Disease Gene Mapping By The Application Of Next-generation Genomic Assays

Profiting by the rapid development of genomic technologies, high-throughput sequencing and SNP genotyping have become essential tools in the investigations of disease gene mapping. In this dissertation, I will describe the study in cancer genome of esophageal squamous-cell carcinomas by exome sequencing and genome-wide SNP array, and another work about verification of high-grade myopia susceptibility loci in Chinese Han by using the mass-spectrometry based SNP genotyping.Esophageal squamous-cell carcinoma (ESCC) is a common cancer with high associated mortality, but the principal causes of this disease remain elusive. To investigate the characteristic of genomic changes and identify the major alterations in ESCC, both exome sequencing and whole genome SNP genotyping were conducted. Firstly, exome sequencing was applied in nine pairs of ESCC and matched blood samples. In the analysis of point mutations, TP53was the most frequently mutated gene, and the chromatin modification process was found to be enriched in the GO analysis. In the analysis of exome sequencing data, prevalent events of large alterations characterized by allelic imbalance were detected, using the minor allele fraction of each heterozygous SNP. Next, SNP arrays were employed in55ESCCs and several matched blood samples. From the array data, we found the large scale alterations in ESCCs were very prevalent and complex, which is different from the spectrum of point mutations. The copy number alterations across55ESCC genomes highlighted six minimal common regions, which is including known cancer related genes like CCND1and CDKN2A/B, also several genes with limited studies in cancer, especially in ESCCs, such as YAPI, BIRC2/3, and CADM2, etc. The association analysis of the alterations with clinical outcome showed that, there are strong relations between genome-wide fraction of instabilities (also some common regions with copy number alteration) and lymph node metastasis. Besides, there are some impacts of these alterations on the post surgery survival. With the integration of TP53mutation and the structural alteration data, we found that genomes of ESCCs with TP53mutations were much more unstable than those without mutations. More importantly, result from the analysis of point mutations and copy number aberrations indicating that most of the ESCCs (65.45%) have alterations in p53signaling pathway, with the major consequence of deregulation in cell cycle, which would promote the cancer progression.Myopia is the most common ocular disorder, with an extreme form called high-grade myopia. Although genetic factors had been proved to play important role, the major related genes remain unclear in high-grade myopia. Here, we picked19highly informative tagSNPs from the associated region, MIR100HG and BLID loci, according to a GWAS of high-grade myopia in Japanese population; these tagSNPs were genotyped by Sequenom in751Chinese Han subjects (476with high myopia,275controls). Results of the association analysis indicated that neither single SNPs nor haplotypes in this region were significantly associated with high-grade myopia in Chinese Han population. This emphasized that high myopia is a complex disease which related with many different genetic factors, and it may have etiological heterogeneity in populations with different genetic backgrounds. Also, the negative signal in this region illustrated that GWAS of high-grade myopia is needed in Chinese Han population.