ArticleBMC proceedings2007
Analysis of high-density single-nucleotide polymorphism data: three novel methods that control for linkage disequilibrium between markers in a linkage analysis.
Article in BMC proceedings, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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
8 citing papers in PubMed.
- An intronic variant in the CELF4 gene is associated with risk for colorectal cancer.Cancer epidemiology · 2021Article
- Analysis of malaria parasite phenotypes using experimental genetic crosses of Plasmodium falciparum.International journal for parasitology · 2012Review
- Finding disease genes: a fast and flexible approach for analyzing high-throughput data.European journal of human genetics : EJHG · 2011Article
- Strategies for selection of subjects for sequencing after detection of a linkage peak.BMC proceedings · 2011Article
- Genome-wide linkage in Utah autism pedigrees.Molecular psychiatry · 2010Article
- Genome-wide linkage using the Social Responsiveness Scale in Utah autism pedigrees.Molecular autism · 2010Article
- Significant linkage evidence for a predisposition gene for pelvic floor disorders on chromosome 9q21.American journal of human genetics · 2009Article
- Linkage analysis with dense SNP maps in isolated populations.Human heredity · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
We performed a multipoint linkage analysis for rheumatoid arthritis (RA) using high-density single-nucleotide polymorphism (SNP) data for chromosome 6 and chromosome 21 using Genetic Analysis Workshop 15 (GAW15) data. These regions were previously shown to have high LOD scores, not accounting for linkage disequilibrium (LD). We propose three novel methods to control for LD in a linkage analysis: allow for LD between markers using graphical modeling, eliminate high-LD markers by principal-component analysis (PCA) using haplotype data, and eliminate high-LD markers by PCA using genotype data. All three novel methods were compared to the previously published SNPLINK high-LD elimination method. Although all four methods verified the previous results, differences in linkage peak height and position were observed across methods. Additional work is required to further understand the effects of LD on linkage results and explore LD control methodology.
Identifiers
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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.