ArticleGenetic epidemiology2014
TARV: tree-based analysis of rare variants identifying risk modifying variants in CTNNA2 and CNTNAP2 for alcohol addiction.
Article in Genetic epidemiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Identification and validation of supervariants reveal novel loci associated with human white matter microstructure.Genome research · 2024Pooled it
- Extensive genetic interactions (epistasis) linked to alcohol use disorder in a high-risk population.Communications biology · 2026Article
- Genetic modifiers of frequent vaso-occlusive hospitalizations among individuals with sickle cell disease (SCD).Annals of hematology · 2025Article
- Empowering genome-wide association studies via a visualizable test based on the regional association score.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Identifying genetic variants for brain connectivity using Ball Covariance Ranking and Aggregation.Journal of the American Statistical Association · 2025Article
- Deep learning identified genetic variants for COVID-19-related mortality among 28,097 affected cases in UK Biobank.Genetic epidemiology · 2023Article
- Catenin Alpha 2 May Be a Biomarker or Potential Drug Target in Psychiatric Disorders with Perseverative Negative Thinking.Pharmaceuticals (Basel, Switzerland) · 2021Article
- Super-variants identification for brain connectivity.Human brain mapping · 2021Article
- Genetic variants are identified to increase risk of COVID-19 related mortality from UK Biobank data.Human genomics · 2021Article
- Genetic variants are identified to increase risk of COVID-19 related mortality from UK Biobank data.medRxiv : the preprint server for health sciences · 2020Article
- Supervariants identification for breast cancer.Genetic epidemiology · 2020Article
- Adaptive Fisher method detects dense and sparse signals in association analysis of SNV sets.BMC medical genomics · 2020Article
- Association of GDNF and CNTNAP2 gene variants with gambling.Journal of behavioral addictions · 2019Article
- Prenatal Alcohol Exposure Is Associated With Adverse Cognitive Effects and Distinct Whole-Genome DNA Methylation Patterns in Primary School Children.Frontiers in behavioral neuroscience · 2018Article
- Genome-Wide Study of Response to Platinum, Taxane, and Combination Therapy in Ovarian Cancer: In vitro Phenotypes, Inherited Variation, and Disease Recurrence.Frontiers in genetics · 2016Article
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2 authors.
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Abstract
Since the development of next generation sequencing (NGS) technology, researchers have been extending their efforts on genome-wide association studies (GWAS) from common variants to rare variants to find the missing inheritance. Although various statistical methods have been proposed to analyze rare variants data, they generally face difficulties for complex disease models involving multiple genes. In this paper, we propose a tree-based analysis of rare variants (TARV) that adopts a nonparametric disease model and is capable of exploring gene-gene interactions. We found that TARV outperforms the sequence kernel association test (SKAT) in most of our simulation scenarios, and by notable margins in some cases. By applying TARV to the study of addiction: genetics and environment (SAGE) data, we successfully detected gene CTNNA2 and its 43 specific variants that increase the risk of alcoholism in women, with an odds ratio (OR) of 1.94. This gene has not been detected in the SAGE data. Post hoc literature search also supports the role of CTNNA2 as a likely risk gene for alcohol addiction. In addition, we also detected a plausible protective gene CNTNAP2, whose 97 rare variants can reduce the risk of alcoholism in women, with an OR of 0.55. These findings suggest that TARV can be effective in dissecting genetic variants for complex diseases using rare variants data.
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