ArticleBMC genetics2008
A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples.
Article in BMC genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Genetic Variation and Sickle Cell Disease Severity: A Systematic Review and Meta-Analysis.JAMA network open · 2023Pooled it
- Pooled genome-wide analysis to identify novel risk loci for pediatric allergic asthma.PloS one · 2011Pooled it
- Automatic block-wise genotype-phenotype association detection based on hidden Markov model.BMC bioinformatics · 2023Article
- Association of theJournal of cardiovascular and thoracic research · 2019Article
- A genome-wide association study of essential hypertension in an Australian population using a DNA pooling approach.Molecular genetics and genomics : MGG · 2017Article
- Bayesian methods for multivariate modeling of pleiotropic SNP associations and genetic risk prediction.Frontiers in genetics · 2012Article
- RNA surveillance-an emerging role for RNA regulatory networks in aging.Ageing research reviews · 2011Review
- Severe sickle cell anemia is associated with increased plasma levels of TNF-R1 and VCAM-1.American journal of hematology · 2011Article
- Scanning for genomic regions subject to selective sweeps using SNP-MaP strategy.Genomics, proteomics & bioinformatics · 2010Article
- Genetic modifiers of the severity of sickle cell anemia identified through a genome-wide association study.American journal of hematology · 2010Article
- RNA editing genes associated with extreme old age in humans and with lifespan in C. elegans.PloS one · 2009Article
- Methodological Issues in Multistage Genome-wide Association Studies.Statistical science : a review journal of the Institute of Mathematical Statistics · 2009Article
- Use of pathway information in molecular epidemiology.Human genomics · 2009Review
- Association of the VEGFR2 gene His472Gln polymorphism with endurance-related phenotypes.European journal of applied physiology · 2009Article
- Genome-wide association studies and the genetic dissection of complex traits.American journal of hematology · 2009Review
- Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies.Journal of neural transmission (Vienna, Austria : 1996) · 2008Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors.
Funding
Abstract
backgroundOne of the challenges of the analysis of pooling-based genome wide association studies is to identify authentic associations among potentially thousands of false positive associations.
resultsWe present a hierarchical and modular approach to the analysis of genome wide genotype data that incorporates quality control, linkage disequilibrium, physical distance and gene ontology to identify authentic associations among those found by statistical association tests. The method is developed for the allelic association analysis of pooled DNA samples, but it can be easily generalized to the analysis of individually genotyped samples. We evaluate the approach using data sets from diverse genome wide association studies including fetal hemoglobin levels in sickle cell anemia and a sample of centenarians and show that the approach is highly reproducible and allows for discovery at different levels of synthesis.
conclusionResults from the integration of Bayesian tests and other machine learning techniques with linkage disequilibrium data suggest that we do not need to use too stringent thresholds to reduce the number of false positive associations. This method yields increased power even with relatively small samples. In fact, our evaluation shows that the method can reach almost 70% sensitivity with samples of only 100 subjects.
Indexed as
Identifiers
What OpenQuestion holds
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.