ArticlePloS one2013
Rare variant analysis for family-based design.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers, 4 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
60 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Region-based analysis of rare genomic variants in whole-genome sequencing datasets reveal two novel Alzheimer's disease-associated genes: DTNB and DLG2.Molecular psychiatry · 2022Pooled it
- Gene-based genome-wide association studies and meta-analyses of conotruncal heart defects.PloS one · 2019Pooled it
- Methods for association analysis and meta-analysis of rare variants in families.Genetic epidemiology · 2015Pooled it
- Pooled it
- MIRAGE: A Bayesian statistical method for gene-level rare-variant analysis incorporating functional annotations.American journal of human genetics · 2026Article
- KnockoffHybrid: A knockoff framework for hybrid analysis of trio and population designs in genome-wide association studies.American journal of human genetics · 2024Article
- Article
- KnockoffTrio: A knockoff framework for the identification of putative causal variants in genome-wide association studies with trio design.American journal of human genetics · 2022Article
- Replication study of AD-associated rare variants.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2022Article
- Recent advances and challenges of rare variant association analysis in the biobank sequencing era.Frontiers in genetics · 2022Review
- Whole-genome sequencing reveals new Alzheimer's disease-associated rare variants in loci related to synaptic function and neuronal development.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2021Article
- The Complex and Diverse Genetic Architecture of Dilated Cardiomyopathy.Circulation research · 2021Review
- A unifying framework for rare variant association testing in family-based designs, including higher criticism approaches, SKATs, and burden tests.Bioinformatics (Oxford, England) · 2021Article
- Gene-Based Association Testing of Dichotomous Traits With Generalized Functional Linear Mixed Models Using Extended Pedigrees: Applications to Age-Related Macular Degeneration.Journal of the American Statistical Association · 2021Article
- A Rare Variant Nonparametric Linkage Method for Nuclear and Extended Pedigrees with Application to Late-Onset Alzheimer Disease via WGS Data.American journal of human genetics · 2019Article
- A comparison of popular TDT-generalizations for family-based association analysis.Genetic epidemiology · 2019Article
- Exome genotyping and linkage analysis identifies two novel linked regions and replicates two others for myopia in Ashkenazi Jewish families.BMC medical genetics · 2019Article
- Article
- Advances in the Genetics of Hypertension: The Effect of Rare Variants.International journal of molecular sciences · 2018Review
- Association of ARID5B Genetic Variants with Risk of Childhood B Cell Precursor Acute Lymphoblastic Leukaemia in LatviaAsian Pacific journal of cancer prevention : APJCP · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Genome-wide association studies have been able to identify disease associations with many common variants; however most of the estimated genetic contribution explained by these variants appears to be very modest. Rare variants are thought to have larger effect sizes compared to common SNPs but effects of rare variants cannot be tested in the GWAS setting. Here we propose a novel method to test for association of rare variants obtained by sequencing in family-based samples by collapsing the standard family-based association test (FBAT) statistic over a region of interest. We also propose a suitable weighting scheme so that low frequency SNPs that may be enriched in functional variants can be upweighted compared to common variants. Using simulations we show that the family-based methods perform at par with the population-based methods under no population stratification. By construction, family-based tests are completely robust to population stratification; we show that our proposed methods remain valid even when population stratification is present.
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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.