ArticleGenome biology2012
An integrative probabilistic model for identification of structural variation in sequencing data.
Article in Genome biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed.
- Long-Read Sequencing and Structural Variant Detection: Unlocking the Hidden Genome in Rare Genetic Disorders.Diagnostics (Basel, Switzerland) · 2025Review
- A Systematic Review of the Advances and New Insights into Copy Number Variations in Plant Genomes.Plants (Basel, Switzerland) · 2025Review
- Transposable Element Insertions Are Associated with Batesian Mimicry in the Pantropical Butterfly Hypolimnas misippus.Molecular biology and evolution · 2024Article
- Detecting genomic deletions from high-throughput sequence data with unsupervised learning.BMC bioinformatics · 2023Article
- Current status of structural variation studies in plants.Plant biotechnology journal · 2021Review
- R-loops and regulatory changes in chronologically ageing fission yeast cells drive non-random patterns of genome rearrangements.PLoS genetics · 2021Article
- GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing.Genome biology · 2021Article
- Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples.Genome research · 2020Article
- Structural variation in the sequencing era.Nature reviews. Genetics · 2020Review
- Meltos: multi-sample tumor phylogeny reconstruction for structural variants.Bioinformatics (Oxford, England) · 2020Article
- Article
- Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software.Nature communications · 2019Article
- Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine.Science China. Life sciences · 2019Review
- Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing.Genome biology · 2019Article
- Article
- Analysis of the human Y-chromosome haplogroup Q characterizes ancient population movements in Eurasia and the Americas.BMC biology · 2019Article
- Molecular Cytogenetics Guides Massively Parallel Sequencing of a Radiation-Induced Chromosome Translocation in Human Cells.Radiation research · 2018Article
- Computational identification of micro-structural variations and their proteogenomic consequences in cancer.Bioinformatics (Oxford, England) · 2018Article
- MSeq-CNV: accurate detection of Copy Number Variation from Sequencing of Multiple samples.Scientific reports · 2018Article
- Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes.Nature communications · 2018Article
8 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
Paired-end sequencing is a common approach for identifying structural variation (SV) in genomes. Discrepancies between the observed and expected alignments indicate potential SVs. Most SV detection algorithms use only one of the possible signals and ignore reads with multiple alignments. This results in reduced sensitivity to detect SVs, especially in repetitive regions. We introduce GASVPro, an algorithm combining both paired read and read depth signals into a probabilistic model which can analyze multiple alignments of reads. GASVPro outperforms existing methods with a 50-90% improvement in specificity on deletions and a 50% improvement on inversions.
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