ArticleBioinformatics (Oxford, England)2016
RVTESTS: an efficient and comprehensive tool for rare variant association analysis using sequence data.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 273 papers, 26 of them syntheses that pooled it.
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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.
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Who cites it
273 citing papers in PubMed, 26 syntheses or guidelines pooled it.
- Genome wide association study meta-analysis of neuropathologic lesions of Alzheimer's disease and related dementias in a multi-site autopsy cohort.PLoS genetics · 2026Pooled it
- Multi-ancestry whole genome sequencing analysis of lean body mass.Genome biology · 2025Pooled it
- Assessment of the functionality and usability of open-source rare variant analysis pipelines.Briefings in bioinformatics · 2025Pooled it
- Genome-Wide Interaction Analyses of Serum Calcium on Ventricular Repolarization Time in 125 393 Participants.Journal of the American Heart Association · 2024Pooled it
- 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
- Association of genetic variation on X chromosome with systemic lupus erythematosus in both Thai and Chinese populations.Lupus science & medicine · 2024Pooled it
- Germline Genetic Variants Associated with Somatic TMPRSS2:ERG Fusion Status in Prostate Cancer: A Genome-Wide Association Study.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2023Pooled it
- Association of Rare Variants in ARSA with Parkinson's Disease.Movement disorders : official journal of the Movement Disorder Society · 2023Pooled it
- Genome-wide contribution of common short-tandem repeats to Parkinson's disease genetic risk.Brain : a journal of neurology · 2023Pooled it
- Increased soluble urokinase plasminogen activator levels modulate monocyte function to promote atherosclerosis.The Journal of clinical investigation · 2022Pooled it
- Genome-wide Association and Meta-analysis of Age at Onset in Parkinson Disease: Evidence From the COURAGE-PD Consortium.Neurology · 2022Pooled it
- Genome-wide meta-analysis of iron status biomarkers and the effect of iron on all-cause mortality in HUNT.Communications biology · 2022Pooled it
- Multi-ancestry genome-wide association study of asthma exacerbations.Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology · 2022Pooled it
- Genome-wide association study meta-analysis identifies three novel loci for circulating anti-Müllerian hormone levels in women.Human reproduction (Oxford, England) · 2022Pooled it
- A multiethnic whole genome sequencing study to identify novel loci for bone mineral density.Human molecular genetics · 2022Pooled it
- A large-scale transcriptome-wide association study (TWAS) of 10 blood cell phenotypes reveals complexities of TWAS fine-mapping.Genetic epidemiology · 2022Pooled it
- Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4.Nature communications · 2021Pooled it
- Genetic factors affect the susceptibility to bacterial infections in diabetes.Scientific reports · 2021Pooled it
- Genome-wide search for genes affecting the age at diagnosis of type 1 diabetes.Journal of internal medicine · 2021Pooled it
- A multi-ethnic genome-wide association study implicates collagen matrix integrity and cell differentiation pathways in keratoconus.Communications biology · 2021Pooled it
213 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
motivationNext-generation sequencing technologies have enabled the large-scale assessment of the impact of rare and low-frequency genetic variants for complex human diseases. Gene-level association tests are often performed to analyze rare variants, where multiple rare variants in a gene region are analyzed jointly. Applying gene-level association tests to analyze sequence data often requires integrating multiple heterogeneous sources of information (e.g. annotations, functional prediction scores, allele frequencies, genotypes and phenotypes) to determine the optimal analysis unit and prioritize causal variants. Given the complexity and scale of current sequence datasets and bioinformatics databases, there is a compelling need for more efficient software tools to facilitate these analyses. To answer this challenge, we developed RVTESTS, which implements a broad set of rare variant association statistics and supports the analysis of autosomal and X-linked variants for both unrelated and related individuals. RVTESTS also provides useful companion features for annotating sequence variants, integrating bioinformatics databases, performing data quality control and sample selection. We illustrate the advantages of RVTESTS in functionality and efficiency using the 1000 Genomes Project data. AVAILABILITY AND IMPLEMENTATION: RVTESTS is available on Linux, MacOS and Windows. Source code and executable files can be obtained at https://github.com/zhanxw/rvtests CONTACT: zhanxw@gmail.com; goncalo@umich.edu; dajiang.liu@outlook.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.