ArticleGenetics2005
Tree scanning: a method for using haplotype trees in phenotype/genotype association studies.
Article in Genetics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT00005209 (Genetic Epidemiology of Coronary Heart Disease), which is not on this map. Cited by 43 papers, 1 of them a synthesis that pooled it.
What it found
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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.
Genetic Epidemiology of Coronary Heart Disease
Who cites it
43 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Genome-wide analysis identified abundant genetic modulators of contributions of the apolipoprotein E alleles to Alzheimer's disease risk.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2022Article
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- Assembly of 809 whole mitochondrial genomes with clinical, imaging, and fluid biomarker phenotyping.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2018Article
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- Allele-specific network reveals combinatorial interaction that transcends small effects in psoriasis GWAS.PLoS computational biology · 2014Article
- Mitochondrial genomic variation associated with higher mitochondrial copy number: the Cache County Study on Memory Health and Aging.BMC bioinformatics · 2014Article
- APOE modulates the correlation between triglycerides, cholesterol, and CHD through pleiotropy, and gene-by-gene interactions.Genetics · 2013Article
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Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
We use evolutionary trees of haplotypes to study phenotypic associations by exhaustively examining all possible biallelic partitions of the tree, a technique we call tree scanning. If the first scan detects significant associations, additional rounds of tree scanning are used to partition the tree into three or more allelic classes. Two worked examples are presented. The first is a reanalysis of associations between haplotypes at the Alcohol Dehydrogenase locus in Drosophila melanogaster that was previously analyzed using a nested clade analysis, a more complicated technique for using haplotype trees to detect phenotypic associations. Tree scanning and the nested clade analysis yield the same inferences when permutation testing is used with both approaches. The second example is an analysis of associations between variation in various lipid traits and genetic variation at the Apolipoprotein E (APOE) gene in three human populations. Tree scanning successfully identified phenotypic associations expected from previous analyses. Tree scanning for the most part detected more associations and provided a better biological interpretative framework than single SNP analyses. We also show how prior information can be incorporated into the tree scan by starting with the traditional three electrophoretic alleles at APOE. Tree scanning detected genetically determined phenotypic heterogeneity within all three electrophoretic allelic classes. Overall, tree scanning is a simple, powerful, and flexible method for using haplotype trees to detect phenotype/genotype associations at candidate loci.
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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.