ArticleAmerican journal of human genetics2022
A phenome-wide association study identifies effects of copy-number variation of VNTRs and multicopy genes on multiple human traits.
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 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed.
- Trial
- A phenome-wide association study of CNVs genotyped from genome sequencing read depth in the UK Biobank.American journal of human genetics · 2026Article
- Genome-wide characterization of lumpy skin disease virus isolate from Bangladesh.Scientific reports · 2025Article
- Structure of a polymorphic repeat at theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Structure of a polymorphic repeat at themedRxiv : the preprint server for health sciences · 2025Article
- Core biological principles and tools stemming from basic Arabidopsis research.The Plant cell · 2025Review
- Genome-wide investigation of VNTR motif polymorphisms in 8,222 genomes: Implications for biological regulation and human traits.Cell genomics · 2024Article
- A phenome-wide association study of tandem repeat variation in 168,554 individuals from the UK Biobank.Nature communications · 2024Article
- A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 associated with intellectual disability.Nature genetics · 2024Article
- TRGT-ing the dark genome to accurately characterize tandem repeats at scale.Nature biotechnology · 2024Article
- Biostatistical Aspects of Whole Genome Sequencing Studies: Preprocessing and Quality Control.Biometrical journal. Biometrische Zeitschrift · 2024Article
- Review
- SUMO protease FUG1, histone reader AL3 and chromodomain protein LHP1 are integral to repeat expansion-induced gene silencing in Arabidopsis thaliana.Nature plants · 2024Article
- Rediscovering tandem repeat variation in schizophrenia: challenges and opportunities.Translational psychiatry · 2023Review
- Article
- Differences in the intraspecies copy number variation of Arabidopsis thaliana conserved and nonconserved miRNA genes.Functional & integrative genomics · 2023Article
- Recent advances and current challenges in population genomics of structural variation in animals and plants.Frontiers in genetics · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
The human genome contains tens of thousands of large tandem repeats and hundreds of genes that show common and highly variable copy-number changes. Due to their large size and repetitive nature, these variable number tandem repeats (VNTRs) and multicopy genes are generally recalcitrant to standard genotyping approaches and, as a result, this class of variation is poorly characterized. However, several recent studies have demonstrated that copy-number variation of VNTRs can modify local gene expression, epigenetics, and human traits, indicating that many have a functional role. Here, using read depth from whole-genome sequencing to profile copy number, we report results of a phenome-wide association study (PheWAS) of VNTRs and multicopy genes in a discovery cohort of ∼35,000 samples, identifying 32 traits associated with copy number of 38 VNTRs and multicopy genes at 1% FDR. We replicated many of these signals in an independent cohort and observed that VNTRs showing trait associations were significantly enriched for expression QTLs with nearby genes, providing strong support for our results. Fine-mapping studies indicated that in the majority (∼90%) of cases, the VNTRs and multicopy genes we identified represent the causal variants underlying the observed associations. Furthermore, several lie in regions where prior SNV-based GWASs have failed to identify any significant associations with these traits. Our study indicates that copy number of VNTRs and multicopy genes contributes to diverse human traits and suggests that complex structural variants potentially explain some of the so-called "missing heritability" of SNV-based GWASs.
Indexed as
Identifiers
What OpenQuestion holds
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.