Initial Studies And Realization Based On SNPs Of Schizophrenia

Schizophrenia is a polygenic inheritance disease that is not agreement with the Mendelian genetic law, and is also a serious mental disorder with a lifetime prevalence rate of 1% in the general population worldwide. Because the illness causes heavy economical and social burdens to families and societies, it is very important to establish a procedure of treating and preventing schizophrenia. However, the research on gene mapping of schizophrenia susceptibility genes has not make significant breakthrough, one of the most important reasons is that the disease susceptibility is determined by several genes with each susceptibility gene having only a modest individual effect. Therefore, it has important theoretical significance and practical value for diagnosis, prevention of the disease and drug screening to study the combined effects between genes.With the development of bioinformatics, and the completion of human genome project and international HapMap project, the SNP——which is not only the marker of human race and individual differences, but also the marker of disease susceptibility and drug sensitivity——plays an important role in looking for disease susceptibility genes. Linkage analysis on genome-wide scan and association analysis make the study more powerful and reliable. Through the experiment of mixing simulated data and real data, it has been demonstrated that in the process of looking for susceptibility genes, the method of multi-locus association analysis can often provide more information than single marker method. Therefore, the method based on multi-locus association analysis, that is, the haplotype analysis, has become a main research approach in studying complex disease susceptibility genes.In this paper, a total of 195 family trios of Chinese Han descent, consisting of fathers, mothers, and affected offspring with schizophrenia, were recruited for the genetic analysis. By using bioinformatics methods, 13 SNPs on 8 genes of cPLA2 gene family and 5 SNPs on PNPLA8 gene family were chosen. The genetic loci associated with schizophrenia were chose by using merging algorithm which is based on variable-length Markov chains.The process of research included: The paper used Excel 2003 text editor to establish pedigree database, and used PHASE software to estimate missing data and unresolved phase. The research adopted the idea of case-parental control studies to design the virtual control group, used the goodness-of-fit chi-square test to verify whether each SNP genotype in the sample distribution could accord with Hardy-Weinberg equilibrium,and then the paper studied the association analysis between single SNP and schizophrenia. In addition, the paper made use of the online SHEsis software to test the haplotype significance and linkage disequilibrium.The followings are the major results obtained in this study:(1) The Hardy-Weinberg equilibrium result Except gene loci rs2162886, rs891014, rs2303744 on the PLA2G4C and rs2396001, rs6466240 on the PNPLA8, all the other 13 loci were not deviated from the Hardy- Weinberg equilibrium, thus the 13-SNPs sample pool was suitable for the genetic analysis.(2) Correlation analysis between single SNP and schizophrenia The research showed that there was no significant difference for the frequencies of alleles of these 13 SNPs between the case and the control (P>0.05), which indicated no association between each SNP and schizophrenia.(3) Haplotype analysis resultThe paper adopted merging algorithm which is based on variable-length Markov chains to make haplotype analysis and generate parsimonious haplotype tree graphs. The Fisher's exact test was used to test the merging edge whose total count >50. The result showed that there were four gene loci, including rs3816533(C, T), rs1668589(C, T), rs1356410(G) and rs40848(G), were associated with positive symptoms of schizophrenia.(4) The results of the haplotype significance and linkage disequilibrium The online SHEsis program was used to estimate the haplotype significance and linkage disequilibrium of the four positive gene loci. Analysis for haplotype significance test showed that there were six haplotypes, through gene loci rs3816533, rs1668589 and rs1356410, were associated with schizophrenia, they were rs3816533(C)-rs4924595(C)-rs1668589(T)-rs1356410(G), rs3816533(T)-rs4924595(C) -rs1668589(C)-rs1356410(G), rs3816533(T)-rs4924595(C)-rs1668589(C), rs4924595 (C)-rs1668589(C)-rs1356410(G), rs4924595(C)-rs1668589(T)-rs1356410(G) and rs4924595(C)-rs1668589(T). There were two haplotypes through rs40848, were associated with schizophrenia, they were rs10249427(C)-rs40848(T)-rs40876(G), rs10249427(C)-rs40848(T). The linkage disequilibrium analysis indicated that beyond middle degree linkage disequilibrium were existed in pairwise loci, rs10249427 and rs40848, rs40848 and rs40876, rs10249427 and rs40876. Thus they possibly carry susceptibility genes to their offspring.The characteristics of this paper are as follows:(1) The paper adopted merging algorithm which is based on variable-length Markov chains for multi-locus of schizophrenia to make haplotype analysis. There are mainly two effects: First, at present, few reports about the application of VLMC in the research of schizophrenia were seen both at home and abroad. The research promotes the application of VLMC model in the field of schizophrenia. Second, the using of merging algorithm introduced a new computer model to the genetic research of schizophrenia, which laid a good foundation for the construction of genetic model of schizophrenia, and also emphasized the important roles that computer and bioinformatics playing in the research of complex diseases.(2) The paper described the construction of control group separately. In this paper, a new design based on case-parental control studies was used to create virtual control. This method is simple, and because of the similar genetic background between the patients and their parents, it can eliminate population stratification and overcome the false association caused by mixture effects of ethnic differences existed in the traditional case-control study.(3) The use of computer-aided software improved the efficiency of data processing. During the experiment of association analysis, several computer-aided software were used for processes such as the construction of control group and the Hardy-Weinberg equilibrium test, to avoid confusion arising from manual operation to derive wrong results. This has improved the efficiency of data processing effectively, and also laid a good foundation for obtaining correct experimental conclusions.The research thoroughly suggests that these loci on genes of cPLA2 and PNPLA8 gene families are associated with schizophrenia, the haplotype analysis based on merging algorithm has better power than the single-marker association analysis. It is also strongly demonstrated that the variable-length Markov chains model has great potential on the prediction and modeling of complex diseases. With the development of bioinformatics, it is predicted that the variable-length Markov chains will be widely used.Schizophrenia is a most serious mental disorder in the population worldwide, the research on the disease-causing genes of schizophrenia is an important content in post-genomic era, which has made use of the findings of HGP and supplemented to it as well. These findings will be very important for elucidating the etiology and genetic mechanisms of schizophrenia, and also for the development of genetic diagnosis, new drugs for the treatment of the illness and prediction of schizophrenia risk. The current study would also provide study strategy and precious experience for other complex genetic disorders.