of intermediate-sized insertions using whole-genome sequencing data and analysis of their functional impact on gene expression.Human genetics · 2021Article
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Authors and funding
3 authors at 3 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSince 2009, numerous tools have been developed to detect structural variants using short read technologies. Insertions >50 bp are one of the hardest type to discover and are drastically underrepresented in gold standard variant callsets. The advent of long read technologies has completely changed the situation. In 2019, two independent cross technologies studies have published the most complete variant callsets with sequence resolved insertions in human individuals. Among the reported insertions, only 17 to 28% could be discovered with short-read based tools.
resultsIn this work, we performed an in-depth analysis of these unprecedented insertion callsets in order to investigate the causes of such failures. We have first established a precise classification of insertion variants according to four layers of characterization: the nature and size of the inserted sequence, the genomic context of the insertion site and the breakpoint junction complexity. Because these levels are intertwined, we then used simulations to characterize the impact of each complexity factor on the recall of several structural variant callers. We showed that most reported insertions exhibited characteristics that may interfere with their discovery: 63% were tandem repeat expansions, 38% contained homology larger than 10 bp within their breakpoint junctions and 70% were located in simple repeats. Consequently, the recall of short-read based variant callers was significantly lower for such insertions (6% for tandem repeats vs 56% for mobile element insertions). Simulations showed that the most impacting factor was the insertion type rather than the genomic context, with various difficulties being handled differently among the tested structural variant callers, and they highlighted the lack of sequence resolution for most insertion calls.
conclusionsOur results explain the low recall by pointing out several difficulty factors among the observed insertion features and provide avenues for improving SV caller algorithms and their combinations.
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