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Search Results: 1 - 10 of 96980 matches for " Yuan-Tsong Chen "
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A large-scale survey of genetic copy number variations among Han Chinese residing in Taiwan
Chien-Hsing Lin, Ling-Hui Li, Sheng-Feng Ho, Tzu-Po Chuang, Jer-Yuarn Wu, Yuan-Tsong Chen, Cathy SJ Fann
BMC Genetics , 2008, DOI: 10.1186/1471-2156-9-92
Abstract: Using stringent selection criteria, 230 regions with variable copy numbers were identified in the Han Chinese population; 133 (57.83%) had been reported previously, 64 displayed greater than 1% CNV allele frequency. The average size of the CNV regions was 322 kb (ranging from 1.48 kb to 5.68 Mb) and covered a total of 2.47% of the human genome. A total of 196 of the CNV regions were simple deletions and 27 were simple amplifications. There were 449 genes and 5 microRNAs within these CNV regions; some of these genes are known to be associated with diseases.The identified CNVs are characteristic of the Han Chinese population and should be considered when genetic studies are conducted. The CNV distribution in the human genome is still poorly characterized, and there is much diversity among different ethnic populations.The human genome contains many DNA sequence variations, including single nucleotide polymorphisms (SNPs), short nucleotide insertions or deletions, tandem repeat sequences, and transposable elements [1]. Recent human genome studies have revealed that copy number variations (CNVs) are more common than previously thought. Some CNVs are associated with gene expression levels and thus may contribute to phenotypic differences [2-7]. Each CNV is a DNA segment > 1 kb that shows variation within the population in terms of a deletion and/or an amplification. Although SNPs are regarded as the main source of phenotypic differences among humans, CNVs also have a large impact on differential gene expression [2].Microarray-based approaches, so called "molecular karyotyping", have been used to detect subtle chromosomal structure variations on the genome-wide scale [8]. SNP microarrays are high-resolution tools for genotyping that can be used to simultaneously detect copy number (CN) alterations and loss-of-heterozygosity [9,10]. The copy number inferring tool (CNIT), an algorithm recently developed for use with Affymetrix GeneChips, efficiently predicts regions with sub
A new analysis tool for individual-level allele frequency for genomic studies
Hsin-Chou Yang, Hsin-Chi Lin, Mei-Chu Huang, Ling-Hui Li, Wen-Harn Pan, Jer-Yuarn Wu, Yuan-Tsong Chen
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-415
Abstract: This study utilizes a unified intensity-measuring approach to estimating individual-level allele frequencies for 1,104 and 1,270 samples genotyped with the single-nucleotide-polymorphism arrays of the Affymetrix Human Mapping 100K and 500K Sets, respectively. Allele frequencies of all samples are estimated and adjusted by coefficients of preferential amplification/hybridization (CPA), and large ethnicity-specific and cross-ethnicity databases of CPA and allele frequency are established. The results show that using the CPA significantly improves the accuracy of allele frequency estimates; moreover, this paramount factor is insensitive to the time of data acquisition, effect of laboratory site, type of gene chip, and phenotypic status. Based on accurate allele frequency estimates, analytic methods based on individual-level allele frequencies are developed and successfully applied to discover genomic patterns of allele frequencies, detect chromosomal abnormalities, classify sample groups, identify outlier samples, and estimate the purity of tumor samples. The methods are packaged into a new analysis tool, ALOHA (Allele-frequency/Loss-of-heterozygosity/Allele-imbalance).This is the first time that these important genetic/genomic applications have been simultaneously conducted by the analyses of individual-level allele frequencies estimated by a unified intensity-measuring approach. We expect that additional practical applications for allele frequency analysis will be found. The developed databases and tools provide useful resources for human genome analysis via high-throughput single-nucleotide-polymorphism arrays. The ALOHA software was written in R and R GUI and can be downloaded at http://www.stat.sinica.edu.tw/hsinchou/genetics/aloha/ALOHA.htm webcite.Allele frequency denotes the relative frequency of an allele compared with the total frequency of all alleles at a marker locus. It is one of the most important population indices and has been broadly applied to geneti
SLC2A10 genetic polymorphism predicts development of peripheral arterial disease in patients with type 2 diabetes. SLC2A10 and PAD in type 2 diabetes
Yi-Der Jiang, Yi-Cheng Chang, Yen-Feng Chiu, Tien-Jyun Chang, Hung-Yuan Li, Wen-Hsing Lin, Hsiang-Yu Yuan, Yuan-Tsong Chen, Lee-Ming Chuang
BMC Medical Genetics , 2010, DOI: 10.1186/1471-2350-11-126
Abstract: We genotyped 10 single nucleotide polymorphisms and one microsatellite spanning 34 kb across the SLC2A10 gene in a prospective cohort of 372 diabetic patients. Their association with the development of peripheral arterial disease (PAD) in type 2 diabetic patients was analyzed.At baseline, several common SNPs of SLC2A10 gene were associated with PAD in type 2 diabetic patients. A common haplotype was associated with higher risk of PAD in type 2 diabetic patients (haplotype frequency: 6.3%, P = 0.03; odds ratio [OR]: 14.5; 95% confidence interval [CI]: 1.3- 160.7) at baseline. Over an average follow-up period of 5.7 years, carriers with the risk-conferring haplotype were more likely to develop PAD (P = 0.007; hazard ratio: 6.78; 95% CI: 1.66- 27.6) than were non-carriers. These associations remained significant after adjustment for other risk factors of PAD.Our data demonstrate that genetic polymorphism of the SLC2A10 gene is an independent risk factor for PAD in type 2 diabetes.Peripheral arterial disease (PAD), defined as lower extremity arterial atherosclerosis, is one of most common diseases of the arteries and is a major complication of type 2 diabetes [1]. Conventional cardiovascular risk factors such as aging, smoking, hyperglycemia, hypertension and dyslipidemia have been shown to be associated with PAD [1]. However, the increased risk for atherosclerotic diseases in diabetic patients can be only partially explained by the conventional risk factors [2]. In fact, a high heritability for ankle-brachial blood pressure index (ABI), an index of PAD, has been obtained in Twin studies in Caucasians [3], indicating that additional genetic factors might be involved in the pathogenesis of PAD. In this respect, the search for genetic causes of PAD remains limited [4].Recently, a genetic form of arterial tortuosity syndrome (ATS; OMIM 208050) was reported to be caused by loss-of-function mutations in the SLC2A10 gene encoding the facilitative glucose transporter GLUT10. A
Garlic Accelerates Red Blood Cell Turnover and Splenic Erythropoietic Gene Expression in Mice: Evidence for Erythropoietin-Independent Erythropoiesis
Bünyamin Akgül,Kai-Wei Lin,Hui-Mei Ou Yang,Yen-Hui Chen,Tzu-Huan Lu,Chien-Hsiun Chen,Tateki Kikuchi,Yuan-Tsong Chen,Chen-Pei D. Tu
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0015358
Abstract: Garlic (Allium sativum) has been valued in many cultures both for its health effects and as a culinary flavor enhancer. Garlic's chemical complexity is widely thought to be the source of its many health benefits, which include, but are not limited to, anti-platelet, procirculatory, anti-inflammatory, anti-apoptotic, neuro-protective, and anti-cancer effects. While a growing body of scientific evidence strongly upholds the herb's broad and potent capacity to influence health, the common mechanisms underlying these diverse effects remain disjointed and relatively poorly understood. We adopted a phenotype-driven approach to investigate the effects of garlic in a mouse model. We examined RBC indices and morphologies, spleen histochemistry, RBC half-lives and gene expression profiles, followed up by qPCR and immunoblot validation. The RBCs of garlic-fed mice register shorter half-lives than the control. But they have normal blood chemistry and RBC indices. Their spleens manifest increased heme oxygenase 1, higher levels of iron and bilirubin, and presumably higher CO, a pleiotropic gasotransmitter. Heat shock genes and those critical for erythropoiesis are elevated in spleens but not in bone marrow. The garlic-fed mice have lower plasma erythropoietin than the controls, however. Chronic exposure to CO of mice on garlic-free diet was sufficient to cause increased RBC indices but again with a lower plasma erythropoietin level than air-treated controls. Furthermore, dietary garlic supplementation and CO treatment showed additive effects on reducing plasma erythropoietin levels in mice. Thus, garlic consumption not only causes increased energy demand from the faster RBC turnover but also increases the production of CO, which in turn stimulates splenic erythropoiesis by an erythropoietin-independent mechanism, thus completing the sequence of feedback regulation for RBC metabolism. Being a pleiotropic gasotransmitter, CO may be a second messenger for garlic's other physiological effects.
SAQC: SNP Array Quality Control
Hsin-Chou Yang, Hsin-Chi Lin, Meijyh Kang, Chun-Houh Chen, Chien-Wei Lin, Ling-Hui Li, Jer-Yuarn Wu, Yuan-Tsong Chen, Wen-Harn Pan
BMC Bioinformatics , 2011, DOI: 10.1186/1471-2105-12-100
Abstract: We developed new quality indices to measure the quality of SNP arrays and/or DNA samples and investigated their statistical properties. The indices quantify a departure of estimated individual-level allele frequencies (AFs) from expected frequencies via standardized distances. The proposed quality indices followed lognormal distributions in several large genomic studies that we empirically evaluated. AF reference data and quality index reference data for different SNP array platforms were established based on samples from various reference populations. Furthermore, a confidence interval method based on the underlying empirical distributions of quality indices was developed to identify poor-quality SNP arrays and/or DNA samples. Analyses of authentic biological data and simulated data show that this new method is sensitive and specific for the detection of poor-quality SNP arrays and/or DNA samples.This study introduces new quality indices, establishes references for AFs and quality indices, and develops a detection method for poor-quality SNP arrays and/or DNA samples. We have developed a new computer program that utilizes these methods called SNP Array Quality Control (SAQC). SAQC software is written in R and R-GUI and was developed as a user-friendly tool for the visualization and evaluation of data quality of genome-wide SNP arrays. The program is available online (http://www.stat.sinica.edu.tw/hsinchou/genetics/quality/SAQC.htm webcite).Single-nucleotide polymorphisms (SNPs), the most abundant genetic markers in the human genome, have been widely used in genetic and genomic research such as studies of disease gene mapping [1-6], medical and clinical diagnostics [7-9], forensic tests [10-12], genome structure of linkage disequilibrium and recombination [13-18], chromosomal aberrations [19-24], and genetic diversity [25-27]. Modern high-throughput and high-resolution SNP array genotyping techniques, such as the Affymetrix GeneChip (Affymetrix Inc., Santa Clara, CA
Molecular profile and copy number analysis of sporadic colorectal cancer in Taiwan
Chien-Hsing Lin, Jen-Kou Lin, Shih-Ching Chang, Ya-Hui Chang, Hwey-May Chang, Jin-Hwang Liu, Ling-Hui Li, Yuan-Tsong Chen, Shih-Feng Tsai, Wei-Shone Chen
Journal of Biomedical Science , 2011, DOI: 10.1186/1423-0127-18-36
Abstract: 1,173 CRC tumors were collected from the Taiwan population, and sequencing-based microsatellite typing assay was used to determine MSI and MSS. Genome-wide SNP array was used to detect CN alterations in 16 MSI-H and 13 MSS CRCs and CN variations in 424 general controls. Gene expression array was used to evaluate the effects of CN alterations, and quantitative PCR methods were used to replicate the findings in independent clinical samples.These 1,173 CRC tumors can be classified into 75 high-frequency MSI (MSI-H) (6.4%), 96 low-frequency MSI (8.2%) and 1,002 MSS (85.4%). Of the 75 MSI-H tumors, 22 had a BRAF mutation and 51 showed MLH1 promoter hypermethylation. There were distinctive differences in the extent of CN alterations between CRC MSS and MSI-H subtypes (300 Mb vs. 42 Mb per genome, p-value < 0.001). Also, chr7, 8q, 13 and 20 gains, and 8p and 18 losses were frequently found in MSS but not in MSI-H. Nearly a quarter of CN alterations were smaller than 100 kb, which might have been missed in previous studies due to low-resolution technology. 514 expressed genes showed CN differences between subtypes, and 271 of them (52%) were differentially expressed.Sporadic CRCs with MSI-H displayed distinguishable clinicopathologic features, which differ from those of MSS. Genomic profiling of the two types of sporadic CRCs revealed significant differences in the extent and distribution of CN alterations in the cancer genome. More than half of expressed genes showing CN differences can directly contribute to their expressional diversities, and the biological functions of the genes associated with CN changes in sporadic CRCs warrant further investigation to establish their possible clinical implications.Colorectal cancer (CRC) is one of the major leading causes of cancer deaths around the world, and is the most common cancer in Taiwan [1]. Two different genetic pathways have been described for tumorigenesis of CRC. The most frequent pathway is the chromosomal instability p
MPDA: Microarray pooled DNA analyzer
Hsin-Chou Yang, Mei-Chu Huang, Ling-Hui Li, Chien-Hsing Lin, Alice LT Yu, Mitchell B Diccianni, Jer-Yuarn Wu, Yuan-Tsong Chen, Cathy SJ Fann
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-196
Abstract: We propose a generalized concept of pooled DNA and present a user-friendly tool named Microarray Pooled DNA Analyzer (MPDA) that we developed to analyze hybridization intensity data from microarray-based pooled DNA experiments. MPDA enables whole-genome DNA preferential amplification/hybridization analysis, allele frequency estimation, association mapping, allelic imbalance detection, and permits integration with shared data resources online. Graphic and numerical outputs from MPDA support global and detailed inspection of large amounts of genomic data. Four whole-genome data analyses are used to illustrate the major functionalities of MPDA. The first analysis shows that MPDA can characterize genomic patterns of preferential amplification/hybridization and provide calibration information for pooled DNA data analysis. The second analysis demonstrates that MPDA can accurately estimate allele frequencies. The third analysis indicates that MPDA is cost-effective and reliable for association mapping. The final analysis shows that MPDA can identify regions of chromosomal aberration in cancer without paired-normal tissue.MPDA, the software that integrates pooled DNA association analysis and allelic imbalance analysis, provides a convenient analysis system for extensive whole-genome pooled DNA data analysis. The software, user manual and illustrated examples are freely available online at the MPDA website listed in the Availability and requirements section.Since the pioneering work of Arnheim et al. in 1985 [1], the analysis of pooled DNA samples has undergone extensive development over the past two decades [2,3]. The main applications of pooled DNA techniques in genomic/genetic studies include association mapping [4,5], polymorphism identification/validation [6,7], genetic diversity [8,9] and mutation detection [10,11]. The millennium revolution of the pooled DNA technique was its integration with microarrays [12], and the performance of which has been examined broadly [13
Identification of Novel Susceptibility Loci for Kawasaki Disease in a Han Chinese Population by a Genome-Wide Association Study
Fuu-Jen Tsai,Yi-Ching Lee,Jeng-Sheng Chang,Li-Min Huang,Fu-Yuan Huang,Nan-Chang Chiu,Ming-Ren Chen,Hsin Chi,Yann-Jinn Lee,Li-Ching Chang,Yi-Min Liu,Hsiang-Hua Wang,Chien-Hsiun Chen,Yuan-Tsong Chen,Jer-Yuarn Wu
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0016853
Abstract: Kawasaki disease (KD) is an acute systemic vasculitis syndrome that primarily affects infants and young children. Its etiology is unknown; however, epidemiological findings suggest that genetic predisposition underlies disease susceptibility. Taiwan has the third-highest incidence of KD in the world, after Japan and Korea. To investigate novel mechanisms that might predispose individuals to KD, we conducted a genome-wide association study (GWAS) in 250 KD patients and 446 controls in a Han Chinese population residing in Taiwan, and further validated our findings in an independent Han Chinese cohort of 208 cases and 366 controls. The most strongly associated single-nucleotide polymorphisms (SNPs) detected in the joint analysis corresponded to three novel loci. Among these KD-associated SNPs three were close to the COPB2 (coatomer protein complex beta-2 subunit) gene: rs1873668 (p = 9.52×10?5), rs4243399 (p = 9.93×10?5), and rs16849083 (p = 9.93×10?5). We also identified a SNP in the intronic region of the ERAP1 (endoplasmic reticulum amino peptidase 1) gene (rs149481, pbest = 4.61×10?5). Six SNPs (rs17113284, rs8005468, rs10129255, rs2007467, rs10150241, and rs12590667) clustered in an area containing immunoglobulin heavy chain variable regions genes, with pbest-values between 2.08×10?5 and 8.93×10?6, were also identified. This is the first KD GWAS performed in a Han Chinese population. The novel KD candidates we identified have been implicated in T cell receptor signaling, regulation of proinflammatory cytokines, as well as antibody-mediated immune responses. These findings may lead to a better understanding of the underlying molecular pathogenesis of KD.
Palmitoyl Acyltransferase, Zdhhc13, Facilitates Bone Mass Acquisition by Regulating Postnatal Epiphyseal Development and Endochondral Ossification: A Mouse Model
I-Wen Song, Wei-Ru Li, Li-Ying Chen, Li-Fen Shen, Kai-Ming Liu, Jeffrey J. Y. Yen, Yi-Ju Chen, Yu-Ju Chen, Virginia Byers Kraus, Jer-Yuarn Wu, M. T. Michael Lee, Yuan-Tsong Chen
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0092194
Abstract: ZDHHC13 is a member of DHHC-containing palmitoyl acyltransferases (PATs) family of enzymes. It functions by post-translationally adding 16-carbon palmitate to proteins through a thioester linkage. We have previously shown that mice carrying a recessive Zdhhc13 nonsense mutation causing a Zdhcc13 deficiency develop alopecia, amyloidosis and osteoporosis. Our goal was to investigate the pathogenic mechanism of osteoporosis in the context of this mutation in mice. Body size, skeletal structure and trabecular bone were similar in Zdhhc13 WT and mutant mice at birth. Growth retardation and delayed secondary ossification center formation were first observed at day 10 and at 4 weeks of age, disorganization in growth plate structure and osteoporosis became evident in mutant mice. Serial microCT from 4-20 week-olds revealed that Zdhhc13 mutant mice had reduced bone mineral density. Through co-immunoprecipitation and acyl-biotin exchange, MT1-MMP was identified as a direct substrate of ZDHHC13. In cells, reduction of MT1-MMP palmitoylation affected its subcellular distribution and was associated with decreased VEGF and osteocalcin expression in chondrocytes and osteoblasts. In Zdhhc13 mutant mice epiphysis where MT1-MMP was under palmitoylated, VEGF in hypertrophic chondrocytes and osteocalcin at the cartilage-bone interface were reduced based on immunohistochemical analyses. Our results suggest that Zdhhc13 is a novel regulator of postnatal skeletal development and bone mass acquisition. To our knowledge, these are the first data to suggest that ZDHHC13-mediated MT1-MMP palmitoylation is a key modulator of bone homeostasis. These data may provide novel insights into the role of palmitoylation in the pathogenesis of human osteoporosis.
Longitudinal Evaluation of an N-Ethyl-N-Nitrosourea-Created Murine Model with Normal Pressure Hydrocephalus
Ming-Jen Lee,Ching-Pang Chang,Yi-Hsin Lee,Yi-Chih Wu,Hsu-Wen Tseng,Yu-Ying Tung,Min-Tzu Wu,Yen-Hui Chen,Lu-Ting Kuo,Dennis Stephenson,Shuen-Iu Hung,Jer-Yuarn Wu,Chen Chang,Yuan-Tsong Chen,Yijuang Chern
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0007868
Abstract: Normal-pressure hydrocephalus (NPH) is a neurodegenerative disorder that usually occurs late in adult life. Clinically, the cardinal features include gait disturbances, urinary incontinence, and cognitive decline.
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