ArticleGenome research2017
Discovery and genotyping of structural variation from long-read haploid genome sequence data.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 232 papers, 1 of them a synthesis that pooled it.
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Who cites it
232 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Application value of long-read sequencing in full characterization of thalassemia-associated structural variations: identifying a novel large segmental duplication and literature review.Orphanet journal of rare diseases · 2025Pooled it
- dicast: a machine learning method for accurate structural variant detection from short-read sequencing data.Genome biology · 2026Article
- A pangenome framework uncovers the role of deletions in repeated evolution of cave-derived traits.Genome research · 2026Article
- Structural Variant benchmarking frameworks: Parameterization, matching logic, and evaluation assumptions presented through HG002 and NA12878.PLoS computational biology · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Evaluation of acute myeloid leukemia using genomic proximity mapping-based next generation cytogenomics.Haematologica · 2026Article
- Pervasive genome structure heterogeneity iniScience · 2026Article
- Neoantigen Targeting as a Novel Approach for Therapy-Resistant Tumors.Molecular diagnosis & therapy · 2026Review
- Benchmarking of sequencing technologies defines optimal strategies for genetic variants detection in a human genome.Genome biology · 2026Article
- Haplotype-Resolved Genome Assemblies for Norwegian Red Cattle.Animal genetics · 2026Article
- MASTR-seq enables multiplexed analysis of short tandem repeats with sequencing.Cell reports methods · 2026Article
- The evolving landscape of pharmacogenomics: Current achievements and future directions.Pharmacological reviews · 2026Review
- Phased-assembly-driven pangenome graphs for structural variant genotyping and complex trait mapping in dairy cattle.Nature communications · 2026Article
- Molecular QTL are enriched for structural variants in a cattle long-read cohort.Communications biology · 2026Article
- Systematic fusion transcript discovery in mantle cell lymphoma using long-read sequencing.bioRxiv : the preprint server for biology · 2026Article
- Evolutionary Balancing of Genetic Consequence and Innovation in Mammals Through Variable Number Tandem Repeats.Genome biology and evolution · 2026Review
- 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
- Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle.Journal of advanced research · 2026Article
- Chromosome-specific epigenetic control and transmission of ribosomal DNA arrays in Hominidae genomes.Cell genomics · 2025Article
- Structural Variants Contribute to Phenotypic Variation in Maize.Molecular ecology · 2025Article
172 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
16 authors.
Funding
Abstract
In an effort to more fully understand the full spectrum of human genetic variation, we generated deep single-molecule, real-time (SMRT) sequencing data from two haploid human genomes. By using an assembly-based approach (SMRT-SV), we systematically assessed each genome independently for structural variants (SVs) and indels resolving the sequence structure of 461,553 genetic variants from 2 bp to 28 kbp in length. We find that >89% of these variants have been missed as part of analysis of the 1000 Genomes Project even after adjusting for more common variants (MAF > 1%). We estimate that this theoretical human diploid differs by as much as ∼16 Mbp with respect to the human reference, with long-read sequencing data providing a fivefold increase in sensitivity for genetic variants ranging in size from 7 bp to 1 kbp compared with short-read sequence data. Although a large fraction of genetic variants were not detected by short-read approaches, once the alternate allele is sequence-resolved, we show that 61% of SVs can be genotyped in short-read sequence data sets with high accuracy. Uncoupling discovery from genotyping thus allows for the majority of this missed common variation to be genotyped in the human population. Interestingly, when we repeat SV detection on a pseudodiploid genome constructed in silico by merging the two haploids, we find that ∼59% of the heterozygous SVs are no longer detected by SMRT-SV. These results indicate that haploid resolution of long-read sequencing data will significantly increase sensitivity of SV detection.
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