ArticleBMC genomics2015
Assessing structural variation in a personal genome-towards a human reference diploid genome.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers.
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Who cites it
96 citing papers in PubMed.
- Structural Variant benchmarking frameworks: Parameterization, matching logic, and evaluation assumptions presented through HG002 and NA12878.PLoS computational biology · 2026Article
- Pervasive genome structure heterogeneity iniScience · 2026Article
- Review
- The promise and challenges of characterizing genome-wide structural variants: A case study in a critically endangered parrot.Molecular ecology resources · 2025Article
- Optical genome mapping unveils hidden structural variants in neurodevelopmental disorders.Scientific reports · 2024Article
- A comparative study of structural variant calling in WGS from Alzheimer's disease families.Life science alliance · 2024Article
- Kled: an ultra-fast and sensitive structural variant detection tool for long-read sequencing data.Briefings in bioinformatics · 2024Article
- Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithms.bioRxiv : the preprint server for biology · 2024Article
- HapKled: a haplotype-aware structural variant calling approach for Oxford nanopore sequencing data.Frontiers in genetics · 2024Article
- Variants in ATP5F1B are associated with dominantly inherited dystonia.Brain : a journal of neurology · 2023Article
- Variant calling and benchmarking in an era of complete human genome sequences.Nature reviews. Genetics · 2023Review
- Benchmarking datasets for assembly-based variant calling using high-fidelity long reads.BMC genomics · 2023Article
- Initial Analysis of Structural Variation Detections in Cattle Using Long-Read Sequencing Methods.Genes · 2022Article
- TT-Mars: structural variants assessment based on haplotype-resolved assemblies.Genome biology · 2022Article
- StructuralVariantAnnotation: a R/Bioconductor foundation for a caller-agnostic structural variant software ecosystem.Bioinformatics (Oxford, England) · 2022Article
- Review
- Comprehensive analysis of structural variants in chickens using PacBio sequencing.Frontiers in genetics · 2022Article
- The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.F1000Research · 2022Article
- BreakNet: detecting deletions using long reads and a deep learning approach.BMC bioinformatics · 2021Article
- Comprehensive characterization of copy number variation (CNV) called from array, long- and short-read data.BMC genomics · 2021Article
36 more citing papers are in PubMed but not listed here.
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Authors and funding
31 authors.
Funding
Abstract
backgroundCharacterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and methods are available to detect these structural variants (SVs), they remain less characterized than smaller variants because of SV diversity, complexity, and size. These challenges are exacerbated by the experimental and computational demands of SV analysis. Here, we characterize the SV content of a personal genome with Parliament, a publicly available consensus SV-calling infrastructure that merges multiple data types and SV detection methods.
resultsWe demonstrate Parliament's efficacy via integrated analyses of data from whole-genome array comparative genomic hybridization, short-read next-generation sequencing, long-read (Pacific BioSciences RSII), long-insert (Illumina Nextera), and whole-genome architecture (BioNano Irys) data from the personal genome of a single subject (HS1011). From this genome, Parliament identified 31,007 genomic loci between 100 bp and 1 Mbp that are inconsistent with the hg19 reference assembly. Of these loci, 9,777 are supported as putative SVs by hybrid local assembly, long-read PacBio data, or multi-source heuristics. These SVs span 59 Mbp of the reference genome (1.8%) and include 3,801 events identified only with long-read data. The HS1011 data and complete Parliament infrastructure, including a BAM-to-SV workflow, are available on the cloud-based service DNAnexus.
conclusionsHS1011 SV analysis reveals the limits and advantages of multiple sequencing technologies, specifically the impact of long-read SV discovery. With the full Parliament infrastructure, the HS1011 data constitute a public resource for novel SV discovery, software calibration, and personal genome structural variation analysis.
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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.