RVTESTS: an efficient and comprehensive tool for rare variant association analysis using sequence data.
paper
Cited
Public
- Authors
- Zhan, Xiaowei; Hu, Youna; Li, Bingshan; Abecasis, Goncalo R; Liu, Dajiang J
- Year
- 2016
- Journal
- Bioinformatics (Oxford, England)
- PMID
- 27153000
- DOI
- 10.1093/bioinformatics/btw079
- PMCID
- PMC4848408
MOTIVATION: Next-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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| Common and Rare Variants Genetic Association Analysis of Circulating Neutrophil Extracellular Traps. | Donkel SJ et al. | β | 2021 | β |
| Common and rare variants in HFE are not associated with Parkinson's disease in Europeans. | Saini P et al. | β | 2021 | β |
| Drinking and smoking polygenic risk is associated with childhood and early-adulthood psychiatric and behavioral traits independently of substance use and psychiatric genetic risk. | De Angelis F et al. | β | 2021 | β |
| Epigenome-wide association study identifies DNA methylation sites associated with target organ damage in older African Americans. | Ammous F et al. | β | 2021 | β |
| Exome sequencing in high and low fetal haemoglobin Arab-Indian haplotype sickle cell disease. | Alnafie AN et al. | β | 2021 | β |
| Genetic factors affect the susceptibility to bacterial infections in diabetes. | Simonsen JR et al. | β | 2021 | β |
| Genetic Profile of Endotoxemia Reveals an Association With Thromboembolism and Stroke. | LeskelΓ€ J et al. | β | 2021 | β |
| Genetics of facial telangiectasia in the Rotterdam Study: a genome-wide association study and candidate gene approach. | MekiΔ S et al. | β | 2021 | β |
| Genetic Susceptibility to Dry Skin in a General Middle-Aged to Elderly Population: A GWAS. | MekiΔ S et al. | β | 2021 | β |
| Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic architecture. | Chia R et al. | β | 2021 | β |
| Genome-wide admixture mapping of DSM-IV alcohol dependence, criterion count, and the self-rating of the effects of ethanol in African American populations. | Lai D et al. | β | 2021 | β |
| Genome-wide association of phenotypes based on clustering patterns of hand osteoarthritis identify <i>WNT9A</i> as novel osteoarthritis gene. | Boer CG et al. | β | 2021 | β |
| Genome-Wide Association Studies of Cognitive and Motor Progression in Parkinson's Disease. | Tan MMX et al. | β | 2021 | β |
| Genome-Wide Association Study Meta-Analysis for Parkinson Disease Motor Subtypes. | Alfradique-Dunham I et al. | β | 2021 | β |
| Genome-wide association study on coronary artery disease in type 1 diabetes suggests beta-defensin 127 as a risk locus. | Antikainen AAV et al. | β | 2021 | β |
| Genome-wide landscape establishes novel association signals for metabolic traits in the Arab population. | Hebbar P et al. | β | 2021 | β |
| Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries. | Gharahkhani P et al. | β | 2021 | β |
| Genome-wide search for genes affecting the age at diagnosis of type 1 diabetes. | Syreeni A et al. | β | 2021 | β |
| Hearing Function: Identification of New Candidate Genes Further Explaining the Complexity of This Sensory Ability. | Concas MP et al. | β | 2021 | β |
| Identification of Genetic Predispositions Related to Ionizing Radiation in Primary Human Skin Fibroblasts From Survivors of Childhood and Second Primary Cancer as Well as Cancer-Free Controls: Protocol for the Nested Case-Control Study KiKme. | Marron M et al. | β | 2021 | β |
| Investigation of Autosomal Genetic Sex Differences in Parkinson's Disease. | Blauwendraat C et al. | β | 2021 | β |
| Lack of evidence for association of UQCRC1 with Parkinson's disease in Europeans. | Senkevich K et al. | β | 2021 | β |
| Low frequency variants associated with leukocyte telomere length in the Singapore Chinese population. | Chang X et al. | β | 2021 | β |
| Metabolic Syndrome Parameters, Determinants, and Biomarkers in Adult Survivors of Childhood Cancer: Protocol for the Dutch Childhood Cancer Survivor Study on Metabolic Syndrome (Dutch LATER METS). | Pluimakers V et al. | β | 2021 | β |
| Metabolomic architecture of obesity implicates metabolonic lactone sulfate in cardiometabolic disease. | Das SK et al. | β | 2021 | β |
| MHC Variants Associated With Symptomatic <i>Versus</i> Asymptomatic SARS-CoV-2 Infection in Highly Exposed Individuals. | Castelli EC et al. | β | 2021 | β |
| Potential causal role of l-glutamine in sickle cell disease painful crises: A Mendelian randomization analysis. | Ilboudo Y et al. | β | 2021 | β |
| Prioritizing the Role of Major Lipoproteins and Subfractions as Risk Factors for Peripheral Artery Disease. | Levin MG et al. | β | 2021 | β |
| Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4. | Grosche S et al. | β | 2021 | β |
| Size matters: Large copy number losses in Hirschsprung disease patients reveal genes involved in enteric nervous system development. | Kuil LE et al. | β | 2021 | β |
| SORL1 mutation in a Greek family with Parkinson's disease and dementia. | Xiromerisiou G et al. | β | 2021 | β |
| Targeted whole exome sequencing and Drosophila modelling to unveil the molecular basis of primary ovarian insufficiency. | Bestetti I et al. | β | 2021 | β |
| Tensin 1 (TNS1) is a modifier gene for low body mass index (BMI) in homozygous [F508del]CFTR patients. | Walton NI et al. | β | 2021 | β |
| The Contribution of Known Familial Cardiovascular Disease Genes to Sudden Cardiac Death in Patients Undergoing Hemodialysis. | Schwantes-An TH et al. | β | 2021 | β |
| The role of RHOT1 and RHOT2 genetic variation on Parkinson disease risk and onset. | PeriΓ±Γ‘n MT et al. | β | 2021 | β |
| The trans-omics landscape of COVID-19. | Wu P et al. | β | 2021 | β |
| Variable Effects of PD-Risk Associated SNPs and Variants in Parkinsonism-Associated Genes on Disease Phenotype in a Community-Based Cohort. | Markopoulou K et al. | β | 2021 | β |
| Whole-exome sequencing reveals a role of HTRA1 and EGFL8 in brain white matter hyperintensities. | Malik R et al. | β | 2021 | β |
| A joint study of whole exome sequencing and structural MRI analysis in major depressive disorder. | Zhang Y et al. | β | 2020 | β |
| A Mendelian Randomization Study Provides Evidence That Adiposity and Dyslipidemia Lead to Lower Urinary Albumin-to-Creatinine Ratio, a Marker of Microvascular Function. | Casanova F et al. | β | 2020 | β |
| Association Analysis and Meta-Analysis of Multi-Allelic Variants for Large-Scale Sequence Data. | Jiang Y et al. | β | 2020 | β |
| Association of <i>G6PD</i> variants with hemoglobin A1c and impact on diabetes diagnosis in East Asian individuals. | Leong A et al. | β | 2020 | β |
| Cardiovascular disease risk and pathophysiology in South Asians: can longitudinal multi-omics shed light? | Sun YV et al. | β | 2020 | β |
| CDH6 and HAGH protein levels in plasma associate with Alzheimer's disease in APOE Ξ΅4 carriers. | Ahmad S et al. | β | 2020 | β |
| Comprehensive assessment of PINK1 variants in Parkinson's disease. | Krohn L et al. | β | 2020 | β |
| Discovery of rare coding variants in OGDHL and BRCA2 in relation to breast cancer risk in Chinese women. | Guo X et al. | β | 2020 | β |
| Distinct Subsets of Noncoding RNAs Are Strongly Associated With BMD and Fracture, Studied in Weight-Bearing and Non-Weight-Bearing Human Bone. | Gautvik KM et al. | β | 2020 | β |
| Epigenetic loci for blood pressure are associated with hypertensive target organ damage in older African Americans from the genetic epidemiology network of Arteriopathy (GENOA) study. | Kho M et al. | β | 2020 | β |
| Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy. | Kousi M et al. | β | 2020 | β |
| Exome-Based Case-Control Analysis Highlights the Pathogenic Role of Ciliary Genes in Transposition of the Great Arteries. | Liu X et al. | β | 2020 | β |
| Exome-chip association analysis of intracranial aneurysms. | van 't Hof FNG et al. | β | 2020 | β |
| Exome Sequencing Analysis Identifies Rare Variants in <i>ATM</i> and <i>RPL8</i> That Are Associated With Shorter Telomere Length. | van der Spek A et al. | β | 2020 | β |
| Exome Sequencing in Individuals with Isolated Biliary Atresia. | Rajagopalan R et al. | β | 2020 | β |
| Exome Sequencing Reveals Common and Rare Variants in F5 Associated With ACE Inhibitor and Angiotensin Receptor Blocker-Induced Angioedema. | Maroteau C et al. | β | 2020 | β |
| Genetic modifiers of risk and age at onset in GBA associated Parkinson's disease and Lewy body dementia. | Blauwendraat C et al. | β | 2020 | β |
| Genetics of renovascular hypertension in children. | Viering DHHM et al. | β | 2020 | β |
| Genetic Studies of Leptin Concentrations Implicate Leptin in the Regulation of Early Adiposity. | Yaghootkar H et al. | β | 2020 | β |
| Genetic variants affecting bone mineral density and bone mineral content at multiple skeletal sites in Hispanic children. | Hou R et al. | β | 2020 | β |
| Genome-wide association meta-analysis for early age-related macular degeneration highlights novel loci and insights for advanced disease. | Winkler TW et al. | β | 2020 | β |
| Genome-wide association studies of the self-rating of effects of ethanol (SRE). | Lai D et al. | β | 2020 | β |
| Genome-Wide Association Study for Urinary and Fecal Incontinence in Women. | Penney KL et al. | β | 2020 | β |
| Genome-Wide Association Study of Wood Anatomical and Morphological Traits in <i>Populus trichocarpa</i>. | Chhetri HB et al. | β | 2020 | β |
| Identification of Genetic Variants for Female Obesity and Evaluation of the Causal Role of Genetically Defined Obesity in Polycystic Ovarian Syndrome. | Ahn Y et al. | β | 2020 | β |
| Identification of Maturity-Onset Diabetes of the Young Caused by Mutation in <i>FOXM1 via</i> Whole-Exome Sequencing in Northern China. | Zhong L et al. | β | 2020 | β |
| Identification of Novel Loci and New Risk Variant in Known Loci for Colorectal Cancer Risk in East Asians. | Lu Y et al. | β | 2020 | β |
| Initial whole-genome sequencing and analysis of the host genetic contribution to COVID-19 severity and susceptibility. | Wang F et al. | β | 2020 | β |
| Large-scale pathway specific polygenic risk and transcriptomic community network analysis identifies novel functional pathways in Parkinson disease. | Bandres-Ciga S et al. | β | 2020 | β |
| Large-Scale Whole-Genome Sequencing Reveals the Genetic Architecture of Primary Membranoproliferative GN and C3 Glomerulopathy. | Levine AP et al. | β | 2020 | β |
| Letter to the editor regarding "TGM6 variants in Parkinson's disease: clinical findings and functional evidence". | Hall A et al. | β | 2020 | β |
| Meta-analysis of up to 622,409 individuals identifies 40 novel smoking behaviour associated genetic loci. | Erzurumluoglu AM et al. | β | 2020 | β |
| Multi-level evidence of an allelic hierarchy of USH2A variants in hearing, auditory processing and speech/language outcomes. | Perrino PA et al. | β | 2020 | β |
| Nasopharyngeal carcinoma MHC region deep sequencing identifies HLA and novel non-HLA TRIM31 and TRIM39 loci. | Ning L et al. | β | 2020 | β |
| Natural variation in a glucuronosyltransferase modulates propionate sensitivity in a C. elegans propionic acidemia model. | Na H et al. | β | 2020 | β |
| Population genetic simulation study of power in association testing across genetic architectures and study designs. | Tong DMH et al. | β | 2020 | β |
| Predicting and elucidating the etiology of fatty liver disease: A machine learning modeling and validation study in the IMI DIRECT cohorts. | Atabaki-Pasdar N et al. | β | 2020 | β |
| The Polygenic and Monogenic Basis of Blood Traits and Diseases. | Vuckovic D et al. | β | 2020 | β |
| Whole exome sequencing in patients with Williams-Beuren syndrome followed by disease modeling in mice points to four novel pathways that may modify stenosis risk. | Parrish PCR et al. | β | 2020 | β |
| A gene-based recessive diplotype exome scan discovers <i>FGF6</i>, a novel hepcidin-regulating iron-metabolism gene. | Guo S et al. | β | 2019 | β |
| A genome-wide association study implicates multiple mechanisms influencing raised urinary albumin-creatinine ratio. | Casanova F et al. | β | 2019 | β |
| Appraising the causal relevance of DNA methylation for risk of lung cancer. | Battram T et al. | β | 2019 | β |
| Assessment of Novel Genome-Wide Significant Gene Loci and Lesion Growth in Geographic Atrophy Secondary to Age-Related Macular Degeneration. | Grassmann F et al. | β | 2019 | β |
| Association of low-frequency genetic variants in regulatory regions with nonsyndromic orofacial clefts. | Shaffer JR et al. | β | 2019 | β |
| Association studies of up to 1.2 million individuals yield new insights into the genetic etiology of tobacco and alcohol use. | Liu M et al. | β | 2019 | β |
| Efficient Variant Set Mixed Model Association Tests for Continuous and Binary Traits in Large-Scale Whole-Genome Sequencing Studies. | Chen H et al. | β | 2019 | β |
| Exome-chip meta-analysis identifies association between variation in ANKRD26 and platelet aggregation. | Chen MH et al. | β | 2019 | β |
| Exome-Derived Adiponectin-Associated Variants Implicate Obesity and Lipid Biology. | Spracklen CN et al. | β | 2019 | β |
| Exome Sequencing in Individuals with Isolated Biliary Atresia | Rajagopalan R et al. | β | 2019 | β |
| Finding New Cell Wall Regulatory Genes in <i>Populus trichocarpa</i> Using Multiple Lines of Evidence. | Furches A et al. | β | 2019 | β |
| Genetic Regulation of Pigment Epithelium-Derived Factor (PEDF): An Exome-Chip Association Analysis in Chinese Subjects With Type 2 Diabetes. | Cheung CYY et al. | β | 2019 | β |
| Genome wide analysis for mouth ulcers identifies associations at immune regulatory loci. | Dudding T et al. | β | 2019 | β |
| Genome-wide association studies identify polygenic effects for completed suicide in the Japanese population. | Otsuka I et al. | β | 2019 | β |
| Genome-wide association studies of alcohol dependence, DSM-IV criterion count and individual criteria. | Lai D et al. | β | 2019 | β |
| Genome-wide Association Study Identifies Genetic Variants Associated With Early and Sustained Response to (Pegylated) Interferon in Chronic Hepatitis B Patients: The GIANT-B Study. | Brouwer WP et al. | β | 2019 | β |
| Genome-wide association study in Finnish twins highlights the connection between nicotine addiction and neurotrophin signaling pathway. | HΓ€llfors J et al. | β | 2019 | β |
| Genome-wide Association Study of Maximum Habitual Alcohol Intake in >140,000 U.S. European and African American Veterans Yields Novel Risk Loci. | Gelernter J et al. | β | 2019 | β |
| Genomewide association study of Parkinson's disease clinical biomarkers in 12 longitudinal patients' cohorts. | Iwaki H et al. | β | 2019 | β |
| Genome-wide association study of post-traumatic stress disorder reexperiencing symptoms in >165,000 US veterans. | Gelernter J et al. | β | 2019 | β |
| Genomics of posttraumatic stress disorder in veterans: Methods and rationale for Veterans Affairs Cooperative Study #575B. | Radhakrishnan K et al. | β | 2019 | β |
| <i>CACNB2</i> Is a Novel Susceptibility Gene for Diabetic Retinopathy in Type 1 Diabetes. | Vuori N et al. | β | 2019 | β |
| Increased frequency of rare missense PPP1R3B variants among Danish patients with type 2 diabetes. | Niazi RK et al. | β | 2019 | β |
| International meta-analysis of PTSD genome-wide association studies identifies sex- and ancestry-specific genetic risk loci. | Nievergelt CM et al. | β | 2019 | β |
| Large-Scale Genome-Wide Association Study of East Asians Identifies Loci Associated With Risk for Colorectal Cancer. | Lu Y et al. | β | 2019 | β |
| Methods for the Analysis and Interpretation for Rare Variants Associated with Complex Traits. | Weissenkampen JD et al. | β | 2019 | β |
| Natural Variation and Genetic Determinants of <i>Caenorhabditis elegans</i> Sperm Size. | Gimond C et al. | β | 2019 | β |
| Parkinson's disease age at onset genome-wide association study: Defining heritability, genetic loci, and Ξ±-synuclein mechanisms. | Blauwendraat C et al. | β | 2019 | β |
| Sequencing reveals protective and pathogenic effects on development of diabetes of rare GLIS3 variants. | Sun J et al. | β | 2019 | β |
| Target genes, variants, tissues and transcriptional pathways influencing human serum urate levels. | Tin A et al. | β | 2019 | β |
| The Genetic Architecture of Parkinson Disease in Spain: Characterizing Population-Specific Risk, Differential Haplotype Structures, and Providing Etiologic Insight. | Bandres-Ciga S et al. | β | 2019 | β |
| Truncating variant burden in high-functioning autism and pleiotropic effects of LRP1 across psychiatric phenotypes | Torrico B et al. | β | 2019 | β |
| Variants in the fetal genome near pro-inflammatory cytokine genes on 2q13 associate with gestational duration. | Liu X et al. | β | 2019 | β |
| Another Round of "Clue" to Uncover the Mystery of Complex Traits. | Verma SS et al. | β | 2018 | β |
| Confirmation of GLRA3 as a susceptibility locus for albuminuria in Finnish patients with type 1 diabetes. | Sandholm N et al. | β | 2018 | β |
| Deep-coverage whole genome sequences and blood lipids among 16,324 individuals. | Natarajan P et al. | β | 2018 | β |
| Effect of Damaging Rare Mutations in Synapse-Related Gene Sets on Response to Short-term Antipsychotic Medication in Chinese Patients With Schizophrenia: A Randomized Clinical Trial. | Wang Q et al. | β | 2018 | β |
| Exome-wide analysis of mutational burden in patients with typical and atypical Rolandic epilepsy. | Bobbili DR et al. | β | 2018 | β |
| Extreme allelic heterogeneity at a Caenorhabditis elegans beta-tubulin locus explains natural resistance to benzimidazoles. | Hahnel SR et al. | β | 2018 | β |
| Frequency of Loss of Function Variants in LRRK2 in Parkinson Disease. | Blauwendraat C et al. | β | 2018 | β |
| GRIPT: a novel case-control analysis method for Mendelian disease gene discovery. | Wang J et al. | β | 2018 | β |
| Identification of Genes Associated With Hirschsprung Disease, Based on Whole-Genome Sequence Analysis, and Potential Effects on Enteric Nervous System Development. | Tang CS et al. | β | 2018 | β |
| Identification of rare sequence variation underlying heritable pulmonary arterial hypertension. | GrΓ€f S et al. | β | 2018 | β |
| Meta-analysis of exome array data identifies six novel genetic loci for lung function. | Jackson VE et al. | β | 2018 | β |
| Proper conditional analysis in the presence of missing data: Application to large scale meta-analysis of tobacco use phenotypes. | Jiang Y et al. | β | 2018 | β |
| Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity. | Turcot V et al. | β | 2018 | β |
| Rare coding variants in genes encoding GABA<sub>A</sub> receptors in genetic generalised epilepsies: an exome-based case-control study. | May P et al. | β | 2018 | β |
| Rare germline variants in DNA repair genes and the angiogenesis pathway predispose prostate cancer patients to develop metastatic disease. | Mijuskovic M et al. | β | 2018 | β |
| Reply: No evidence for rare TRAP1 mutations influencing the risk of idiopathic Parkinson's disease. | Fitzgerald JC et al. | β | 2018 | β |
| Stage 2 Registered Report: Variation in neurodevelopmental outcomes in children with sex chromosome trisomies: testing the double hit hypothesis. | Newbury DF et al. | β | 2018 | β |
| Whole-Genome Linkage Scan Combined With Exome Sequencing Identifies Novel Candidate Genes for Carotid Intima-Media Thickness. | Vojinovic D et al. | β | 2018 | β |
| WISARD: workbench for integrated superfast association studies for related datasets. | Lee S et al. | β | 2018 | β |
| A heterozygous mutation in GOT1 is associated with familial macro-aspartate aminotransferase. | Kulecka M et al. | β | 2017 | β |
| Analysis of neurodegenerative Mendelian genes in clinically diagnosed Alzheimer Disease. | FernΓ‘ndez MV et al. | β | 2017 | β |
| Association of gene coding variation and resting metabolic rate in a multi-ethnic sample of children and adults. | Hellwege JN et al. | β | 2017 | β |
| Association studies of low-frequency coding variants in nonsyndromic cleft lip with or without cleft palate. | Leslie EJ et al. | β | 2017 | β |
| Burden of rare variants in ALS genes influences survival in familial and sporadic ALS. | Pang SY et al. | β | 2017 | β |
| Current Scope and Challenges in Phenome-Wide Association Studies. | Verma A et al. | β | 2017 | β |
| Genome-wide association study of erythrocyte density in sickle cell disease patients. | Ilboudo Y et al. | β | 2017 | β |
| Identifying Genetic Sources of Phenotypic Heterogeneity in Orofacial Clefts by Targeted Sequencing. | Carlson JC et al. | β | 2017 | β |
| Possible role of rare variants in Trace amine associated receptor 1 in schizophrenia. | John J et al. | β | 2017 | β |
| Robust and rapid algorithms facilitate large-scale whole genome sequencing downstream analysis in an integrative framework. | Li M et al. | β | 2017 | β |
| Utility of Post-Mortem Genetic Testing in Cases of Sudden Arrhythmic Death Syndrome. | Lahrouchi N et al. | β | 2017 | β |