ArticleEuropean journal of human genetics : EJHG2014
A fast multilocus test with adaptive SNP selection for large-scale genetic-association studies.
Article in European journal of human genetics : EJHG, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it, 20 citations in OpenAlex.
- A Powerful Procedure for Pathway-Based Meta-analysis Using Summary Statistics Identifies 43 Pathways Associated with Type II Diabetes in European Populations.PLoS genetics · 2016Pooled it
- Simultaneous selection of multiple important single nucleotide polymorphisms in familial genome wide association studies data.Scientific reports · 2023Article
- Speeding up Monte Carlo simulations for the adaptive sum of powered score test with importance sampling.Biometrics · 2022Article
- JEM: A joint test to estimate the effect of multiple genetic variants on DNA methylation.Genetic epidemiology · 2021Article
- Statistical Method Based on Bayes-Type Empirical Score Test for Assessing Genetic Association with Multilocus Genotype Data.International journal of genomics · 2020Article
- Association of Selenoprotein and Selenium Pathway Genotypes with Risk of Colorectal Cancer and Interaction with Selenium Status.Nutrients · 2019Article
- Genetic variation in the Hippo pathway and breast cancer risk in women of African ancestry.Molecular carcinogenesis · 2018Article
- A multi-locus genetic association test for a dichotomous trait and its secondary phenotype.Statistical methods in medical research · 2018Article
- Genetic variation in the vitamin D related pathway and breast cancer risk in women of African ancestry in the root consortium.International journal of cancer · 2018Article
- Association of breast cancer risk and the mTOR pathway in women of African ancestry in 'The Root' Consortium.Carcinogenesis · 2017Article
- Pathway, in silico and tissue-specific expression quantitative analyses of oesophageal squamous cell carcinoma genome-wide association studies data.International journal of epidemiology · 2016Article
- Genetic variation in the insulin, insulin-like growth factor, growth hormone, and leptin pathways in relation to breast cancer in African-American women: the AMBER consortium.NPJ breast cancer · 2016Article
- Gene-based analysis of the fibroblast growth factor receptor signaling pathway in relation to breast cancer in African American women: the AMBER consortium.Breast cancer research and treatment · 2016Article
- Common genetic variants in epigenetic machinery genes and risk of upper gastrointestinal cancers.International journal of epidemiology · 2015Article
- A fast and powerful tree-based association test for detecting complex joint effects in case-control studies.Bioinformatics (Oxford, England) · 2014Article
- A symbiotic liaison between the genetic and epigenetic code.Frontiers in genetics · 2014Review
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
Abstract
As increasing evidence suggests that multiple correlated genetic variants could jointly influence the outcome, a multilocus test that aggregates association evidence across multiple genetic markers in a considered gene or a genomic region may be more powerful than a single-marker test for detecting susceptibility loci. We propose a multilocus test, AdaJoint, which adopts a variable selection procedure to identify a subset of genetic markers that jointly show the strongest association signal, and defines the test statistic based on the selected genetic markers. The P-value from the AdaJoint test is evaluated by a computationally efficient algorithm that effectively adjusts for multiple-comparison, and is hundreds of times faster than the standard permutation method. Simulation studies demonstrate that AdaJoint has the most robust performance among several commonly used multilocus tests. We perform multilocus analysis of over 26,000 genes/regions on two genome-wide association studies of pancreatic cancer. Compared with its competitors, AdaJoint identifies a much stronger association between the gene CLPTM1L and pancreatic cancer risk (6.0 × 10(-8)), with the signal optimally captured by two correlated single-nucleotide polymorphisms (SNPs). Finally, we show AdaJoint as a powerful tool for mapping cis-regulating methylation quantitative trait loci on normal breast tissues, and find many CpG sites whose methylation levels are jointly regulated by multiple SNPs nearby.
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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.