Genome-Wide Copy Number Variations And SNPs Association Study On Osteoporosis And Obesity

Copy number variation (CNV) is a common type of genomic variability, with variations in the size of DNA fragments ranging from 1 kilobase (Kb) to several megabases (Mb). CNVs encompass more DNA than single nucleotide polymorphisms, they may be important in genetics and evolution. Previous study also showed that CNVs account for nearly 20% of the total detected genetic variation in gene expression, which futher conform the importance of CNVs in genetics. Now, geneticists are still seeking CNV analysis approach for complex disease, therefore, CNV analysis is a most advanced method to study genetic factor on human complex disease. While genome-wide associaiton study (GWAS) is a most hot and powerful approach to find susceptibility gene of complex disease.Osteoporosis and obesity are two common diseases, which have already become the major public health problems. These two diseases have high heritability. In the past decades, extensive efforts have been dedicated to the search of DNA sequence variations to impact these two diseases. However, the achievement is not satisfied. Collectively, all of these implicated genes or SNPs can only account for a small part of genetic variation. Consequently, it has become important to explore the possibility that some of the remaining undiscovered genetic factors that influence risk of osteoporosis and obesity.In this dissertation, first, we firstly performed case-control genome-wide CNV analyses using Affymetrix Human Mapping 500K arrays. The study population included 700 elderly Chinese Han subjects comprising 350 cases with a history of hip osteoporotic fracture (OF) and 350 healthy and matched controls. Based on the mapping results for genomic CNVs, we conducted association analyses to identify CNVs underlying susceptibility to OF. For those CNVs that were significantly associated with OF, we performed further analysis using PCR and electrophoresis, and real time PCR to validate and fine map the CNV region for specific genes involved. We identified a CNV of UGT2B17 gene (UDP glucuronosyltransferase 2 family, polypeptide B17) that was associated with risk of OF. More importantly, this CNV’s association with OF was successfully replicated in an independent Chinese sample consisting of 399 cases with hip OF and 400 controls. We further detected the significant relevance of this CNV to hip BMD and femoral neck (FN) bone geometry using two independent samples of 689 unrelated Chinese subjects and 1,000 unrelated white subjects. Since UGT2B17 encodes an enzyme catabolizing steroid hormones, we measured the concentrations of serum testosterone and estradiol for 236 Chinese young males and assessed their UGT2B17 copy number. Subjects without UGT2B17 had significantly higher concentrations of testosterone and estradiol. Our findings suggest the important effect of the CNV of UGT2B17 to the pathogenesis of osteoporosis.Second, we firstly conducted genome-wide CNV analyses for obesity using Affymetrix SNP 6.0 arrays in 2,286 US white subjects. We found two CNVs, CNP1670 and CNP1669 located in chromosome 10q24.3, have significant associaiton with obesity related phenotypes. These two CNVs contain both deletion and duplication. Our results showed that subjects had more copies of these two CNV would increase the risk of obesity. Then, this result was replicated in two independent US white samples. However, we did not detect signifiant association between these two CNVs and obesity in Chinese Han subject, which suggested that these two CNVs had ethnic differentiation. Interestingly, CNP1670 contains a gene named, CYP2E1, which encodes Cytochrome P450 2E1 involved in the oxidative metabolism process.Third, using the same sample containg 2,286 US white subjects, we performed GWAS for obesity. Two genes, GPC5 and FTO were detected to be significantly associated with obesity related phenotype. GPC5 encodes glypican proteoglycan 5. Glypicans are a class of heparan sulfate proteoglycans bound to the external surface of plasma membranes that play an important role in the control of cell division and growth regulation, and alos affect neuronal growth and repair. FTO is a new famous gene which is identified by several GWAS.Population genetics analysis has suggested a functional role for common variants in mitochondrial DNA (mtDNA). Finally, to extend our analysis from nuclear DNA to mtDNA, we fristly performed associaiton between mitochondrial SNP (mtSNP) and obesity in 2,286 unrelated Caucasian subjects, and further explored interactions between mitochondrial genes and nuclear genes. We found that ND2 gene and ATPase6 gene were signifiantly associated with obesity related phenotype. We further indicated that the interation between nuclear gene CPT1B and 12SrRNA in mitochondrial can affect obesity.In summary, this work used most advanced approaches to identify susceptibility genes for osteoporosis and obesity. we detected a serious of valuable results, which open a new avenue to understand the genetic determination for these two diseases.