Association mapping of complex traits typically employs tagSNP genotype data to identify a trait locus within a region of interest. However, considerable debate exists regarding the most powerful strategy for utilizing such tagSNP data for inference. A popular approach tests each tagSNP within the region individually, but such tests could lose power as a result of incomplete linkage disequilibr...

The TagSNP problem is a specific form of compression problem arising in genetics. Given a very large set of SNP (genomic positions where polymorphism is observed in a given population), the aim is to select a smallest subset of SNPs which represents the complete set of tagSNP reliably. This is possible because strong correlations existing between neighboring SNPs. Typically, besides minimizing ...

The TagSNP problem is a specific form of compression problem arising in genetics. Given a very large set of SNP (genomic positions where polymorphism is observed in a given population), the aim is to select a smallest subset of SNPs which represents the complete set of tagSNP reliably. This is possible because strong correlations existing between neighboring SNPs. Typically, besides minimizing ...

MOTIVATION Selecting SNP markers for genome-wide association studies is an important and challenging task. The goal is to minimize the number of markers selected for genotyping in a particular platform and therefore reduce genotyping cost while simultaneously maximizing the information content provided by selected markers. RESULTS We devised an improved algorithm for tagSNP selection using th...

In this paper, we study the tagSNP selection problem on multiple populations using the pairwise r(2) linkage disequilibrium criterion. We propose a novel combinatorial optimization model for the tagSNP selection problem, called the minimum common tagSNP selection (MCTS) problem, and present efficient solutions for MCTS. Our approach consists of three main steps including (i) partitioning the SN...

In this article, we studied the tag single-nucleotide polymorphism (tagSNP) selection problem on multiple populations using the pairwise r(2) linkage disequilibrium criterion. We proposed a novel combinatorial optimization model for the tagSNP selection problem, called the minimum common tagSNP selection (MCTS) problem, and presented efficient solutions for MCTS. Our approach consists of the fo...

DNA-methyltransferase (DNMT)-3A which contains DNMT3A1 and DNMT3A2 isoforms have been suggested to play a crucial role in carcinogenesis and showed aberrant expression in most cancers. Accumulated evidences also indicated that single nucleotide polymorphisms (SNP) in DNMT genes were associated with susceptibility to different tumors. We hypothesized that genetic variants in DNMT3A1 promoter reg...

In the normal intestinal epithelium transforming growth factor beta-1 (TGFbeta-1) acts as a growth inhibitor, but in malignant cells it may act as a tumor promoter. However, only limited information is available on genetic variation in the TGFB1 gene and its relationship to circulating levels and risk of colorectal cancer. To characterize associations of genetic variation [tagging single-nucleo...

Stearoyl-CoA desaturase 1 (SCD1) activity, a key regulator of lipid metabolism, may be associated with the development of metabolic syndrome (MetS). We examined the association of genetic variation in the SCD1 gene with the occurrence of MetS and its five components in a population of Costa Rican adults (n = 2152; mean age, 58 y; range, 18-86 y). Associations of tag single nucleotide polymorphi...