ArticleGenome biology2021
Hidden biases in germline structural variant detection.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- dicast: a machine learning method for accurate structural variant detection from short-read sequencing data.Genome biology · 2026Article
- Benchmarking Q40 sequencing for sensitive and efficient detection of rare genomic variants.Genome biology · 2026Article
- Comprehensive benchmarking of somatic structural variant detection at ultra-low allele fractions.bioRxiv : the preprint server for biology · 2025Article
- Computational analysis of DNA methylation from long-read sequencing.Nature reviews. Genetics · 2025Review
- The nature of complex structural variations in tomatoes.Horticulture research · 2025Article
- Reference Materials for Improving Reliability of Multiomics Profiling.Phenomics (Cham, Switzerland) · 2024Review
- Genomic reproducibility in the bioinformatics era.Genome biology · 2024Review
- The impact of FASTQ and alignment read order on structural variant calling from long-read sequencing data.PeerJ · 2024Article
- Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet.Genome biology · 2023Article
- The Quartet Data Portal: integration of community-wide resources for multiomics quality control.Genome biology · 2023Article
- Genomic variant benchmark: if you cannot measure it, you cannot improve it.Genome biology · 2023Review
- Population history modulates the fitness effects of Copy Number Variation in the Roma.Human genetics · 2023Article
- Detection of trait-associated structural variations using short-read sequencing.Cell genomics · 2023Article
- SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads.Nature methods · 2023Article
- Truvari: refined structural variant comparison preserves allelic diversity.Genome biology · 2022Article
- Towards accurate and reliable resolution of structural variants for clinical diagnosis.Genome biology · 2022Review
- Assessing reproducibility of inherited variants detected with short-read whole genome sequencing.Genome biology · 2022Article
- Recent advances and current challenges in population genomics of structural variation in animals and plants.Frontiers in genetics · 2022Review
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Authors and funding
11 authors.
Funding
Abstract
backgroundGenomic structural variations (SV) are important determinants of genotypic and phenotypic changes in many organisms. However, the detection of SV from next-generation sequencing data remains challenging.
resultsIn this study, DNA from a Chinese family quartet is sequenced at three different sequencing centers in triplicate. A total of 288 derivative data sets are generated utilizing different analysis pipelines and compared to identify sources of analytical variability. Mapping methods provide the major contribution to variability, followed by sequencing centers and replicates. Interestingly, SV supported by only one center or replicate often represent true positives with 47.02% and 45.44% overlapping the long-read SV call set, respectively. This is consistent with an overall higher false negative rate for SV calling in centers and replicates compared to mappers (15.72%). Finally, we observe that the SV calling variability also persists in a genotyping approach, indicating the impact of the underlying sequencing and preparation approaches.
conclusionsThis study provides the first detailed insights into the sources of variability in SV identification from next-generation sequencing and highlights remaining challenges in SV calling for large cohorts. We further give recommendations on how to reduce SV calling variability and the choice of alignment methodology.
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