ArticlePLoS genetics2013
A hybrid likelihood model for sequence-based disease association studies.
Article in PLoS genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 24 citations in OpenAlex.
- Mutations in the pancreatic secretory enzymesProceedings of the National Academy of Sciences of the United States of America · 2018Trial
- Molecular Modeling and In Vitro Functional Analysis of the RGS12 PDZ Domain Variant Associated with High-Penetrance Familial Bipolar Disorder.International journal of molecular sciences · 2024Article
- Endoplasmic stress-inducing variants in carboxyl ester lipase and pancreatic cancer risk.Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.] · 2022Article
- Genomic and neuroimaging approaches to bipolar disorder.BJPsych open · 2022Review
- An interpretable low-complexity machine learning framework for robust exome-basedNAR genomics and bioinformatics · 2020Article
- Whole-exome sequencing of 81 individuals from 27 multiply affected bipolar disorder families.Translational psychiatry · 2020Article
- Article
- The impact of a fine-scale population stratification on rare variant association test results.PloS one · 2018Article
- [Genetics of bipolar disorder].Der Nervenarzt · 2017Review
- DoEstRare: A statistical test to identify local enrichments in rare genomic variants associated with disease.PloS one · 2017Article
- Filtering genetic variants and placing informative priors based on putative biological function.BMC genetics · 2016Article
- Whole Genome Sequencing Defines the Genetic Heterogeneity of Familial Pancreatic Cancer.Cancer discovery · 2016Article
- Incorporation of protein binding effects into likelihood ratio test for exome sequencing data.BMC proceedings · 2016Article
- New developments in the genetics of bipolar disorder.Current psychiatry reports · 2014Review
- Identifying rare and common disease associated variants in genomic data using Parkinson's disease as a model.Journal of biomedical science · 2014Article
- The Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation.Frontiers in genetics · 2013Article
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
Abstract
In the past few years, case-control studies of common diseases have shifted their focus from single genes to whole exomes. New sequencing technologies now routinely detect hundreds of thousands of sequence variants in a single study, many of which are rare or even novel. The limitation of classical single-marker association analysis for rare variants has been a challenge in such studies. A new generation of statistical methods for case-control association studies has been developed to meet this challenge. A common approach to association analysis of rare variants is the burden-style collapsing methods to combine rare variant data within individuals across or within genes. Here, we propose a new hybrid likelihood model that combines a burden test with a test of the position distribution of variants. In extensive simulations and on empirical data from the Dallas Heart Study, the new model demonstrates consistently good power, in particular when applied to a gene set (e.g., multiple candidate genes with shared biological function or pathway), when rare variants cluster in key functional regions of a gene, and when protective variants are present. When applied to data from an ongoing sequencing study of bipolar disorder (191 cases, 107 controls), the model identifies seven gene sets with nominal p-values < 0.05, of which one MAPK signaling pathway (KEGG) reaches trend-level significance after correcting for multiple testing.
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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.