ArticleNature communications2023
INSurVeyor: improving insertion calling from short read sequencing data.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed.
- Comparative evaluation of GWAS-prioritized SNP, SSR, and insertion-type structural variant marker panels for genomic prediction in soybean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- A blended genome and exome sequencing method captures genetic variation in an unbiased and cost-effective manner.Nature genetics · 2026Article
- The influence of structural variants from 2445 pigs on gene expression and complex traits.Nature communications · 2026Article
- Insertion sequence elements associated with Staphylococcus epidermidis evolution in persistent orthopaedic device-related infections.BMC genomics · 2026Article
- Population-scale genomic medicine with the Hong Kong Genome Project.Nature medicine · 2026Article
- TEPEAK: A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations.PLoS computational biology · 2026Article
- PoolSeq Genome-Wide Association Studies and Microbial Signature Analyses Identify Novel Candidates Associated With Pyrethroid Resistance Evolution in Anopheles funestus in Cameroon.Molecular ecology · 2026Article
- Jumping in the human brain: A review on somatic transposition.Fundamental research · 2026Review
- The continued promise of genomic technologies and software in neurogenetics.Journal of neuromuscular diseases · 2025Review
- Brain somatic mutations in Alzheimer's disease: linking genetic mosaicism to neurodegeneration.Molecular neurodegeneration · 2025Review
- Genomic Drivers of Pyrethroid Resistance Escalation in the Malaria Vector Anopheles funestus Across Africa.Molecular biology and evolution · 2025Article
- SV-MeCa: an XGBoost-based meta-caller approach for structural variant calling from short-read data.BMC bioinformatics · 2025Article
- Identification of technically challenging variants: Whole-genome sequencing improves diagnostic yield in patients with high clinical suspicion of rare diseases.HGG advances · 2025Article
- Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis.Genome research · 2025Article
- Long-Read Sequencing Outperforms Short-Read Sequencing in Detecting Most Structural Variations.Serican journal of medicine · 2025Article
- The implementation of genome sequencing in rare genetic diseases diagnosis: a pilot study from the Hong Kong genome project.The Lancet regional health. Western Pacific · 2025Article
- Comparisons of performances of structural variants detection algorithms in solitary or combination strategy.PloS one · 2025Article
- Genome-wide association studies unveil major genetic loci driving insecticide resistance in Anopheles funestus in four eco-geographical settings across Cameroon.BMC genomics · 2024Article
- SurVIndel2: improving copy number variant calling from next-generation sequencing using hidden split reads.Nature communications · 2024Article
- ProcaryaSV: structural variation detection pipeline for bacterial genomes using short-read sequencing.BMC bioinformatics · 2024Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Insertions are one of the major types of structural variations and are defined as the addition of 50 nucleotides or more into a DNA sequence. Several methods exist to detect insertions from next-generation sequencing short read data, but they generally have low sensitivity. Our contribution is two-fold. First, we introduce INSurVeyor, a fast, sensitive and precise method that detects insertions from next-generation sequencing paired-end data. Using publicly available benchmark datasets (both human and non-human), we show that INSurVeyor is not only more sensitive than any individual caller we tested, but also more sensitive than all of them combined. Furthermore, for most types of insertions, INSurVeyor is almost as sensitive as long reads callers. Second, we provide state-of-the-art catalogues of insertions for 1047 Arabidopsis Thaliana genomes from the 1001 Genomes Project and 3202 human genomes from the 1000 Genomes Project, both generated with INSurVeyor. We show that they are more complete and precise than existing resources, and important insertions are missed by existing methods.
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