ArticleAmerican journal of human genetics2005
The effect of single-nucleotide polymorphism marker selection on patterns of haplotype blocks and haplotype frequency estimates.
Article in American journal of human genetics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed.
- GWAS on early sexual maturation across freshwater and seawater environments in domesticated Lochy strain of Atlantic salmon.Genetics, selection, evolution : GSE · 2026Article
- A Single-Nucleotide Polymorphism in the Promoter of PorcineFrontiers in cell and developmental biology · 2022Article
- Single Nucleotide Polymorphisms ofGenes · 2019Article
- Genetic and phenotypic landscape of the major histocompatibilty complex region in the Japanese population.Nature genetics · 2019Article
- Identification of single nucleotide polymorphisms ofJournal of animal science and biotechnology · 2019Article
- eLD: entropy-based linkage disequilibrium index between multiallelic sites.Human genome variation · 2018Article
- Determination of genetic effects of ATF3 and CDKN1A genes on milk yield and compositions in Chinese Holstein population.BMC genetics · 2017Article
- Construction of a population-specific HLA imputation reference panel and its application to Graves' disease risk in Japanese.Nature genetics · 2015Article
- A multilocus linkage disequilibrium measure based on mutual information theory and its applications.Genetica · 2009Article
- GENOMEPOP: a program to simulate genomes in populations.BMC bioinformatics · 2008Article
- Pharmacogenetics and pharmacogenomics of schizophrenia: a review of last decade of research.Molecular psychiatry · 2007Review
- Evaluation of sample size effect on the identification of haplotype blocks.BMC bioinformatics · 2007Article
- Efficacy assessment of SNP sets for genome-wide disease association studies.Nucleic acids research · 2007Article
- Association of Neuregulin 1 with schizophrenia and bipolar disorder in a second cohort from the Scottish population.Molecular psychiatry · 2007Article
- The genetics of autistic disorders and its clinical relevance: a review of the literature.Molecular psychiatry · 2007Review
- A model-based approach to selection of tag SNPs.BMC bioinformatics · 2006Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The definition of haplotype blocks of single-nucleotide polymorphisms (SNPs) has been proposed so that the haplotypes can be used as markers in association studies and to efficiently describe human genetic variation. The International Haplotype Map (HapMap) project to construct a comprehensive catalog of haplotypic variation in humans is underway. However, a number of factors have already been shown to influence the definition of blocks, including the population studied and the sample SNP density. Here, we examine the effect that marker selection has on the definition of blocks and the pattern of haplotypes by using comparable but complementary SNP sets and a number of block definition methods in various genomic regions and populations that were provided by the Encyclopedia of DNA Elements (ENCODE) project. We find that the chosen SNP set has a profound effect on the block-covered sequence and block borders, even at high marker densities. Our results question the very concept of discrete haplotype blocks and the possibility of generalizing block findings from the HapMap project. We comparatively apply the block-free tagging-SNP approach and discuss both the haplotype approach and the tagging-SNP approach as means to efficiently catalog genetic variation.
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.