ArticleGenome research2022
A framework to score the effects of structural variants in health and disease.
Article in Genome research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers, 1 of them a synthesis that pooled it.
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Who cites it
43 citing papers in PubMed, 1 synthesis or guideline pooled it, 58 citations in OpenAlex.
- Mutations in the tail and rod domains of the neurofilament heavy-chain gene increase the risk of ALS.Annals of clinical and translational neurology · 2024Pooled it
- Comprehensive evaluation of structural variation detection for germline and somatic analysis with long-read sequencing data.Briefings in bioinformatics · 2026Article
- Complementarity of Long-Reads and Optical Mapping in Parkinson's Disease for Structural Variants.Annals of clinical and translational neurology · 2026Article
- Rare protein-disrupting variants inmedRxiv : the preprint server for health sciences · 2026Article
- Genetic analysis of neurodegenerative diseases.The Journal of clinical investigation · 2026Review
- BICEP: an extension to indels and copy number variants for rare variant prioritisation in pedigree analysis.bioRxiv : the preprint server for biology · 2026Article
- Predicting the functional impact of single nucleotide variants in Drosophila melanogaster with FlyCADD.Genetics · 2026Article
- A generic pipeline for CADD score generation: chickenCADD and turkeyCADD.G3 (Bethesda, Md.) · 2026Article
- Machine learning-based prediction of human structural variation and characterization of associated sequence determinants.bioRxiv : the preprint server for biology · 2026Article
- Genome region aware CADD thresholds for noncoding variant prioritization.NAR genomics and bioinformatics · 2025Article
- Structural variants in the 3D genome as drivers of disease.Nature reviews. Genetics · 2025Review
- Direct identification ofbioRxiv : the preprint server for biology · 2025Article
- Population-scale Long-read Sequencing in themedRxiv : the preprint server for health sciences · 2025Article
- Pangenome discovery of missing autism variants.medRxiv : the preprint server for health sciences · 2025Article
- Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease.Genome research · 2025Article
- A Hitchhiker's Guide to long-read genomic analysis.Genome research · 2025Review
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
- Rare pathogenic structural variants show potential to enhance prostate cancer germline testing for African men.Nature communications · 2025Article
- Systematic assessment of structural variant annotation tools for genomic interpretation.Life science alliance · 2025Article
- Identification of novel variants underlying non-syndromic primary ovarian insufficiency using a targeted NGS gene panel.Frontiers in endocrinology · 2025Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although technological advances improved the identification of structural variants (SVs) in the human genome, their interpretation remains challenging. Several methods utilize individual mechanistic principles like the deletion of coding sequence or 3D genome architecture disruptions. However, a comprehensive tool using the broad spectrum of available annotations is missing. Here, we describe CADD-SV, a method to retrieve and integrate a wide set of annotations to predict the effects of SVs. Previously, supervised learning approaches were limited due to a small number and biased set of annotated pathogenic or benign SVs. We overcome this problem by using a surrogate training objective, the Combined Annotation Dependent Depletion (CADD) of functional variants. We use human- and chimpanzee-derived SVs as proxy-neutral and contrast them with matched simulated variants as proxy-deleterious, an approach that has proven powerful for short sequence variants. Our tool computes summary statistics over diverse variant annotations and uses random forest models to prioritize deleterious structural variants. The resulting CADD-SV scores correlate with known pathogenic and rare population variants. We further show that we can prioritize somatic cancer variants as well as noncoding variants known to affect gene expression. We provide a website and offline-scoring tool for easy application of CADD-SV.
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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.