| Chronic myeloid leukemia (CML) may well be the most extensively studied human neoplasm, and it is characterized by the BCR-ABL fusion gene from t(9;22) translocation. Although the fusion gene is regarded as the molecular hallmark of the disease, the mechanisms responsible for its forming remain elusive. People have now come to accept the idea that the diversity or polymorphism of genes in individuals are responsible for the difference of phenotype, susceptibility to complex diseases such as cancer, and it may also interpret the different response of individuals to drugs and environmental factors. We investigated the polymorphism of the BCR, ABL and HLA-DPB1 genes in order to gain some knowledge of the molecular mechanisms of the disease.We screened 9 sequence-tagged sites (STS) in BCR and ABL gene by DMA pooling and denaturing high performance liquid chromatography (dHPLC), and the results were verified by sequencing. We found polymorphism sites in 4 out of the 9 fragments and there are 3 bases different from the reference sequence found in 3 fragments. The novel SNP in U07000 fragment has significantly different frequencies between CML and control people.A 1.13kb part of the BCR promotor region was amplified and sequenced from 30 CML patients and 19 controls. Here we got 4 novel SNPs and 3 different bases. We analysed the transcription factor binding sites in the region and found 2 novel SNPs and 1 different base are located in or tightly near some of the sites.We screened a 3.12 kb region spanning from exon13 to exon15 in the M-bcr. The region was divided into 8 fragments by overlapping PCR primers. Direct sequencing or dHPLC was used according to the size of fragments. We found 6 novel SNPs (including one cSNP)and 2 different bases, also the frequencies of the SNPs in the populations. The sequence diversity was analysed using DnaSP Ver3.5, the nucleotide diversity (TT) and 6 were 0.00066 and 0.00047+0.00019, respectively. Departure from neutrality was tested byTajima's D and Fu and Li's D and F, none of them showed significant differences, so the region we analysed evolved neutrally in the population. The sequence analysis of the region reveals sequences associated to recombination such as heptamer, poly purine/poly pyrimidine sequences, and Alu repeats in it, and one of the SNP is located in the conserved sequence of Alu repeat.We also analysed the polymorphism of HLA-DPB1 in CML patients using sequencing-based typing. We found a total of 22 alleles in the patients, and the frequencies of HLA-DPBT1301 and DPB1*20011 were higher in CML patients than those of healthy individuals.To sum up, we have established the screening method by using DMA pooling and dHPLC, and it had proved very successfully. We have found sequence polymorphisms in the regions investigated, most of them being SNPs, and we have got the frequencies of the SNPs in the population. It appears that some SNPs in BCR gene might have the probability of bringing influence to the transcription and function of the gene. Studied of the HLA-DPB1 gene in CML patients suggest there may be positive associations between certain HLA-DPB1 alleles and CML.
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