AI-SNPs screening based on the whole genome data and research on genetic structure differences of subcontinent populations.

The genetic structure differences in population is one of the key elements in medical research involving multi-population samples. A set of ancestry-informative single nucleotide polymorphisms (AI-SNPs) can be utilized to analyze genetic component of a population, infer ancestral origin of individuals and pre-filter samples to reduce the impact of population genetic structure differences on medical research. However, most of the published studies were focused on revealing the differences between populations of continents or regions of a continent. In this paper, AI-SNPs were screened by calculating FST value in each pair of five East Asian populations: Japanese in Tokyo (JPT), Han Chinese in Beijing (CHB), Southern Han Chinese (CHS), Chinese Dai in Xishuangbanna (CDX) and Kinh in Ho Chi Minh City (KHV) in the 1000 Genomes Project phase 3 (GRCh37.p13) to analyze differences in subcontinent populations. The results demonstrate that the five East Asian populations in our study were assigned to three clusters: JPT, CHB and CHS, CDX and KHV. A set of AI-SNPs can be used for analysis of individual genetic composition and selection of representative individuals. Individuals with over 80% population representative genetic components have good representativeness of a population. This paper demonstrated the practical value of the method, which was performed to verify the ancestral composition and select representative samples with a panel of screened AI-SNPs by FST value, thereby reducing the influence of genetic structure differences in subcontinent populations on population-related medical research.

Forensic genomics research on microhaplotypes.

Microhaplotype loci (microhaplotype, MHs), defined by two or more closely linked single nucleotide polymorphisms, are a type of molecular marker within a short segment of DNA. As emerging forensic genetic markers, MHs have no stutter artefacts and higher polymorphism, and permit the design of smaller amplicons. In order to identify the markers from a genome wide perspective and explore their potential application further, we constructed the most comprehensive MH dataset to date, based on the whole genome sequencing data of 105 Han individuals in Southern China from 1000 Genomes Project. The results showed that there were 9,490,075 MH loci in the range of 350 bp in the human genome, and the distribution density of microhaplotypes suggests gene variation. Polymorphism analysis of MHs from various base spans showed that the polymorphism of MHs could reach or exceed common short tandem repeat sites. In addition, based on their flexible assembly, a scheme to build the public database of microhaplotypes was proposed.

[Correlation of K-ras Gene Mutations with the Protein Expressions of TAK1 and MAP4K2 in Colorectal Cancer].

OBJECTIVE: To analyze the correlation of K-ras gene mutations with the protein expressions of transforming growth factor-ß activating kinase 1 (TAK1) protein and mitogen-activated protein kinase kinase kinase kinase 2 (MAP4K2) protein in colorectal cancer. METHODS: K-ras gene mutations were detected by DNA sequencing analysis, and the expressions of TAK1 protein and MAP4K2 protein were detected by immunohistochemical method in 76 cases of colorectal cancer tissues. RESULTS: In 76 cases of colorectal cancer tissues, the mutation rate of K-ras gene was 32.89% (25 cases), and K-ras gene mutations were correlated with the degrees of cell differentiation ( P<0.05). The positive rates of TAK1 protein and MAP4K2 protein were 48.68% and 46.05%, respectively. The protein expressions of TAK1 and MAP4K2 were positively correlated with the degrees of cell differentiation and lymph node metastases, respectively ( P<0.05). There was no correlation between K-ras gene mutation and either TAK1 protein or MAP4K2 protein expression ( P>0.05). In 25 cases of colorectal cancer with K-ras mutation, the expression of TAK1 protein was positively correlated with the expression of MAP4K2 protein ( P<0.05). CONCLUSION: K-ras gene mutation, TAK1 and MAP4K2 protein expressions were related to the degree of differentiation of colorectal cancer, but not to the depth of invasion. In colorectal cancer with K-ras gene mutation, the expression of TAK1 protein was positively correlated with the expression of MAP4K2 protein.