Mononucleotide A-repeats may Play a Regulatory Role in Endothermic Housekeeping Genes.

Background: Coding and non-coding short tandem repeats (STRs) facilitate a great diversity of phenotypic traits. The imbalance of mononucleotide A-repeats around transcription start sites (TSSs) was found in 3 mammals: , and .

Principal Findings: We found that the imbalance pattern originated in some vertebrates.

Effect of gene polymorphisms in ADAM33, TGFβ1, VEGFA, and PLAUR on asthma in Thai population.

Background: Most of the asthma susceptibility genes have demonstrated moderate effect. Gene-gene interaction may play a role in asthma.

Objective: To investigate the genetic and gene-gene interaction effects of single nucleotide polymorphisms (SNPs) in the ADAM33, TGFβ1, VEGFA, and PLAUR genes on asthma in Thai population.

Upstream mononucleotide A-repeats play a cis-regulatory role in mammals through the DICER1 and Ago proteins.

A-repeats are the simplest form of tandem repeats and are found ubiquitously throughout genomes. These mononucleotide repeats have been widely believed to be non-functional 'junk' DNA. However, studies in yeasts suggest that A-repeats play crucial biological functions, and their role in humans remains largely unknown.

Small Ancestry Informative Marker panels for complete classification between the original four HapMap populations.

A protocol for the identification of Ancestry Informative Markers (AIMs) from genome-wide Single Nucleotide Polymorphism (SNP) data is proposed. The protocol consists of three main steps: identification of potential positive selection regions via F(ST) extremity measurement, SNP screening via two-stage attribute selection and classification model construction using a Naïve Bayes classifier. The two-stage attribute selection is composed of a newly developed round robin Symmetrical Uncertainty (SU) ranking technique and a wrapper embedded with a Naïve Bayes classifier.

An omnibus permutation test on ensembles of two-locus analyses can detect pure epistasis and genetic heterogeneity in genome-wide association studies.

This article presents the ability of an omnibus permutation test on ensembles of two-locus analyses (2LOmb) to detect pure epistasis in the presence of genetic heterogeneity. The performance of 2LOmb is evaluated in various simulation scenarios covering two independent causes of complex disease where each cause is governed by a purely epistatic interaction. Different scenarios are set up by varying the number of available single nucleotide polymorphisms (SNPs) in data, number of causative SNPs and ratio of case samples from two affected groups.

Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses.

Background: Purely epistatic multi-locus interactions cannot generally be detected via single-locus analysis in case-control studies of complex diseases. Recently, many two-locus and multi-locus analysis techniques have been shown to be promising for the epistasis detection. However, exhaustive multi-locus analysis requires prohibitively large computational efforts when problems involve large-scale or genome-wide data.

Association between ADAM33 polymorphisms and asthma in a Thai population.

ADAM33 (A Disintegrin And Metalloprotease 33) is an asthma susceptibility gene found across several human populations. However, no information on ADAM33 exists for Thai population. The objective of this study was to determine the association, if any, between ADAM33 polymorphisms and asthma in Thai subjects.