Endometriosis has a genetic component, and significant linkage has been found to a region on chromosome 10q. Two candidate genes, EMX2 and PTEN, implicated in both endometriosis and endometrial cancer, lie on chromosome 10q. We hypothesized that variation in EMX2 and/or PTEN could contribute to the risk of endometriosis and may account for some of the linkage signal on 10q. We genotyped single ...

Linkage disequilibrium study represents a major issue in statistical genetics as it plays a fundamental role in gene mapping and helps us to learn more about human history. The linkage disequilibrium complex structure makes its exploratory data analysis essential yet challenging. Visualization methods, such as the triangular heat map implemented in Haploview, provide simple and useful tools to ...

Models of background variation in genomic regions form the basis of linkage disequilibrium mapping methods. In this work we analyze a background model that groups SNPs into haplotype blocks and represents the dependencies between blocks by a Markov chain. We develop an error measure to compare the performance of this model against the common model that assumes that blocks are independent. By ex...

Improvements in technology have made it possible to conduct genome-wide association mapping at costs within reach of academic investigators, and experiments are currently being conducted with a variety of high-throughput platforms. To provide an appropriate context for interpreting results of such studies, we summarize here results of an investigation of one of the first of these technologies t...

We have investigated the pattern of DNA sequence variation at the exuperantia2 locus in Drosophila pseudoobscura. This adds to the increasing dataset of genetic variation in D. pseudoobscura, a useful model species for evolutionary genetic studies. The level of silent site nucleotide diversity and the divergence from an outgroup Drosophila miranda are comparable with those for other X-linked lo...

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We examine overlapping clustering schemes with functorial constraints, in the spirit of Carlsson–Mémoli. This avoids issues arising from the chaining required by partition-based methods. Our principal result shows that any clustering functor is naturally constrained to refine single-linkage clusters and be refined by maximal-linkage clusters. We work in the context of metric spaces with non-exp...

On typing a large number of SNPs within a small genomic region in European populations it is commonly found that there is rather little haplotype diversity — the observed haplotypes fall into rather few major groups with only minor differences between haplotypes within groups. Johnson et al. [1] suggested that linkage disequilibrium and haplotype diversity within the region can be captured by a...

Numerical methods of solving the inverse light scattering problem for spheres are presented. The methods are based on two stochastic global optimization techniques: Deep’s random search and the multilevel single-linkage clustering analysis due to Rinnooy Kan and Timmer. Computational examples show that the radius and the refractive index of spheres comparable with or larger than the wavelength ...

There is considerable interest in the potential of single nucleotide polymorphisms (SNPs) for mapping complex traits which are determined by genes of small individual effect (oligogenes). It is thought likely that many oligogenes are themselves common polymorphisms, perhaps biallelic, for which there is effectively neutral selection reflected in late age of onset. The extent of detectable linka...