We show that the statistical power of a single single-nucleotide polymorphism (SNP) score test for genetic association reflects the cumulative effect of all causal SNPs that are correlated with the test SNP. Statistical significance of a score test can sometimes be explained by the collective effect of weak correlations between the test SNP and multiple causal SNPs. In a finite population, weak...

The relationship between human inherited genomic variations and phenotypic differences has been the focus of much research effort in recent years. These studies benefit from millions of single-nucleotide polymorphism (SNP) records available in public databases, such as dbSNP. The importance of identifying false dbSNP records increases with the growing role played by SNPs in linkage analysis for...

Recently, there has been increased interest in using Single Nucleotide Polymorphisms (SNPs) as a method for detecting genes for complex traits. SNPs are diallelic markers that have the potential to be inexpensively produced using chip technology. It has been suggested that SNPs will be beneficial in study designs that utilize trio data (father, mother, child). In our previous work, we calculate...

The presence of linkage disequilibrium violates the underlying assumption of linkage equilibrium in most traditional multipoint linkage approaches. Studies have shown that such violation leads to bias in qualitative trait linkage analysis when parental genotypes are unavailable. Appropriate handling of marker linkage disequilibrium can avoid such false positive evidence. Using the rheumatoid ar...

UNLABELLED Linkage disequilibrium (LD) is an important measure used in the analysis of single-nucleotide polymorphism (SNP) data. We used the Genetic Analysis Workshop 16 (GAW16) Framingham Heart Study 500 k SNP data to explore the effect of sampling methods on estimating of LD for SNP data. METHOD AND DATA We found 332 trios in the GAW16 Framingham SNP data. Repeated random samples without r...

Parent-offspring trios are widely collected for disease gene-mapping studies and are being extensively genotyped as part of the International HapMap Project. With dense maps of markers on trios, the effects of LD and linkage can be separated, allowing estimation of recombination rates in a model-free setting. Here we define a model-free multipoint method on the basis of dense sequence polymorph...

Phylogenetic patterns show the presence or absence of certain genes in a set of full genomes derived from different species. They can also be used to determine sets of genes that occur only in certain evolutionary branches. Previously, we presented a database named PhyloPat which allows the complete Ensembl gene database to be queried using phylogenetic patterns. Here, we describe an updated ve...

dermatophytes are a group of keratinophilic fungi capable of invading keratinized tissues (skin, hair and nails). they cause dermatophytosis (commonly known as tinea or ring worm) in human and animals. in this report, dna similarities and genomic linkage of 40 dermatophytes strains was obtained from different universities, were studied by random amplified polymorphic dna (rapd–pcr) using 11 ran...

BACKGROUND The regulation of gene expression is an emerging area of investigation. Increased knowledge can deepen our understanding of the genetic contributions to variations in complex traits. The purpose of this study is to explore the feasibility of detecting regulatory elements of gene expression with multivariate analyses. METHODS Peripheral blood lymphocyte expression levels of 30 genes...

the domesticated silkworm, bombyx mori, is of high commercial importance as a silk producer and is also widely used for implementation of basic and applied research. it is important to understand its genome organization using molecular markers for genetic studies and for breeding purposes. in this study, a genetic linkage map using 204 amplified fragment length polymorphism (aflp) markers was d...