ArticleGenome research2009
Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 153 papers, 1 of them a synthesis that pooled it.
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Who cites it
153 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Copy Number Variants in Alzheimer's Disease.Journal of Alzheimer's disease : JAD · 2017Pooled it
- Structural Variant benchmarking frameworks: Parameterization, matching logic, and evaluation assumptions presented through HG002 and NA12878.PLoS computational biology · 2026Article
- Tracing the evolution of sequencing into the era of genomic medicine.Nature reviews. Genetics · 2025Review
- A Systematic Review of the Advances and New Insights into Copy Number Variations in Plant Genomes.Plants (Basel, Switzerland) · 2025Review
- ECOLE: Learning to call copy number variants on whole exome sequencing data.Nature communications · 2024Article
- Potentials and challenges of chromosomal microarray analysis in prenatal diagnosis.Frontiers in genetics · 2022Review
- Comprehensive characterization of copy number variation (CNV) called from array, long- and short-read data.BMC genomics · 2021Article
- A Cluster-Based Approach for the Discovery of Copy Number Variations From Next-Generation Sequencing Data.Frontiers in genetics · 2021Article
- AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome.The Plant cell · 2020Article
- VALOR2: characterization of large-scale structural variants using linked-reads.Genome biology · 2020Article
- Meltos: multi-sample tumor phylogeny reconstruction for structural variants.Bioinformatics (Oxford, England) · 2020Article
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- PostSV: A Post-Processing Approach for Filtering Structural Variations.Bioinformatics and biology insights · 2020Article
- Discovery of tandem and interspersed segmental duplications using high-throughput sequencing.Bioinformatics (Oxford, England) · 2019Article
- Article
- Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing.Genome biology · 2019Article
- Structural variation and fusion detection using targeted sequencing data from circulating cell free DNA.Nucleic acids research · 2019Article
- Exploring the landscape of focal amplifications in cancer using AmpliconArchitect.Nature communications · 2019Article
- TDNAscan: A Software to Identify Complete and Truncated T-DNA Insertions.Frontiers in genetics · 2019Article
93 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Recent studies show that along with single nucleotide polymorphisms and small indels, larger structural variants among human individuals are common. The Human Genome Structural Variation Project aims to identify and classify deletions, insertions, and inversions (>5 Kbp) in a small number of normal individuals with a fosmid-based paired-end sequencing approach using traditional sequencing technologies. The realization of new ultra-high-throughput sequencing platforms now makes it feasible to detect the full spectrum of genomic variation among many individual genomes, including cancer patients and others suffering from diseases of genomic origin. Unfortunately, existing algorithms for identifying structural variation (SV) among individuals have not been designed to handle the short read lengths and the errors implied by the "next-gen" sequencing (NGS) technologies. In this paper, we give combinatorial formulations for the SV detection between a reference genome sequence and a next-gen-based, paired-end, whole genome shotgun-sequenced individual. We describe efficient algorithms for each of the formulations we give, which all turn out to be fast and quite reliable; they are also applicable to all next-gen sequencing methods (Illumina, 454 Life Sciences [Roche], ABI SOLiD, etc.) and traditional capillary sequencing technology. We apply our algorithms to identify SV among individual genomes very recently sequenced by Illumina technology.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.