ArticleNucleic acids research2022
GREEN-DB: a framework for the annotation and prioritization of non-coding regulatory variants from whole-genome sequencing data.
Article in Nucleic acids research, 2022. 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, 28 citations in OpenAlex.
- Incremental yield of genome sequencing after exome sequencing for nonimmune hydrops fetalis spectrum.American journal of obstetrics & gynecology MFM · 2026Article
- Genome Sequencing of Undiagnosed European Patients Suspected of Hereditary Cancer: Diagnostic Yield and Identification of Candidate Causative Variants.JCO precision oncology · 2026Article
- Accelerating rare disease diagnostics by linking DNA and RNA through an explainable and interactive RNA-guided workflow.NAR genomics and bioinformatics · 2026Article
- Gene4Denovo2: an updated platform for human de novo mutations discovery and interpretation.Nucleic acids research · 2026Article
- A multidisciplinary RNA-guided approach to complement genomic analysis of unsolved patients with an inborn error of immunity.Frontiers in immunology · 2026Article
- Decoding structural birth defects through genomic landscapes: Innovative frameworks for diagnosis (Review).International journal of molecular medicine · 2026Review
- AI-powered precision medicine: utilizing genetic risk factor optimization to revolutionize healthcare.NAR genomics and bioinformatics · 2025Review
- Article
- Noncoding variants are a rare cause of recessive developmental disorders in trans with coding variants.Genetics in medicine : official journal of the American College of Medical Genetics · 2024Article
- Diagnostic utility of DNA methylation analysis in genetically unsolved pediatric epilepsies and CHD2 episignature refinement.Nature communications · 2024Article
- The Immunometabolic Gene N-Acetylglucosamine Kinase Is Uniquely Involved in the Heritability of Multiple Sclerosis Severity.International journal of molecular sciences · 2024Article
- VarCards2: an integrated genetic and clinical database for ACMG-AMP variant-interpretation guidelines in the human whole genome.Nucleic acids research · 2024Article
- Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases.Genome medicine · 2023Article
- Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant's Abiotic Stress Tolerance Responses.Genes · 2023Review
- Recommendations for clinical interpretation of variants found in non-coding regions of the genome.Genome medicine · 2022Article
- Newborn Screening by Genomic Sequencing: Opportunities and Challenges.International journal of neonatal screening · 2022Article
- DIRECT-NET: An efficient method to discover cis-regulatory elements and construct regulatory networks from single-cell multiomics data.Science advances · 2022Article
- RevUP: an online scoring system for regulatory variants implicated in rare diseases.Bioinformatics (Oxford, England) · 2022Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Non-coding variants have long been recognized as important contributors to common disease risks, but with the expansion of clinical whole genome sequencing, examples of rare, high-impact non-coding variants are also accumulating. Despite recent advances in the study of regulatory elements and the availability of specialized data collections, the systematic annotation of non-coding variants from genome sequencing remains challenging. Here, we propose a new framework for the prioritization of non-coding regulatory variants that integrates information about regulatory regions with prediction scores and HPO-based prioritization. Firstly, we created a comprehensive collection of annotations for regulatory regions including a database of 2.4 million regulatory elements (GREEN-DB) annotated with controlled gene(s), tissue(s) and associated phenotype(s) where available. Secondly, we calculated a variation constraint metric and showed that constrained regulatory regions associate with disease-associated genes and essential genes from mouse knock-outs. Thirdly, we compared 19 non-coding impact prediction scores providing suggestions for variant prioritization. Finally, we developed a VCF annotation tool (GREEN-VARAN) that can integrate all these elements to annotate variants for their potential regulatory impact. In our evaluation, we show that GREEN-DB can capture previously published disease-associated non-coding variants as well as identify additional candidate disease genes in trio analyses.
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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.