Noninvasive prenatal prediction of fetal haplotype with Spearman rank correlation analysis model.

BACKGROUND: Noninvasive prenatal testing (NIPT) has been widely used clinically to detect fetal chromosomal aneuploidy with high accuracy rates, gradually replacing traditional serological screening. However, the application of NIPT for monogenic diseases is still in an immature stage of exploration. The detection of mutations in peripheral blood of pregnant women requires precise qualitative and quantitative techniques, which limits its application. The bioinformatic strategies based on the SNP (single nucleotide polymorphism) linkage analysis are more practical, which can be divided into two types depending on whether proband information is needed. Hidden Markov Mode (HMM) and Sequential probability ratio test (SPRT) are suitable for families with probands. In contrast, methods based on databases and population demographic information are suitable for families without probands. METHODS: In this study, we proposed a Spearman rank correlation analysis method to infer the fetal haplotypes based on core family information. Allele frequencies of SNPs that were used to construct parental haplotypes were calculated as sets of nonparametric variables, in contrast to their theoretical values represented by a fetal fraction (FF). The effects on the calculation of the fetal concentration of two DNA enrichment methods, multiple-PCR amplification, and targeted hybrid capture, were compared, and the heterozygosity distribution of SNPs within pedigrees was analyzed to reveal the best conditions for the model application. RESULTS: Predictions of the paternal haplotype inheritance were in line with expectations for both DNA library construction methods, while for maternal haplotype inheritance prediction, the rates were 96.55% for method multiple-PCR amplification and 95.8% for method targeted hybrid capture. CONCLUSION: Positive prediction rates showed that the maternal haplotype prediction was not as accurate as paternal one, due to the large amount of maternal noise in the mother's peripheral blood. Although this model is relatively immature, it provides a new perspective for noninvasive prenatal clinical tests of monogenic diseases.

Association between promoters polymorphisms of matrix metalloproteinases and risk of digestive cancers: a meta-analysis.

PURPOSE: A variety of studies have been performed to elucidate the polymorphisms in promoter regions of matrix metalloproteinases (MMPs) associated with the risk of digestive cancers, and yet, results remain conflicting and heterogeneous. Thus, we undertook a systematic meta-analysis to determine the genetic susceptibility of MMPs to digestive cancers. METHODS: A computerized literature search was conducted in databases of PubMed, Embase, and ISI Web of Knowledge till October 2012 for any MMP genetic association study in oral squamous, gastric, esophageal, and colorectal carcinomas. Odds ratios (OR) and 95 % confidence interval (CI) were estimated for each gene under dominant and recessive models, and the heterogeneity between studies was assessed using Q test and I (2) value. Overall and subgroup analysis according to anatomical sites and ethnicity was carried out. Statistical analysis was performed with Review Manager 5.0. RESULTS: A total of 40 eligible publications with 68 comparisons were included in this study. For MMP1 nt-1607, individuals with 2G state could increase risk of digestive cancers in total analysis (dominant: OR = 1.31, 95 % CI = 1.16-1.48, P < 0.00001; recessive: OR = 1.29, 95 % CI = 1.11-1.50, P = 0.0009). In the subgroup of tumor sites, significant associations were also observed in esophageal cancer and colorectal cancer under both genetic models. For MMP2 nt-1306, CT or TT carriers performed significant protection against digestive cancer in the dominant model (OR = 0.69, 95 % CI = 0.55-0.85, P = 0.0007) of the overall. In the subgroup analysis, significant association was found in esophageal cancer, with borderline effects in gastric cancer and oral squamous cell carcinoma. For MMP7 -181 A/G, significant association was observed under two genetic models in the overall (dominant: OR = 1.26, 95 % CI = 1.10-1.43, P = 0.0009; recessive: OR = 1.33, 95 % CI = 1.11-1.60, P = 0.002) and in the individual cancer subgroup of esophageal cancer and gastric cancer. For MMP9 -1,562 C/T, a borderline effect was found with digestive cancers in the total and stratified analysis of the colorectal cancer under dominant model. No association was observed in either the overall or subgroup analysis for MMP3 -1,171 5A/6A. CONCLUSIONS: Our meta-analysis demonstrated the fact that polymorphisms in promoter regions of MMP genes might be related to the susceptibility of digestive cancers, with cancer development for MMP1 and MMP7, and a protection against cancer for MMP2 and MMP9. Further evidences with adequate sample sizes need to be conducted.

Association study between single nucleotide polymorphisms on retinol binding protein 4,FOXO1 and type 2 diabetes mellitus / 中华检验医学杂志

Objective To investigate the distribution of single nucleotide polymorphisms(SNPs) on retinol binding protein 4(RBP4) genes and forkhead box O1 (FOXO1) gene, and their relationships with the occurrence of type Ⅱ diabetes mellitus (T2DM) in Chinese Han population. Methods Totally ten SNPs on RBP4 and FOXO1 were determined in 384 T2DM patients and 384 normal controls by TaqMan probe genotyping and agarose gel electrophoresis methods. And their serum level of fasting blood glucose (FBG), total cholesterol (TC) and trigly- ceride (TG) were also estimated. Results For RBP4, there was no significance for various genetypes and alleles including - 803 G > A, + 5169 C > T, and + 6969 G > C between two groups (P > 0.05). Each genotype had no relationships with T2DM (using adjusted logistic regression models). No haplotype was associated with T2DM. For FOXO1, among seven SNPs typed, significant variation was found in the frequency distribution of rs7324943 G/T in the two groups(χ~2=4.02, P = 0.044), and further stratification analysis showed that in subjects of aged 40 and non-hypertension, there was a higher risk of T2DM in GT heterozygous carriers than in GG homozygous carriers (OR = 1.47, 1.80), T allele carriers showed higher risk than non-T carriers (OR = 1.42,1.79). For rs17592236 C/T, though no significant frequency variation was found between two groups (χ~2 = 0.39, P = 0.401), but in subjects of aged ≤ 40, stratification analysis showed dramatically increased risk of T2DM in CT and TT carriers than in CC carriers (OR = 6.33,10.15), T allele carriers showed 7. 11-fold higher risk than non-T carriers. A haplotype CT related to T2DM susceptibility was also found, which could decrease the risk of its carriers by 28%. Conclusions For BBP4, the polymorphisms of - 803 G > A, + 5169 C > T, and + 6969 G > C had no relationships with T2DM in Chinese Han population. For FOXO1, the polymorphism of rs7324943 G/T,rs17592236 C/T and a haplotype CT were found related to the susceptibility of T2DM in Chinese Han population. Yet further studies are necessary to explain the impact of these polymorphisms on the disease occurrence.

Multifractal analysis of genomes sequences' CGR graph / 生物医学工程学杂志

To describe the fractal feature of CGR (Chaos-game representation) graph of genomes sequences, a multifractal theory is presented in the analysis. By studying the effect of three probability sets on the scale invariance range, the probability set with the best scale invariance is chosen, and then the smooth general dimension spectrum and multifractal spectrum are calculated. The experimental result shows that the probability set composed of the relative probability has the best scale-invariance performance. The scale invariance has three different variance regions, which indicate that genomes sequence segments with different lengths have different distribution rules. It is concluded that the multifractal method is effective for describing the fractal feature of CGR graph of genomes sequences.

Alignment-free biomolecular sequence comparison method / 生物医学工程学杂志

Biosequence analysis is the primary research field of bioinformatics. In this field, useful information can be extracted by comparison analysis methods. Among them, sequence alignment is the most common comparison method. However the sequence comparison by alignment, which assumes conservation of contiguity between homologous segments, is at odds with genetic recombination. Especially for the multisequence alignment, there exists the difficulty in the complexity of calculation. Therefore, alignment-free sequence comparison methods are required. In this paper, two main categories of alignment-free sequence comparison methods are reviewed. The first one is based on the word (oligomer) frequency and its distribution. The sequences are compared using the distances defined in a Cartesian space by the frequency vectors. In the second category, sequences are compared using Kolmogorov complexity and chaos theory.

The cloning of human interleukin-10 gene and its expression in eukaryotic cells / 医学研究生学报

Objective: To clone human interleukin 10(hIL-10) gene full-length cDNA sequence and to construct its eukaryotic expression vector in Chinese hamster ovary(CHO) cells. Methods: cDNA fragment encoding hIL-10 gene was amplified from human peripheral normal white blood cells by RT-PCR and confirmed by DNA sequencing.The ds-DNA was inserted into pcDNA3 vector.This recombinant expressing vector was transfected into CHO cell.The IL-10 molecules expressed were detected by ELISA and the role of inhibition of IL-10 was determined with MTT. Results: The cDNA encoding hIL-10 was cloned by RT-PCR and inserted into T-easy vector and sequence analysis verified that the cloned fragment was hIL-10 cDNA.The IL-10 was expressed in the CHO and it blocked the lymphocyte transformation.Conclusion: The eukaryotic expression plasmid was constructed successfully,which will contribute to further studies on the role of hIL-10 in autoimmunity,transplantation immunity and inflammatory disease.

Two single nucleotide polymorphisms of beta 2-adrenoceptor gene in elderly patients with hypertension / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To investigate the association of two single nucleotide polymorphisms (SNPs) of beta 2-adrenoceptor (beta 2-AR) gene with hypertension in elderly patients.</p><p><b>METHODS</b>The study samples were collected from unrelated Chinese Han population of Dabie Mountain in Anhui province. Eighty-six elderly patients with hypertension and 43 controls were selected. Genotypes of +1053 and +1239 SNPs were typed by polymerase chain reaction-restriction fragment length polymorphism.</p><p><b>RESULTS</b>The frequencies of the two SNPs complied well with the Hardy-Weinberg equilibrium in normal group. The distribution of genotypes AA, GA,GG of the SNP at locus +1239 in moderate and severe hypertension group was significantly different from that in normal group (chi square=8.67, P<0.05). There were evident differences in the frequencies of alleles of the two groups (chi square=4.02, P<0.05). No significant difference was observed in the distribution of genotypes of the SNP at locus +1053 between the two groups.</p><p><b>CONCLUSION</b>These data indicate that the SNP at locus +1239 of beta 2-AR gene is associated with hypertension in elderly patients.</p>

Analysis of three Y-STR loci polymorphism in isolated populations / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To figure out the polymorphism of three Y-STR loci in isolated populations and explore the consanguinity of the populations with the use of Y-STR.</p><p><b>METHODS</b>Male samples were selected from two isolated populations(80 and 60 males) in Zhejiang province and one open population (36 males), genescan was performed with males' DNA by genescan technology with ABI PRISM 377 sequencer at Y chromosome loci DYS388, DYS390 and DYS395.</p><p><b>RESULTS</b>DYS388, DYS390, DYS395 allele counts in Yushan island population, Taohua island population and open population were 8, 9, 7, 5, 6, 7 and 6, 6, 5 respectively. Gene diversity was between 0.70-0.80 in the three populations. There was no difference in distribution of allele frequency and shared genotypes between the isolated populations and the open population by statistical test. Genetic distance is long between Taohua island population and open population, short between Yushan island population and open population, and moderate between Yushan island population and Taohua island population.</p><p><b>CONCLUSION</b>The main allele is 129 at DYS388; 215 at DYS390; and 119 at DYS395. The distribution of allele frequency and gene diversity at DYS388, DYS390, DYS395 loci, and the shared genotypes between populations as well as the genetic distance are unable to explain the blood relationship between the isolated and open populations, suggesting the additional studies in large sample size will be necessary to use Y-STR for exploring the blood relationship between populations.</p>

Analysis of mutation sites of BRCA1 gene in Chinese patients with breast cancer / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To detect the mutation sites of exons 2, 20, 11A and 11B in Chinese patients with breast cancer.</p><p><b>METHODS</b>A total of 86 patients with breast cancer without blood relationship were randomly selected. Polymerase chain reaction (PCR) and double-strand DNA direct sequencing were applied.</p><p><b>RESULTS</b>No mutations, especially deletions were found in exons 2, 20 and 11 with carefully checking the sequencing results, although they were reported frequently in Europe populations with breast cancer. We found one polymorphism in exon 11, with high frequency, and in the test of chi-square, the frequencies of two alleles had no significant difference between the patients and controls.</p><p><b>CONCLUSION</b>The above results suggest this SNP may not be associated with the breast cancer in Chinese population, and indicates that the gene sequence of what we have studied doesn't account much for occurrence of the breast cancer in the population of China.</p>

Construction and Expression of Retroviral Vector Encoding Enhanced Green Fluorescent Protein / 中国实验血液学杂志

Retroviral vectors are wildly used as vehicles for gene transfer into hematopoietic cells based on its potency for efficient gene delivery and integration of transgene in host genome. The development of better transduction protocols depends on gene markers that allow a rapid detection and effective selection of genetically transduced cells. In this study, the enhanced green fluorescent protein (EGFP), a gene that is optimized for detection and expression in mammalian cells, was firstly amplified and cloned by high-fidelity PCR. The vector LGSN carrying EGFP gene was then constructed and the retroviral producer cell lines that yield high titers of LGSN vector in supernatants were developed by liposome-mediated transfection in combination with cross infection. Both GP + envAm12 murine fibroblasts and K562 leukemic cells transduced with EGFP virus demonstrated a stable green fluorescence signal readily detectable by flow cytometry or fluorescence microscopy in up to 97% and 86% of examined cells, respectively. The integration of LGSN provirus in transduced cells was confirmed by PCR analysis. These results indicate EGFP is a suitable reporter molecule for gene transfer and expression in hematopoietic cells. Therefore, the bright and long-term expression of EGFP in living cells will advance the study of gene therapy in vitro and in vivo, particularly for human applications.

Gene expression of tyrosine kinase receptor pathway in primary glioblastoma and its significance / 中国癌症杂志

Background and purpose:Glioblastoma is one of the most common intracranial tumors, the morbidity and mortality are both high, and the molecular biological mechanism of the disease is still unclear. In this study, we detected the gene expression of tyrosine kinase receptor (TKR) pathway in primary glioblastoma(GBM) with low-density array, furthermore we analyzed the significance of the gene expression change. Methods:We detected 26 genes of RTK pathway in 10 primary GBM tissues and 9 normal brain tissues (gained from the decompression operation of brain trauma), and analyzed the different expressions of these two kinds of tissues by statistic method.Results:The Ct values of MAP2K1 and MAP2K4 in normal brain tissues were 1.6?1.7 and 2.2?2.1, the Ct values of MAP2K1 and MAP2K4 in primary GBM tissues were 3.9?1.5 and 5.0?2.0, and the Ct different values between normal brain tissues and primary GBM tissues of both genes were -2.3 and -2.8(P

Gene Therapy of Mice Melanoma by HSV-tk/ACV System / 中国肿瘤生物治疗杂志

This is the first report on gene therapy of mice melanoma by HSV - tk/ACV system. The sensitivity to ACV of genetically modified B16 cells (B16LNTK) was much higher than that of the parental cells. The sensitivity to ACV of B16 cells was increased when they were co - cultured with B16LNTK cells with various ratios. which showed the exist of the by stander effects. The tumor volume of B16LNTK (0.25cm3) is 94% less than that of B16 in C57BL/6 mice after 20-days ACV treatment. (P

Association between XRCC3 Thr241Met polymorphism and genetic susceptibility to glioma in Chinese Han population living in Shanghai and surrounding provinces in east China / 第二军医大学学报

Objective:To investigate the possible association between Thr241Met polymorphism in the DNA repair gene X-ray repair cross-complementing group 3 (XRCC3) with genetic susceptibility to glioma in a Chinese Han population living in Shanghai and the surrounding provinces in east China. Methods: Genotyping by a TaqMan assay was performed in 771 brain glioma patients living in Shanghai and the surrounding provinces (Jiangsu.Zhejiang, Anhui.etc. )and in 752 control participants matched in age and gender. The genotyping results of TaqMan assay and the association between Thr241Met polymorphism in the DNA repair gene XRCC3 with genetic susceptibility to glioma were statistically analyzed. Results: Genotypes of 1 468 subjects (760 with brain glioma and 708 were cancer-free control) were successfully performed by TaqMan assay, with the successful rate being 96.4%. Statistical analysis result showed that gene(C/T) and genotype(C/CT/CT/T) frequencies of XRCC3 were not significantly different between the glioma and cancer-free groups. Compared with the CC genotype, the variant TC(P = 0. 909; adjusted by age and gender OR = 0. 981; 95%CI = 0. 701-1. 371) or TT(P=0. 642; adjusted by age and gender OR = 0. 7; 95%CI = 0. 156-3. 146) genotypes of XRCC3 Thr241Met were associated with a non-statistically significant increase of glioma risk. Conclusion: The variant TC or TT genotypes of XRCC3 Thr241Met may not be risk factors for brain glioma in Chinese Han population living in Shanghai and the surrounding provinces in east China.