Relationship Between Breast Cancer And Polymorphism Of DNA Repair Genes

Background: Breast Cancer is the most common tumor in female, and it damages the health of large number of women. The etiology of breast cancer is associated with several factors, while the most important factor is susceptible gene. Constructing a system of diagnosis and treatment of breast cancer with certain risk factor is an urgent problem for the medical faculty and society. Until now, BRCA1/BRCA2 genes have been considered to be associated with familial breast cancer, while from recently assays, development of breast cancer is stimulated by several susceptible genes. How to find the key susceptible gene is the most pressing key in clinical and basic research. As achievement of Human Genome Project, more and more genes have been discovered and cloned, In these genes, some mutations have been found. While in the development of human being, these mutations may be good or bad or nothing effect, and do something unknown to diseases. To confirm the interaction of these mutations, can provide much more basic information about prevention and diagnosis of breast cancer. As further medical study, techniques of detection of Single Nucleotide Polymorphism (SNP), the third generation of tag, have been totally improved, and we have constructed a complete set of research system. It is easy to find more susceptible genes from this system and explain the relationship between genes and diseases. For now, breast cancer is associated with DNA repair genes, so this research will try to explain the relationship. We focus on identifying the candidate susceptibility genes using a case-control analysis, and try to find the relation ship of them. Methods: The present study had focused on identifying the candidate susceptibility genes using case-control analysis.A total of 360 bloody samples, consisting of 180 patients with breast cancer and 180 healthy ones. The genetic loci associated with breast cancer and DNA repair functions are chosen by using bioinformatics methods and molecular genetics techniques. Based on NCBFs database called dbSNP(http://www.ncbi.nlm.nih.gov/projects/SNP), there are 874 SNPs on ATM gene, 1251 on ATR gene, 567 on BRCA1 gene, 649 on BRCA2 gene. By software Seqbuilder of Laser gene series pack, we choose 5 SNPs on these 4 genes. These loci included 2 SNPs on the ATM gene and each SNP on the ATR gene, BRCA1 gene, and BRCA2 gene. Totally 5 SNPs on 4 genes are genotyped using PCR-based RFLP analysis. We use these SNPs and restriction enzymes as follows: ATM-rs228593 (BelI), ATM-rs611646 (HinfI), ATR-rs13091637 (EcoRV), BRCAl-rs4793191 (PstI), BRCA2-rs9567623 (Hhal). Genotyping data is put into Excel in Microsoft Office2003 pack, and translate it into different form based on analysis methods. Using SPSS 16 to calculate the frequence data and odds ratio, and tell difference in these groups. The Hardy-Weinberg (H-W) equilibrium is tested for genotype frequency distributions of SNPs using of goodness of fit test. To elucidate genetic heterogeneity, in addition, breast cancer patients are sub-grouped based on their menstruation age. Combined effects of paired SNPs are tested by MDR programs. And try to draw interaction graph using ORANGE software.Results: We genotype 360 sample including 180 in case-group and 180 in control-group, the mininum age is 30, maxinum age is 64, and mean age is 9.60±7.588, the largest group is between age of 40-49. There is no difference between case and control group. The X~2 goodness-of-fit test shows that the genotypic distributions of all 5 SNPs are not deviated from the H-W equilibrium, and thus this sample pool is suitable for the genetic analysis. The ATM-rs228593 is a G to A base change, there are 3 genotypes, G/G, G/A, A/A. when the allele is G, it forms the restriction cleave site for Bell. And like ATM-rs228593, ATM-611646(T/A, HinfI), ATR-rs 13091637 (T/C, EcoRV), BRCAl-rs4793191 (A/G PstI). BRCA2-rs9567623(C/T, Hhal). All these 5 SNPs are not different between case-control groups. From odds ratio analysis, 2 SNPs in homozygote (A/A + T/T) of ATM may increase the risk of breast cancer (ORM). Heterozygote (T/C) of ATR-rs13091637 may decrease the risk of breast cancer (OR=0.615, 95%CI=0.392-0.965, p<0.05), and in postmenstruation group, it becomes more significant. BRCAl's genotype G/G can decrease the risk of breast cancer, and allele G may do better when the amount of G increase. BRCA2rs9567623 shows no associate with breast cancer (p>0.05). With MDR analysis, the best single site model is ATRrs13091637. 2 sites model is ATMrs 611646 and BRCA1rs4793191. 3 sites model is ATMrs611646, ATRrsl3091637 and BRCA2rs9567623. 4 sites model is ATMrs611646, ATRrs 13091637, BRCAlrs4793191 and BRCA2rs9567623. Above all, the best model is 5 sites model (ATMrs228593 ATMrs611646 ATRrs 13091637 BRCAlrs4793191 BRCA2rs9567623), it has topest CV value 10/10. Interaction tree by Hierarchical Clustering methods shows ATMrs611646 and BRCAlrs4793191 in the same branch, and they have the maximum interaction, while ATRrs 13091637 is at a different lonely branch. Using ORANGE software, we construct the interaction graph with 5 SNPs, ATRrs 13091637 gives maximum stand-alone IG value. Although ATMrs611646 gets the lowest IG, it shows the highest interaction IG in 5 SNPs.Conclusion: ATM-rs228593 A/A plus rs611646 T/T may increase the risk of breast cancer, and A/A+T/T is much more significant in menopause group; ATR-rs13091637 T/C genotype can decrease the risk of breast cancer; Allele G in BRCAl-rs4793191 can decrease the risk of breast cancer; BRCA2-rs9567623 shows no association with breast cancer. The best model by MDR methods is 5 sites model, suggesting breast cancer is associated with multi-gene function. In interaction graph, ATR-rs13091637 shows stand-alone effect, while ATM-rs611646 will do best with other related genes.