Detecting SNP combinations discriminating human populations from HapMap data

Correlation between gene polymorphism in angiotensin II type 1 receptor and type 2 diabetes mellitus complicated by hypertension in a population of Inner Mongolia

Background

The role of angiotensin II type 1 receptor (AT1R) as a key player in type 2 diabetes mellitus (T2DM) complicated with hypertension remains controversial. The present case-control study systematically investigated the association between gene the correct variation type in the angiotensin II type 1 receptor (AT1R) gene and type 2 diabetes mellitus complicated with hypertension in the Han population from the Inner Mongolia region, China.

Method

Here, state which variants were analysis, including age, occupation, triglyceride, systolic, diastolic, sex, culture, marital status, smoking, alcohol, BMI (body mass index), SBP (systolic blood pressure), DBP (diastolic blood pressure), TG (triglyceride), TC (total cholesterol), HDL-C (high-density lipoprotein cholesterol), LDL-C (low-density lipoprotein cholesterol), FPG (fasting plasma glucose). Genomic DNA was extracted from samples from 202 type 2 diabetic patients with hypertension and 216 type 2 diabetic patients without hypertension.

Results

Non-conditional regression analysis showed that in comparison with the TT genotype, the presence of the CC genotype for the T573 site of the AT1R gene increased the risk for diabetes mellitus complicated with hypertension by 3.219-fold (OR = 3.219, 95% CI: 1.042–9.941, P = 0.042). The results from multivariate linear regression analysis suggested the rs5182 polymorphism in the AT1R gene to be associated with diastolic blood pressure (P = 0.032). No other associations were found between the incidence of disease and the correct variation type at other sites of the AT1R gene.

Conclusions

Our results suggest that the rs5182 polymorphism in the AT1R gene is associated with diabetes complicated by hypertension in the Han population of Inner Mongolia.

Application of Chaotic Laws to Improve Haplotype Assembly Using Chaos Game Representation

Sequence data are deposited in the form of unphased genotypes and it is not possible to directly identify the location of a particular allele on a specific parental chromosome or haplotype. This study employed nonlinear time series modeling approaches to analyze the haplotype sequences obtained from the NGS sequencing method. To evaluate the chaotic behavior of haplotypes, we analyzed their whole sequences, as well as several subsequences from distinct haplotypes, in terms of the SNP distribution on their chromosomes. This analysis utilized chaos game representation (CGR) followed by the application of two different scaling methods. It was found that chaotic behavior clearly exists in most haplotype subsequences. For testing the applicability of the proposed model, the present research determined the alleles in gap positions and positions with low coverage by using chromosome subsequences in which 10% of each subsequence's alleles are replaced by gaps. After conversion of the subsequences' CGR into the coordinate series, a Local Projection (LP) method predicted the measure of ambiguous positions in the coordinate series. It was discovered that the average reconstruction rate for all input data is more than 97%, demonstrating that applying this knowledge can effectively improve the reconstruction rate of given haplotypes.

Genetic variation and forensic characteristic analysis of 25 STRs of a novel fluorescence co-amplification system in Chinese Southern Shaanxi Han population

We analyzed the genetic polymorphisms of 15 autosomal and 10 Y-chromosomal STR loci in 214 individuals of Han population from Southern Shaanxi of China and studied the genetic relationships between Southern Shaanxi Han and other populations. We observed a total of 150 alleles at 15 autosomal STR loci with the corresponding allelic frequencies ranging from 0.0023 to 0.5210, and the combined power of discrimination and exclusion for the 15 autosomal STR loci were 0.99999999999999998866 and 0.999998491, respectively. For the 10 Y-STR loci, totally 100 different haplotypes were obtained, of which 94 were unique. The discriminatory capacity and haplotype diversity values of the 10 Y-STR loci were 0.9259 and 0.998269, respectively. The results demonstrated high genetic diversities of the 25 STR loci in the population for forensic applications. We constructed neighbor-joining tree and conducted principal component analysis based on 15 autosomal STR loci and conducted multidimensional scaling analysis and constructed neighbor-joining tree based on 10 Y-STR loci. The results of population genetic analyses based on both autosomal and Y-chromosome STRs indicated that the studied Southern Shaanxi Han population had relatively closer genetic relationship with Eastern Han population, and distant relationships with Croatian, Serbian and Moroccan populations.