ArticleGenome research2020
Ultrafast and scalable variant annotation and prioritization with big functional genomics data.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genetic landscape and functional exploration of kidney cancer predisposition in cross-ancestral populations.Nature communications · 2026Pooled it
- Causal association between sleep disorders and nephrolithiasis: a two-sample Mendelian randomization study.International urology and nephrology · 2026Article
- Apiotrichum-Centered Fungal Interaction Network Disturbance Correlates With Increased Arterial Stiffness.Aging cell · 2026Article
- Genetic heterogeneity affects the risk of incident depression, comorbidity, and response to environment: A prospective trajectory study.Psychological medicine · 2026Article
- Inflammatory cytokines are not associated with early age-related macular degeneration: a two-sample Mendelian randomisation study.Eye (London, England) · 2026Article
- Four Pharmacogenomic Variants Strongly Linked to Corticosteroid-Induced Avascular Necrosis in Children with Cancer.Journal of clinical pharmacology · 2025Article
- Stratifying variant deleteriousness and trait-modulating effect under human recent adaptation using the FIND model.Genome biology · 2025Article
- Refining antipsychotic treatment strategies in schizophrenia: discovery of genetic biomarkers for enhanced drug response prediction.Molecular psychiatry · 2025Article
- Identification of shared genetic etiology of cardiovascular and cerebrovascular diseases through common cardiometabolic risk factors.Communications biology · 2024Article
- Best practices for germline variant and DNA methylation analysis of second- and third-generation sequencing data.Human genomics · 2024Review
- TOPMed imputed genomics enhances genomic atlas of the human proteome in brain, cerebrospinal fluid, and plasma.Scientific data · 2024Article
- A genome-wide association study based on the China Kadoorie Biobank identifies genetic associations between snoring and cardiometabolic traits.Communications biology · 2024Article
- Identification and verification of disulfidptosis-related genes in sepsis-induced acute lung injury.Frontiers in medicine · 2024Article
- Revealing the association between East Asian oral microbiome and colorectal cancer through Mendelian randomization and multi-omics analysis.Frontiers in cellular and infection microbiology · 2024Article
- Echtvar: compressed variant representation for rapid annotation and filtering of SNPs and indels.Nucleic acids research · 2023Article
- FAVOR: functional annotation of variants online resource and annotator for variation across the human genome.Nucleic acids research · 2023Article
- QTLbase2: an enhanced catalog of human quantitative trait loci on extensive molecular phenotypes.Nucleic acids research · 2023Article
- Scalable approaches for functional analyses of whole-genome sequencing non-coding variants.Human molecular genetics · 2022Review
- VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases.Nucleic acids research · 2022Article
- From the reference human genome to human pangenome: Premise, promise and challenge.Frontiers in genetics · 2022Article
Corrections and comments
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Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The advances of large-scale genomics studies have enabled compilation of cell type-specific, genome-wide DNA functional elements at high resolution. With the growing volume of functional annotation data and sequencing variants, existing variant annotation algorithms lack the efficiency and scalability to process big genomic data, particularly when annotating whole-genome sequencing variants against a huge database with billions of genomic features. Here, we develop VarNote to rapidly annotate genome-scale variants in large and complex functional annotation resources. Equipped with a novel index system and a parallel random-sweep searching algorithm, VarNote shows substantial performance improvements (two to three orders of magnitude) over existing algorithms at different scales. It supports both region-based and allele-specific annotations and introduces advanced functions for the flexible extraction of annotations. By integrating massive base-wise and context-dependent annotations in the VarNote framework, we introduce three efficient and accurate pipelines to prioritize the causal regulatory variants for common diseases, Mendelian disorders, and cancers.
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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.