Project description:We will explore the genetic (including APC, k-ras, p53, MSI, etc.) and environmental (including family history, life style, diet, nutritional status, DM, serum IGF-I, IGFBP-3, etc.) risk factors of colorectal tumorigenesis. We will accrue approximately 1000 patients as experimental group. The control group consists of 2000 individuals who were confirmed without colorectal cancer or polyps by colonoscopy. We estimated the statistical power of this study will reach more than 90%. In the second year, we will explore the association between various environmental risk factors with the epigenetic changes of various oncogenes and tumor suppressor genes. Firstly, we will study the correlation between hypermethylation of promoter region of hMLH1 gene with various environmental factors. Next, we will explore the genetic polymorphisms of promoter of E-cadherin gene. Recently, it has been reported that the C→A genetic polymorphism in the promoter region of E-cadherin gene in prostate cancer. Since this phenomenon has not been reported in colorectal cancer, it is mandatory for us to extend our research to the E-cadherin polymorphisms of colorectal cancer. Moreover, this project will focus on exploration of the association between the genetic polymorphisms of promoter of TS gene with chemosensitivity to 5-Fu-based therapy. We speculated that the better prognosis in colorectal tumors with MSI is related to their expression of TS gene. In summary, the second year of this project will extend our accumulated experience in the study of genetic polymorphisms to further clarify the association between genetic polymorphisms of TS gene with the prognosis of colorectal cancers after chemotherapy. We believe that this project will facilitate: (1) the further clarification of colorectal cancer tumorigenesis; (2) the establishment of domestic epidemiological data of colorectal cancer of Taiwan, and (3) the improvement of the quality of clinical management of patients with colorectal cancer.
Project description:Various studies have established the role of genetics in the development of type 2 diabetes mellitus (T2DM) across population groups with a reported heritability of 30–70%. These studies highlight the effect of interethnic variability in genetic susceptibility and risk for complications of T2DM. The underrepresentation of Filipinos in current global databases have prompted the goal to identify variants associated with the risk of T2DM among the population. Since the validation of variants associated with one population seems suboptimal if applied to another population, designing a specific set of genetic variants for a particular population poses a challenge. Microarray techniques were used on extracted DNA from whole blood samples using customized microarray beadchips with selected variants from various genome repositories. Customization included candidates from both coding and non-coding regions (e.g. intergenic and intronic SNPs) with statistical evidence of associated to T2DM, its complications, treatment, diagnosis and other related conditions. Incorporation of clinical data from participants can then narrow the significant variants to the population and identify which can be valuable for developing genetic risk prediction models relevant to preventing and diagnosing the disease among Filipinos.
Project description:Various studies have established the role of genetics in the development of type 2 diabetes mellitus (T2DM) across population groups with a reported heritability of 30–70%. These studies highlight the effect of interethnic variability in genetic susceptibility and risk for complications of T2DM. The underrepresentation of Filipinos in current global databases have prompted the goal to identify variants associated with the risk of T2DM among the population. Since the validation of variants associated with one population seems suboptimal if applied to another population, designing a specific set of genetic variants for a particular population poses a challenge. Microarray techniques were used on extracted DNA from whole blood samples using customized microarray beadchips with selected variants from various genome repositories. Customization included candidates from both coding and non-coding regions (e.g. intergenic and intronic SNPs) with statistical evidence of associated to T2DM, its complications, treatment, diagnosis and other related conditions. Incorporation of clinical data from participants can then narrow the significant variants to the population and identify which can be valuable for developing genetic risk prediction models relevant to preventing and diagnosing the disease among Filipinos.
Project description:Direct targeting of noncoding genomic regions harboring common sequence variants associated with human traits through in vivo animal model studies and precise genome editing in human cells is essential for closing the critical gap between genetic discoveries and physiological understanding. However, such investigation has been impractical for most of these variants as they have small effect sizes and are in haplotypes containing multiple single nucleotide polymorphisms (SNPs) spanning thousands of base pairs. We developed an integrated approach to address this challenge, combining an efficient two-step technique to precisely edit large haplotypes in human induced pluripotent stem cells and orthologous region deletion in phenotypically permissive animal models. As proof of principle, we applied this approach to examine a blood pressure associated locus with a noncoding haplotype containing 11 SNPs spanning 17.4 kbp. We found a robust blood pressure effect of nearly 10 mmHg and identified the physiological and molecular mechanisms involved.
Project description:Direct targeting of noncoding genomic regions harboring common sequence variants associated with human traits through in vivo animal model studies and precise genome editing in human cells is essential for closing the critical gap between genetic discoveries and physiological understanding. However, such investigation has been impractical for most of these variants as they have small effect sizes and are in haplotypes containing multiple single nucleotide polymorphisms (SNPs) spanning thousands of base pairs. We developed an integrated approach to address this challenge, combining an efficient two-step technique to precisely edit large haplotypes in human induced pluripotent stem cells and orthologous region deletion in phenotypically permissive animal models. As proof of principle, we applied this approach to examine a blood pressure associated locus with a noncoding haplotype containing 11 SNPs spanning 17.4 kbp. We found a robust blood pressure effect of nearly 10 mmHg and identified the physiological and molecular mechanisms involved.
Project description:We adapted the self-transcribing active regulatory region sequencing (Starr-seq) strategy to systematically identify the SNPs that affect gene expression by modulating activities of regulatory elements. Among 10,673 SNPs linked with 996 GWAS-identified cancer-risk SNPs, we found 70 regulatory variants for which the two alleles conferred different regulatory activities. We analyzed one of them in-depth and confirmed its target by CRIPSR-Cas9 technology. Our results will help the interpretation of GWAS results and better cancer risk assessment.
Project description:Precise identification of causal variants within credible intervals of eQTL associations is needed to identify regulatory GWAS variants. We show that CROPseq, namely multiplex CRISPR-Cas9 genome editing combined with single cell RNAseq, is a viable strategy for fine mapping regulatory SNPs. Mutations were induced nearby 67 SNPs in three genes, two of which, rs2251039 and rs17523802, significantly altered CISD1 and PARK7 expression, respectively, and overlap with chromatin accessibility peaks.
Project description:Most type 1 diabets (T1D) associated SNPs are located in non-coding regions, making it hard to understand their functional impact. We performed epigenomic profiling of two enhancer marks, H3K4me1 and H3K27ac, using primary TH1 and TREG cells from healthy and T1D subjects. By integrating enhancers predicted using these ChIP-Seq data, T1D associated SNPs and additional supporting data, we found and validated several novel risk SNPs for T1D.
Project description:Via a GWA study, several SNPs have been identified as markers capable of predicting prognosis of lung cancer patients receiving TKIs therapy as first-line treatment. In order to get insights into how these genetic variants are linked to traits of interest, we conducted a genome-wide eQTL study by integrated analyses of SNP genotyping array data and gene expression array data of 115 subjects of lung adenocarcinoma. Our study successfully identified several SNPs as eQTLs, whose genotype were significantly associated with expression levels of several already known genes related to lung cancer.
Project description:This experiment was carried out in the context of a pharmacogenetic study of long-term (4-year follow-up) response to Interferon-beta treatment in two cohorts of Italian Multiple Sclerosis patients, to identify genetic variants (SNPs) that may influence response to IFN-beta. We integrated results from meta-analysis of the two cohorts with gene expression profiling of IFNβ stimulated PBMCs from 20 healthy controls and eQTL analyses, to look at possible enrichment of IFN-beta induced genes with genes mapped by top-ranking meta-analyzed SNPs.