ArticleAmerican journal of human genetics2022
TOP-LD: A tool to explore linkage disequilibrium with TOPMed whole-genome sequence data.
Article in American journal of human genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers, 3 of them syntheses that pooled it.
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Who cites it
60 citing papers in PubMed, 3 syntheses or guidelines pooled it, 99 citations in OpenAlex.
- Consensus meta-analysis of genome-wide association studies for Alzheimer's disease and related dementias.Nature genetics · 2026Pooled it
- Multi-ancestry genome-wide association study of severe pregnancy nausea and vomiting.Nature genetics · 2026Pooled it
- Re-analysis and meta-analysis of summary statistics from gene-environment interaction studies.Bioinformatics (Oxford, England) · 2023Pooled it
- Genetic variation in BDNF is associated with opioid use disorder severity.Human genetics · 2026Article
- Cross-population metabolome-wide Mendelian randomization study of prostate cancer risk.Research square · 2026Article
- Multi-omics integration predicts the incidence of 17 diseases in the UK Biobank.Nature communications · 2026Article
- A Novel PTPN2 Isoform Differentially Regulates Immune Response.European journal of immunology · 2026Article
- A reference panel for linkage disequilibrium and genotype imputation using whole-genome sequencing data from 2,680 participants across India.HGG advances · 2026Article
- Cell-specific variant-to-gene mapping identifies conserved neural and glial regulators of sleep.bioRxiv : the preprint server for biology · 2026Article
- Molecular systems, human noncoding sequence variants, and blood pressure.Physiological reviews · 2026Review
- Variant-to-gene mapping identifiesbioRxiv : the preprint server for biology · 2026Article
- eQTL in diseased colon tissue identifies potential target genes associated with IBD.Nature communications · 2026Article
- AncientProxy: A catalog of ancient proxies for modern genetic variants.American journal of human genetics · 2026Article
- PYRAMA: an open-source tool for advanced meta-analysis of genome wide association studies.Bioinformatics (Oxford, England) · 2026Article
- Ethnic-specific effects of the LILRB2-LILRB5 locus and newly identified risk loci for Alzheimer's disease in the East Asian population.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- Liver single-nucleus multiome profiling reveals cell-type mechanisms for cardiometabolic traits.American journal of human genetics · 2026Article
- Global Evaluation of Congenital Heart Disease-Associated Non-Coding Variants.Research square · 2026Article
- DecipheringBioinformatics advances · 2026Article
- 3D chromatin-based variant-to-gene maps across 57 human cell types reveal the cellular and genetic architecture of autoimmune disease susceptibility.Genome biology · 2025Article
- Recommendations for responsible use of population descriptors in polygenic risk score development.Nature genetics · 2025Review
Corrections and comments
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Authors and funding
26 authors at 12 institutions in 2 countries.
Funding
Abstract
Current publicly available tools that allow rapid exploration of linkage disequilibrium (LD) between markers (e.g., HaploReg and LDlink) are based on whole-genome sequence (WGS) data from 2,504 individuals in the 1000 Genomes Project. Here, we present TOP-LD, an online tool to explore LD inferred with high-coverage (∼30×) WGS data from 15,578 individuals in the NHLBI Trans-Omics for Precision Medicine (TOPMed) program. TOP-LD provides a significant upgrade compared to current LD tools, as the TOPMed WGS data provide a more comprehensive representation of genetic variation than the 1000 Genomes data, particularly for rare variants and in the specific populations that we analyzed. For example, TOP-LD encompasses LD information for 150.3, 62.2, and 36.7 million variants for European, African, and East Asian ancestral samples, respectively, offering 2.6- to 9.1-fold increase in variant coverage compared to HaploReg 4.0 or LDlink. In addition, TOP-LD includes tens of thousands of structural variants (SVs). We demonstrate the value of TOP-LD in fine-mapping at the GGT1 locus associated with gamma glutamyltransferase in the African ancestry participants in UK Biobank. Beyond fine-mapping, TOP-LD can facilitate a wide range of applications that are based on summary statistics and estimates of LD. TOP-LD is freely available online.
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Registered trials
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.