175 results on '"Gao, Xiaoyi"'
Search Results
152. A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms
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Gao, Xiaoyi, primary, Starmer, Joshua, additional, and Martin, Eden R., additional
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- 2008
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153. AWclust: point-and-click software for non-parametric population structure analysis
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Gao, Xiaoyi, primary and Starmer, Joshua D, additional
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- 2008
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154. Human population structure detection via multilocus genotype clustering
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Gao, Xiaoyi, primary and Starmer, Joshua, additional
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- 2007
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155. Binary DNA hairpin-based colorimetric biochip for simultaneous detection of Pb2+ and Hg2+ in real-world samples.
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Shi, Xiaoli, Gao, Xiaoyi, Zhang, Lingling, Li, Yunchao, Fan, Louzhen, and Yu, Hua-Zhong
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DNA , *HAIRPIN (Genetics) , *BIOCHIPS , *LEAD , *MERCURY , *METAL ions , *MICROARRAY technology - Abstract
A microarray-format colorimetric biochip was constructed on plastic using two specially-designed DNA hairpin strands as binary probes and a binding-induced conformational switching strategy as the signal generation protocol. Coupled with single- or dual-color staining, we were able to simultaneously detect and quantitate the trace amounts of Pb2+ and Hg2+ in various real-world samples. [ABSTRACT FROM AUTHOR]
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- 2015
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156. UBE3A Hyperactivity as a Driver of Neurodevelopmental Disease.
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Weston, Kellan, Gao, Xiaoyi, Zhao, Jinghan, Kim, Kwang‐Soo, Harrison, Joseph S., Wu, Kuen‐Phon, and Yi, Jason
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R386 --> 668.6 --> UBE3A is a HECT (homologous to E6AP C‐terminus) domain E3 ubiquitin ligase that targets substrate proteins for degradation through the ubiquitin‐proteasome pathway. The UBE3Agene is of unique interest for its gene dosage‐dependent effect in the developing brain: Precise deletion or null mutation of the maternal copy of UBE3A causes a severe intellectual disability known as Angelman syndrome; meanwhile, duplication or triplication of the gene region in which UBE3A resides is linked to a prevalent syndromic form of autism known as Dup15q syndrome. However, little is known about the effects of missense variants which cause a single amino acid change in the enzyme, and prediction of disease outcomes for a given variant remains a challenge. Here, we pose that investigating variants' effects on UBE3A functional activity levels is critical for predicting disease. In order to identify if precise mutations in UBE3A are sufficient to drive disease, we devised a high‐throughput assay to screen the functional consequence of UBE3A missense variants. We screened over 150 variants and identified distinct functional classes of UBE3A mutants based on their effect on enzymatic activity. Importantly, we identified over a dozen novel gain‐of‐functionvariants that aberrantly hyperactivate UBE3A enzyme activity. Through collaborations with clinical centers, we confirm that individuals possessing hyperactivating UBE3A variants exhibited phenotypes that were distinguishable from Angelman. Mice carrying a specific hyperactivating mutation on the maternal allele exhibited aberrant motor and early communication defects, as well as microcephaly. Finally, we mapped the results of our screen to the UBE3A protein structure to reveal a previously‐undefined allosteric regulatory exosite within the catalytic domain that we show to act as a charge‐dependent regulator of enzymatic activity. We found additional HECT domain enzymes to possess disease‐associated variants within their exosites, suggesting that exosite dysfunction is a common mechanism underlying a set of neurodevelopmental disorders. Together, our study indicates that excessive UBE3A activity increases the risk for neurodevelopmental pathology and suggests that deep structure‐functional analysis of protein variants can uncover disease‐relevant regulatory mechanisms. [ABSTRACT FROM AUTHOR]
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- 2022
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157. Potential Early Identification of a Large Campylobacter Outbreak Using Alternative Surveillance Data Sources: Autoregressive Modelling and Spatiotemporal Clustering
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Adnan, Mehnaz, Gao, Xiaoying, Bai, Xiaohan, Newbern, Elizabeth, Sherwood, Jill, Jones, Nicholas, Baker, Michael, Wood, Tim, and Gao, Wei
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Public aspects of medicine ,RA1-1270 - Abstract
BackgroundOver one-third of the population of Havelock North, New Zealand, approximately 5500 people, were estimated to have been affected by campylobacteriosis in a large waterborne outbreak. Cases reported through the notifiable disease surveillance system (notified case reports) are inevitably delayed by several days, resulting in slowed outbreak recognition and delayed control measures. Early outbreak detection and magnitude prediction are critical to outbreak control. It is therefore important to consider alternative surveillance data sources and evaluate their potential for recognizing outbreaks at the earliest possible time. ObjectiveThe first objective of this study is to compare and validate the selection of alternative data sources (general practice consultations, consumer helpline, Google Trends, Twitter microblogs, and school absenteeism) for their temporal predictive strength for Campylobacter cases during the Havelock North outbreak. The second objective is to examine spatiotemporal clustering of data from alternative sources to assess the size and geographic extent of the outbreak and to support efforts to attribute its source. MethodsWe combined measures derived from alternative data sources during the 2016 Havelock North campylobacteriosis outbreak with notified case report counts to predict suspected daily Campylobacter case counts up to 5 days before cases reported in the disease surveillance system. Spatiotemporal clustering of the data was analyzed using Local Moran’s I statistics to investigate the extent of the outbreak in both space and time within the affected area. ResultsModels that combined consumer helpline data with autoregressive notified case counts had the best out-of-sample predictive accuracy for 1 and 2 days ahead of notified case reports. Models using Google Trends and Twitter typically performed the best 3 and 4 days before case notifications. Spatiotemporal clusters showed spikes in school absenteeism and consumer helpline inquiries that preceded the notified cases in the city primarily affected by the outbreak. ConclusionsAlternative data sources can provide earlier indications of a large gastroenteritis outbreak compared with conventional case notifications. Spatiotemporal analysis can assist in refining the geographical focus of an outbreak and can potentially support public health source attribution efforts. Further work is required to assess the location of such surveillance data sources and methods in routine public health practice.
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- 2020
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158. Development and Optimization of Chitosan Nanoparticle-Based Intranasal Vaccine Carrier.
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Gao, Xiaoyi, Liu, Nan, Wang, Zengming, Gao, Jing, Zhang, Hui, Li, Meng, Du, Yimeng, Gao, Xiang, and Zheng, Aiping
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INTRANASAL administration , *NASAL mucosa , *SURFACE charges , *NASAL irrigation , *FLUORESCENCE spectroscopy , *CHITOSAN , *SEASHELLS - Abstract
Chitosan is a natural polysaccharide, mainly derived from the shell of marine organisms. At present, chitosan has been widely used in the field of biomedicine due to its special characteristics of low toxicity, biocompatibility, biodegradation and low immunogenicity. Chitosan nanoparticles can be easily prepared. Chitosan nanoparticles with positive charge can enhance the adhesion of antigens in nasal mucosa and promote its absorption, which is expected to be used for intranasal vaccine delivery. In this study, we prepared chitosan nanoparticles by a gelation method, and modified the chitosan nanoparticles with mannose by hybridization. Bovine serum albumin (BSA) was used as the model antigen for development of an intranasal vaccine. The preparation technology of the chitosan nanoparticle-based intranasal vaccine delivery system was optimized by design of experiment (DoE). The DoE results showed that mannose-modified chitosan nanoparticles (Man-BSA-CS-NPs) had high modification tolerance and the mean particle size and the surface charge with optimized Man-BSA-CS-NPs were 156 nm and +33.5 mV. FTIR and DSC results confirmed the presence of Man in Man-BSA-CS-NPs. The BSA released from Man-BSA-CS-NPs had no irreversible aggregation or degradation. In addition, the analysis of fluorescence spectroscopy of BSA confirmed an appropriate binding constant between CS and BSA in this study, which could improve the stability of BSA. The cell study in vitro demonstrated the low toxicity and biocompatibility of Man-BSA-CS-NPs. Confocal results showed that the Man-modified BSA-FITC-CS-NPs promote the endocytosis and internalization of BSA-FITC in DC2.4 cells. In vivo studies of mice, Man-BSA-CS-NPs intranasally immunized showed a significantly improvement of BSA-specific serum IgG response and the highest level of BSA-specific IgA expression in nasal lavage fluid. Overall, our study provides a promising method to modify BSA-loaded CS-NPs with mannose, which is worthy of further study. [ABSTRACT FROM AUTHOR]
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- 2022
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159. Genome‐wide association analyses identify genes modifying age‐at‐onset of Alzheimer's disease: Genetics/genetic factors of non‐Alzheimer's tauopathies.
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Martin, Eden R., Sun, Shuming, Slifer, Susan H., Naj, Adam C., Gao, Xiaoyi R., and Li, Yi‐Ju
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Background: Several studies have attempted to identify genes for age‐at‐onset (AAO) of dementia symptoms in Alzheimer's disease (AD) through genome‐wide linkage (Daw et al. 1999, Li et al. 2002, Choi et al. 2011) and genome‐wide association studies (Kamboh et al. 2012, Naj et al. 2014). Naj et al. conducted a meta‐analysis of 14 datasets from the Alzheimer's Disease Genetics Consortium (ADGC) with genotype imputation to HapMap2. Using an expanded set of ADGC cohorts, we re‐examined AAO using higher‐quality genome‐wide imputation data and pooled‐data analysis instead of meta‐analysis to identify novel genetic contributors to AAO of AD. Methods: We combined data from 20 non‐Hispanic white prospective and case‐control ADGC datasets, excluding family‐based datasets. Genotype data were imputed to the Haplotype Reference Consortium (HRC) r1.1 reference panel using the Michigan Imputation Server and consistent quality control applied to each dataset, after which genotype data were merged across datasets using QCTOOL and GTOOL. We performed case‐only association analyses for log10(AAO) using multivariable linear regression with covariate adjustment for sex, cohort, and principal components capturing population substructure, and then conducted analyses conditioning on dosage of APOE ε4 alleles. Variants with P < 10−5 from conditional analyses were re‐analyzed using linear mixed modeling treating cohort as a random effect. Results: We used 9,228 AD cases, including 5,307 females (57.4%) with mean (SD) AAO of 74.2(7.7) years. In addition to the APOE region, which reached genome‐wide significance (P < 5 × 10−8), we observed strong novel associations with variants in NTM (encoding neurotrimin) on chr11q25 (rs117589002, P = 1.24 × 10−7) and in an intergenic region on chr3p22.3 (Pmin = 1.89 × 10−7). Other AAO loci previously identified in the smaller ADGC dataset (Naj et al 2014) remained nominally significant. After adjusting for APOE ε4, thirty‐two regions showed suggestive association (P < 10−5), with chr3p22.3 and NTM remaining the top loci. Chromosome 11q25 includes a known AD linkage region (Blacker et al. 2003). In addition, NTM variation has been found to be correlated with cognitive function tests (Liu et al. 2007) and intelligence (Pan et al. 2010). Conclusions: In an expanded ADGC dataset, we confirmed AAO associations in the APOE region and observed evidence for potential novel AD AAO loci including NTM. [ABSTRACT FROM AUTHOR]
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- 2020
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160. Multiple Non-Equivalent Interfaces Mediate Direct Activation of GABAA Receptors by Propofol
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Eaton, Megan M., Germann, Allison L., Arora, Ruby, Cao, Lily Q., Gao, Xiaoyi, Shin, Daniel J., Wu, Albert, Chiara, David C., Cohen, Jonathan B., Steinbach, Joe Henry, Evers, Alex S., and Akk, Gustav
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Activation ,binding site ,GABA ,mutation ,propofol ,structure - Abstract
Background Propofol is a sedative agent that at clinical concentrations acts by allosterically activating or potentiating the γ-aminobutyric acid type A (GABAA) receptor. Mutational, modeling, and photolabeling studies with propofol and its analogues have identified potential interaction sites in the transmembrane domain of the receptor. At the “+” of the β subunit, in the β-α interface, meta-azipropofol labels the M286 residue in the third transmembrane domain. Substitution of this residue with tryptophan results in loss of potentiation by propofol. At the “-” side of the β subunit, in the α-β interface (or β-β interface, in the case of homomeric β receptors), ortho-propofol diazirine labels the H267 residue in the second transmembrane domain. Structural modeling indicates that the β(H267) residue lines a cavity that docks propofol with favorable interaction energy. Method We used two-electrode voltage clamp to determine the functional effects of mutations to the “+” and “-” sides of the β subunit on activation of the α1β3 GABAA receptor by propofol. Results: We found that while the individual mutations had a small effect, the combination of the M286W mutation with tryptophan mutations of selected residues at the α-β interface leads to strong reduction in gating efficacy for propofol. Conclusion: We conclude that α1β3 GABAA receptors can be activated by propofol interactions with the β-β, α-β, and β-α interfaces, where distinct, non-equivalent regions control channel gating. Any interface can mediate activation, hence substitutions at all interfaces are required for loss of activation by propofol.
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- 2016
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161. Avoiding the high Bonferroni penalty in genome-wide association studies.
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Gao, Xiaoyi, Becker, Lewis C., Becker, Diane M., Starmer, Joshua D., and Province, Michael A.
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- 2010
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162. Genome-Wide Association and Functional Follow-Up Reveals New Loci for Kidney Function
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Pattaro, Cristian, Köttgen, Anna, Teumer, Alexander, Böger, Carsten A., Fuchsberger, Christian, Olden, Matthias, Chen, Ming-Huei, Tin, Adrienne, Taliun, Daniel, Li, Man, Gao, Xiaoyi, Gorski, Mathias, Yang, Qiong, Hundertmark, Claudia, Foster, Meredith C., Glazer, Nicole, Isaacs, Aaron, Liu, Ching-Ti, Smith, Albert V., O'Connell, Jeffrey R., Struchalin, Maksim, Tanaka, Toshiko, Gierman, Hinco J., Feitosa, Mary, Hwang, Shih-Jen, Atkinson, Elizabeth J., Lohman, Kurt, Johansson, Åsa, Tönjes, Anke, Dehghan, Abbas, Chouraki, Vincent, Holliday, Elizabeth G., Sorice, Rossella, Kutalik, Zoltan, Lehtimäki, Terho, Esko, Tõnu, Deshmukh, Harshal, Ulivi, Sheila, Murgia, Federico, Trompet, Stella, Imboden, Medea, Kollerits, Barbara, Pistis, Giorgio, Harris, Tamara B., Launer, Lenore J., Aspelund, Thor, Eiriksdottir, Gudny, Mitchell, Braxton D., Boerwinkle, Eric, Schmidt, Helena, Cavalieri, Margherita, Rao, Madhumathi, Demirkan, Ayse, Oostra, Ben A., de Andrade, Mariza, Ding, Jingzhong, Andrews, Jeanette S., Freedman, Barry I., Koenig, Wolfgang, Illig, Thomas, Döring, Angela, Wichmann, H.-Erich, Kolcic, Ivana, Zemunik, Tatijana, Boban, Mladen, Minelli, Cosetta, Wheeler, Heather E., Igl, Wilmar, Zaboli, Ghazal, Wild, Sarah H., Wright, Alan F., Campbell, Harry, Ellinghaus, David, Nöthlings, Ute, Jacobs, Gunnar, Biffar, Reiner, Endlich, Karlhans, Ernst, Florian, Homuth, Georg, Kroemer, Heyo K., Nauck, Matthias, Stracke, Sylvia, Völker, Uwe, Völzke, Henry, Kovacs, Peter, Stumvoll, Michael, Mägi, Reedik, Uitterlinden, Andre G., Rivadeneira, Fernando, Aulchenko, Yurii S., Polasek, Ozren, Hastie, Nick, Vitart, Veronique, Helmer, Catherine, Wang, Jie Jin, Ruggiero, Daniela, Bergmann, Sven, Kähönen, Mika, Viikari, Jorma, Nikopensius, Tiit, Province, Michael, Ketkar, Shamika, Colhoun, Helen, Doney, Alex, Robino, Antonietta, Giulianini, Franco, Krämer, Bernhard K., Portas, Laura, Ford, Ian, Buckley, Brendan M., Adam, Martin, Thun, Gian-Andri, Paulweber, Bernhard, Haun, Margot, Sala, Cinzia, Metzger, Marie, Mitchell, Paul, Ciullo, Marina, Kim, Stuart K., Vollenweider, Peter, Raitakari, Olli, Metspalu, Andres, Palmer, Colin, Gasparini, Paolo, Pirastu, Mario, Jukema, J. Wouter, Probst-Hensch, Nicole M., Kronenberg, Florian, Toniolo, Daniela, Gudnason, Vilmundur, Shuldiner, Alan R., Coresh, Josef, Schmidt, Reinhold, Ferrucci, Luigi, Siscovick, David S., van Duijn, Cornelia M., Borecki, Ingrid, Kardia, Sharon L. R., Liu, Yongmei, Rudan, Igor, Gyllensten, Ulf, Wilson, James F., Franke, Andre, Pramstaller, Peter P., Rettig, Rainer, Prokopenko, Inga, Witteman, Jacqueline C. M., Hayward, Caroline, Parsa, Afshin, Bochud, Murielle, Heid, Iris M., Garnaas, Maija, O'Seaghdha, Conall, Li, Guo, Johnson, Andrew D., Cornelis, Marilyn, Chu, Audrey Yu-lei, Hu, Frank B., Turner, Stephen T., Hofman, Albert, Curhan, Gary Craig, Ridker, Paul M., Goessling, Wolfram, Chasman, Daniel Ian, Kao, W. H. Linda, and Fox, Caroline
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biology ,genetics - Abstract
Chronic kidney disease (CKD) is an important public health problem with a genetic component. We performed genome-wide association studies in up to 130,600 European ancestry participants overall, and stratified for key CKD risk factors. We uncovered 6 new loci in association with estimated glomerular filtration rate (eGFR), the primary clinical measure of CKD, in or near \(MPPED2\), \(DDX1\), \(SLC47A1\), \(CDK12\), \(CASP9\), and \(INO80\). Morpholino knockdown of \(mpped2\) and \(casp9\) in zebrafish embryos revealed podocyte and tubular abnormalities with altered dextran clearance, suggesting a role for these genes in renal function. By providing new insights into genes that regulate renal function, these results could further our understanding of the pathogenesis of CKD.
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- 2012
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163. Statistical Methods in Genetic Association Studies
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Gao, Xiaoyi
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- population structure, multiple testing, genotyping error, single nucleotide polymorphism
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Population structure is a serious confounding factor in genetic association studies. It may lead to false positive results or failure to detect true association. We propose a hierarchical clustering algorithm, AW-clust, for using single nucleotide polymorphism (SNP) genetic data to assign individuals to populations. We show that the algorithm can assign sample individuals highly accurately to their corresponding ethic groups: CEU, YRI, CHB+JPT in our tests using HapMap SNP data and it is also robust to admixed populations when tested on Perlegen SNP data. Moreover, it can detect fine-scale population structure as subtle as that between Chinese and Japanese by using genome-wide hight diversity SNP loci. Genotyping errors exist in most genetic data and can influence the biological conclusions of the studies. A simple method is to conduct the Hardy-Weinberg equilibrium (HWE) test in population-based association studies. We investigated the power issue of using the HWE test on genotyping error detection in the presence of current genotyping technologies. Multiple testing is a challenging issue in genetic studies using SNPs that are in linkage disequilibrium (LD) with each other. Failure to adjust for multiple testing appropriately may produce excess false positives or overlook true positive signals. We propose a new multiple testing correction method, CLDMeff , for association studies using SNP markers. It is shown to be simpler and more accurate than the recently developed methods and is comparable to the permutation-based correction using both simulated and real data. The efficiency and accuracy of the CLDMeff method makes it an attractive choice for multiple testing correction when there is high intermarker LD in the SNP dataset.
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- 2007
164. New loci associated with kidney function and chronic kidney disease
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Susan Campbell, Mladen Boban, Sharon L.R. Kardia, Sandra Wilde, Abbas Dehghan, Christian Fuchsberger, Peter Kovacs, Renate B. Schnabel, Gary C. Curhan, Wolfgang Koenig, Wei Wang, Barbara Kollerits, Talin Haritunians, Evadnie Rampersaud, Philipp S. Wild, Yongmei Liu, Mary F. Feitosa, Sarah H. Wild, Ivana Kolcic, Matthias Olden, Medea Imboden, Tanja Zeller, Albert V. Smith, Stephen T. Turner, Igor Rudan, Thomas Münzel, Francesco Giallauria, Anna Köttgen, Uwe Völker, Elizabeth J. Atkinson, Christa Meisinger, Jeffrey Metter, Paul M. Ridker, Florian Kronenberg, Lyudmyla Kedenko, Anita Brandstätter, Dorothea Nitsch, Cornelia M. van Duijn, H.-Erich Wichmann, Michael A. Province, Alan F. Wright, Harry Campbell, Bruce M. Psaty, Man Li, Alex Parker, Toshiko Tanaka, Jeffrey R. O'Connel, Nicholas D. Hastie, James F. Wilson, Reinhold E. Schmidt, Peter P. Pramstaller, Karlhans Endlich, Frank B. Hu, Inga Prokopenko, Andrew D. Johnson, Sunita Badola, Ozren Polasek, Afshin Parsa, Nicole Probst-Hensch, Albert Hofman, Wilmar Igl, Thomas Lumley, Anke Tönjes, Cosetta Minelli, Ingrid B. Borecki, Marilyn C. Cornelis, Andrew B. Singleton, Michael G. Shlipak, Rainer Rettig, Stefan Blankenberg, Qiong Yang, Lina Zgaga, Thierry Rochat, Vilmundur Gudnason, Margherita Cavalieri, Yurii S. Aulchenko, Iris M. Heid, Thor Aspelund, Heyo K. Kroemer, Caroline Hayward, Tatijana Zemunik, Alan R. Shuldine, Veronique Vitart, Wen Hong L. Kao, Matthias Nauck, Ben A. Oostra, Helena Schmidt, Mariza de Andrade, Thomas Illig, Stefan Schreiber, Jacqueline C. M. Witteman, Alexander Teumer, Ulf Gyllensten, Eric Boerwinkle, Tennille S. Leak, Cristian Pattaro, Michael Stumvoll, David Ellinghaus, Ghazal Zaboli, Arne Schillert, Tamara B. Harris, Aaron Isaacs, Braxton D. Mitchel, Carsten A. Böger, Ian H. de Boer, Dan E. Arking, Kurt Lohman, Andre Franke, Fernando Rivadeneira, Gudny Eiriksdottir, Reedik Mägi, Xiaoyi Gao, Nicole L. Glazer, André G. Uitterlinden, Bernhard K. Krämer, Josef Coresh, Caroline S. Fox, Bernhard Paulweber, Norman Klopp, Andreas Ziegler, Janine F. Felix, Åsa Johansson, Daniel I. Chasman, Maksim Struchalin, David S. Siscovick, Guillaume Paré, Shamika Ketkar, Shih-Jen Hwang, Luigi Ferrucci, Henry Völzke, M. CarolaZillikens, Lenore J. Launer, Rochat, Thierry, Köttgen, Anna, Pattaro, Cristian, Böger, Carsten A., Fuchsberger, Christian, Olden, Matthia, Glazer, Nicole L., Parsa, Afshin, Gao, Xiaoyi, Yang, Qiong, Smith, Albert V., O'Connel, Jeffrey R., Li, Man, Schmidt, Helena, Tanaka, Toshiko, Isaacs, Aaron, Ketkar, Shamika, Hwang, Shih-Jen, Johnson, Andrew D., Dehghan, Abba, Teumer, Alexander, Paré, Guillaume, Atkinson, Elizabeth J., Zeller, Tanja, Lohman, Kurt, Cornelis, Marilyn C., Probst-Hensch, Nicole M., Kronenberg, Florian, Tönjes, Anke, Hayward, Caroline, Aspelund, Thor, Eiriksdottir, Gudny, Launer, Lenore J., Harris, Tamara B., Rampersaud, Evadnie, Mitchel, Braxton D., Arking, Dan E., Boerwinkle, Eric, Struchalin, Maksim, Cavalieri, Margherita, Singleton, Andrew, Giallauria, Francesco, Metter, Jeffrey, De Boer, Ian H., Haritunians, Talin, Lumley, Thoma, Siscovick, David, Psaty, Bruce M., Carolazillikens, M., Oostra, Ben A., Feitosa, Mary, Province, Michael, Andrade, Mariza De, Turner, Stephen T., Schillert, Arne, Ziegler, Andrea, Wild, Philipp S., Schnabel, Renate B., Wilde, Sandra, Munzel, Thomas F., Leak, Tennille S., Illig, Thoma, Klopp, Norman, Meisinger, Christa, Wichmann, H-Erich, Koenig, Wolfgang, Zgaga, Lina, Zemunik, Tatijana, Kolcic, Ivana, Minelli, Cosetta, Hu, Frank B., Johansson, Åsa, Igl, Wilmar, Zaboli, Ghazal, Wild, Sarah H., Wright, Alan F., Campbell, Harry, Ellinghaus, David, Schreiber, Stefan, Aulchenko, Yurii S., Felix, Janine F., Rivadeneira, Fernando, Uitterlinden, Andre G., Hofman, Albert, Imboden, Medea, Nitsch, Dorothea, Brandstätter, Anita, Kollerits, Barbara, Kedenko, Lyudmyla, Mägi, Reedik, Stumvoll, Michael, Kovacs, Peter, Boban, Mladen, Campbell, Susan, Endlich, Karlhan, Völzke, Henry, Kroemer, Heyo K., Nauck, Matthia, Völker, Uwe, Polasek, Ozren, Vitart, Veronique, Badola, Sunita, Parker, Alexander N., Ridker, Paul M., Kardia, Sharon L. R., Blankenberg, Stefan, Liu, Yongmei, Curhan, Gary C., Franke, Andre, Paulweber, Bernhard, Prokopenko, Inga, Wang, Wei, Gudnason, Vilmundur, Shuldine, Alan R., Coresh, Josef, Schmidt, Reinhold, Ferrucci, Luigi, Shlipak, Michael G., Van Duijn, Cornelia M., Borecki, Ingrid, Krämer, Bernhard K., Rudan, Igor, Gyllensten, Ulf, Wilson, James F., Witteman, Jacqueline C., Pramstaller, Peter P., Rettig, Rainer, Hastie, Nick, Chasman, Daniel I., Kao, W. H., Heid, Iris M., Fox, Caroline S., Epidemiology, Erasmus MC other, Internal Medicine, and Clinical Genetics
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medicine.medical_specialty ,GENOME-WIDE ASSOCIATION ,SERUM CREATININE ,PROTEIN ,GENE ,MUTATIONS ,VARIANTS ,POPULATION ,CANDIDATE ,HOMOLOG ,MEGALIN ,Population ,Renal function ,Genome-wide association study ,Biology ,Kidney ,urologic and male genital diseases ,Cohort Studies ,chemistry.chemical_compound ,SDG 3 - Good Health and Well-being ,Risk Factors ,Internal medicine ,Genetic Marker ,medicine ,Genetics ,Humans ,Cystatin C ,education ,Cystatin C/genetics ,ddc:616 ,Genetic Markers/genetics ,Creatinine ,education.field_of_study ,Models, Genetic ,Risk Factor ,chronic kidney disease ,loci ,SNP ,Creatinine/blood ,medicine.disease ,Diet ,Europe ,Kidney/*physiology ,Endocrinology ,medicine.anatomical_structure ,chemistry ,Renal physiology ,biology.protein ,Kidney Failure, Chronic ,Kidney Failure, Chronic/ethnology/*genetics ,Cohort Studie ,Kidney disease ,Human ,Genome-Wide Association Study ,Glomerular Filtration Rate - Abstract
Chronic kidney disease (CKD) is a significant public health problem, and recent genetic studies have identified common CKD susceptibility variants. The CKDGen consortium performed a meta-analysis of genome-wide association data in 67,093 individuals of European ancestry from 20 predominantly population-based studies in order to identify new susceptibility loci for reduced renal function as estimated by serum creatinine (eGFRcrea), serum cystatin c (eGFRcys) and CKD (eGFRcrea 60 ml/min/1.73 m 2; n = 5,807 individuals with CKD (cases)). Follow-up of the 23 new genome-wide-significant loci (P 5 × 10 8) in 22,982 replication samples identified 13 new loci affecting renal function and CKD (in or near LASS2, GCKR, ALMS1, TFDP2, DAB2, SLC34A1, VEGFA, PRKAG2, PIP5K1B, ATXN2, DACH1, UBE2Q2 and SLC7A9) and 7 loci suspected to affect creatinine production and secretion (CPS1, SLC22A2, TMEM60, WDR37, SLC6A13, WDR72 and BCAS3). These results further our understanding of the biologic mechanisms of kidney function by identifying loci that potentially influence nephrogenesis, podocyte function, angiogenesis, solute transport and metabolic functions of the kidney. © 2010 Nature America, Inc. All rights reserved.
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- 2010
165. Erratum: Ancestral diversity improves discovery and fine-mapping of genetic loci for anthropometric traits-The Hispanic/Latino Anthropometry Consortium.
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Fernández-Rhodes L, Graff M, Buchanan VL, Justice AE, Highland HM, Guo X, Zhu W, Chen HH, Young KL, Adhikari K, Palmer ND, Below JE, Bradfield J, Pereira AC, Glover L, Kim D, Lilly AG, Shrestha P, Thomas AG, Zhang X, Chen M, Chiang CWK, Pulit S, Horimoto A, Krieger JE, Guindo-Martínez M, Preuss M, Schumann C, Smit RAJ, Torres-Mejía G, Acuña-Alonzo V, Bedoya G, Bortolini MC, Canizales-Quinteros S, Gallo C, González-José R, Poletti G, Rothhammer F, Hakonarson H, Igo R, Adler SG, Iyengar SK, Nicholas SB, Gogarten SM, Isasi CR, Papnicolaou G, Stilp AM, Qi Q, Kho M, Smith JA, Langefeld CD, Wagenknecht L, Mckean-Cowdin R, Gao XR, Nousome D, Conti DV, Feng Y, Allison MA, Arzumanyan Z, Buchanan TA, Chen YI, Genter PM, Goodarzi MO, Hai Y, Hsueh W, Ipp E, Kandeel FR, Lam K, Li X, Nadler JL, Raffel LJ, Roll K, Sandow K, Tan J, Taylor KD, Xiang AH, Yao J, Audirac-Chalifour A, Peralta Romero JJ, Hartwig F, Horta B, Blangero J, Curran JE, Duggirala R, Lehman DE, Puppala S, Fejerman L, John EM, Aguilar-Salinas C, Burtt NP, Florez JC, García-Ortíz H, González-Villalpando C, Mercader J, Orozco L, Tusié-Luna T, Blanco E, Gahagan S, Cox NJ, Hanis C, Butte NF, Cole SA, Comuzzie AG, Voruganti VS, Rohde R, Wang Y, Sofer T, Ziv E, Grant SFA, Ruiz-Linares A, Rotter JI, Haiman CA, Parra EJ, Cruz M, Loos RJF, and North KE
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[This corrects the article DOI: 10.1016/j.xhgg.2022.100099.]., (© 2022 The Author(s).)
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- 2022
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166. Ancestral diversity improves discovery and fine-mapping of genetic loci for anthropometric traits-The Hispanic/Latino Anthropometry Consortium.
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Fernández-Rhodes L, Graff M, Buchanan VL, Justice AE, Highland HM, Guo X, Zhu W, Chen HH, Young KL, Adhikari K, Palmer ND, Below JE, Bradfield J, Pereira AC, Glover L, Kim D, Lilly AG, Shrestha P, Thomas AG, Zhang X, Chen M, Chiang CWK, Pulit S, Horimoto A, Krieger JE, Guindo-Martínez M, Preuss M, Schumann C, Smit RAJ, Torres-Mejía G, Acuña-Alonzo V, Bedoya G, Bortolini MC, Canizales-Quinteros S, Gallo C, González-José R, Poletti G, Rothhammer F, Hakonarson H, Igo R, Adler SG, Iyengar SK, Nicholas SB, Gogarten SM, Isasi CR, Papnicolaou G, Stilp AM, Qi Q, Kho M, Smith JA, Langefeld CD, Wagenknecht L, Mckean-Cowdin R, Gao XR, Nousome D, Conti DV, Feng Y, Allison MA, Arzumanyan Z, Buchanan TA, Ida Chen YD, Genter PM, Goodarzi MO, Hai Y, Hsueh W, Ipp E, Kandeel FR, Lam K, Li X, Nadler JL, Raffel LJ, Roll K, Sandow K, Tan J, Taylor KD, Xiang AH, Yao J, Audirac-Chalifour A, de Jesus Peralta Romero J, Hartwig F, Horta B, Blangero J, Curran JE, Duggirala R, Lehman DE, Puppala S, Fejerman L, John EM, Aguilar-Salinas C, Burtt NP, Florez JC, García-Ortíz H, González-Villalpando C, Mercader J, Orozco L, Tusié-Luna T, Blanco E, Gahagan S, Cox NJ, Hanis C, Butte NF, Cole SA, Comuzzie AG, Voruganti VS, Rohde R, Wang Y, Sofer T, Ziv E, Grant SFA, Ruiz-Linares A, Rotter JI, Haiman CA, Parra EJ, Cruz M, Loos RJF, and North KE
- Abstract
Hispanic/Latinos have been underrepresented in genome-wide association studies (GWAS) for anthropometric traits despite their notable anthropometric variability, ancestry proportions, and high burden of growth stunting and overweight/obesity. To address this knowledge gap, we analyzed densely imputed genetic data in a sample of Hispanic/Latino adults to identify and fine-map genetic variants associated with body mass index (BMI), height, and BMI-adjusted waist-to-hip ratio (WHRadjBMI). We conducted a GWAS of 18 studies/consortia as part of the Hispanic/Latino Anthropometry (HISLA) Consortium (stage 1, n = 59,771) and generalized our findings in 9 additional studies (stage 2, n = 10,538). We conducted a trans-ancestral GWAS with summary statistics from HISLA stage 1 and existing consortia of European and African ancestries. In our HISLA stage 1 + 2 analyses, we discovered one BMI locus, as well as two BMI signals and another height signal each within established anthropometric loci. In our trans-ancestral meta-analysis, we discovered three BMI loci, one height locus, and one WHRadjBMI locus. We also identified 3 secondary signals for BMI, 28 for height, and 2 for WHRadjBMI in established loci. We show that 336 known BMI, 1,177 known height, and 143 known WHRadjBMI (combined) SNPs demonstrated suggestive transferability (nominal significance and effect estimate directional consistency) in Hispanic/Latino adults. Of these, 36 BMI, 124 height, and 11 WHRadjBMI SNPs were significant after trait-specific Bonferroni correction. Trans-ancestral meta-analysis of the three ancestries showed a small-to-moderate impact of uncorrected population stratification on the resulting effect size estimates. Our findings demonstrate that future studies may also benefit from leveraging diverse ancestries and differences in linkage disequilibrium patterns to discover novel loci and additional signals with less residual population stratification., Competing Interests: S.M.G. and A.M.S. receive funding from Seven Bridges Genomics to develop tools for the NHLBI BioData Catalyst consortium. All others authors declare no competing interests., (© 2022 The Author(s).)
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- 2022
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167. Optimization of Ferroelectric Ordering and Thermal Stability in Na 1/2 Bi 1/2 TiO 3 -Based Lead-Free Single Crystal through Defect Engineering.
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Chen C, Yang L, Cheng Z, Chang S, Jiang X, Jiang X, Wang J, Huang X, Gao X, Dong G, Luo H, Lyu Y, Liu J, and Zhang S
- Abstract
Environmentally friendly lead-free piezoelectric materials have been attracting significant attention in recent years. Na
1/2 Bi1/2 TiO3 -based relaxor ferroelectrics have found acceptance for application in promising lead-free transducers in high-power ultrasonic devices. However, their low thermal stability, i.e., their relatively low ferroelectric-relaxor transition temperature ( TF-R ), hinders their practical application. Herein, a thermal-quenching approach is applied on a Na1/2 Bi1/2 TiO3 (NBT)-based single crystal, which yields a large increase in TF-R and dramatic enhancement of its ferroelectric ordering, leading to excellent thermal stability of its dielectric, ferroelectric, and piezoelectric properties. This behavior is mainly attributed to quenching-induced domain evolution as well as its octahedral tilt, which is linked to the increased oxygen vacancies. The substitution of long-range ordered ferroelectric domains for short-range polar nanodomains contributes to its increased coherence length and, consequently, enhancement of TF-R . This work provides an approach to the optimization of the ferroelectric ordering and thermal stability of NBT as well as an in-depth understanding of the quenching effect on the local structure, which could be applied to other relaxor-based ferroelectrics for optimization of their macroscopic properties.- Published
- 2021
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168. High-Performance Sm-Doped Pb(Mg 1/3 Nb 2/3 )O 3 -PbZrO 3 -PbTiO 3 -Based Piezoceramics.
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Guo Q, Li F, Xia F, Gao X, Wang P, Hao H, Sun H, Liu H, and Zhang S
- Abstract
High-performance piezoelectric materials are pivotal to many electromechanical applications including piezoelectric actuators, sensors, and transducers. However, the general approach to achieve high piezoelectric properties by establishing morphotropic phase boundary (MPB) has limitation due to the weak anisotropy of the Gibbs free energy profile at the MPB region. Here, aliovalent Sm
3+ -doped 0.4Pb(Mg1/3 Nb2/3 )O3 -(0.6- x )PbZrO3 - x PbTiO3 piezoelectric ceramics were fabricated by a solid-state method, where the optimized piezoelectric coefficient d33 = 910 pC/N, dielectric constant εr = 4090, and Curie temperature TC = 184 °C were obtained at x = 0.352, being attributed to the synergistic contributions from the MPB and enhanced local structural heterogeneity. Rayleigh analysis was adopted to study the intrinsic and extrinsic contributions in Sm-doped PMN-PZ-PT ceramics, where the extrinsic contribution was found to be on the order of 25-67% at 4 kV/cm. Of particular significance is that a large signal d33 * = 820 pm/V (at 20 kV/cm) with a minimal strain variation of 5% was achieved for a composition of x = 0.372 over the temperature range of 20-160 °C, being superior to those previously reported piezoelectric ceramic materials. This work offers a good paradigm to simultaneously achieve high piezoelectric properties with good temperature stability in ferroelectric ceramics, which have great potential for piezoelectric application at elevated temperatures.- Published
- 2019
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169. A Genome-Wide Association Study of Vertical Cup-Disc Ratio in a Latino Population.
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Nannini DR, Torres M, Chen YI, Taylor KD, Rotter JI, Varma R, and Gao X
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- Adult, Basic Helix-Loop-Helix Transcription Factors metabolism, California epidemiology, Female, Genotype, Glaucoma diagnosis, Glaucoma ethnology, Helix-Loop-Helix Motifs, Humans, Male, Middle Aged, Polymorphism, Single Nucleotide, Prevalence, Basic Helix-Loop-Helix Transcription Factors genetics, Genome-Wide Association Study methods, Glaucoma genetics, Hispanic or Latino, Intraocular Pressure physiology, Optic Disk pathology
- Abstract
Purpose: Vertical cup-disc ratio (VCDR) is used as a clinical assessment measure to identify and monitor glaucomatous damage to the optic nerve. Previous genetic studies conducted in European and Asian populations have identified many loci associated with VCDR. The genetic factors in other ethnic populations, such as Latino, influencing VCDR remain to be determined. Here, we describe the first genome-wide association study (GWAS) on VCDR in Latino individuals., Methods: We conducted this GWAS on VCDR using 4537 Latino individuals who were genotyped by using either the Illumina OmniExpress BeadChip (∼730K markers) or the Illumina Hispanic/SOL BeadChip (∼2.5 million markers). Study subjects were 40 years of age and older. Linear regression, adjusting for age, sex, and principal components of genetic ancestry, was conducted to assess the associations between single nucleotide polymorphisms (SNPs) and VCDR. We imputed SNPs from the 1000 Genomes Project to integrate additional SNPs not directly genotyped., Results: We replicated two previously reported SNPs that reached GWAS significance, rs1900005 and rs7916697, in the ATOH7-PBLD region, as well as identified two suggestive associations in the CDC7-TGFBR3 region on chromosome 1p22.1 and in the ZNF770-DPH6 region on chromosome 15q14. We discovered a novel SNP, rs56238729 (P = 1.22 × 10-13), in the ATOH7-PBLD region that is significantly associated with VCDR in Latino individuals. We replicated eight previously reported regions, including COL8A1, CDKN2B-CDKN2BAS, BMP2, and CHEK2 (P < 2.17 × 10-3)., Conclusions: Our results discovered a novel SNP that is significantly associated with VCDR in Latino individuals and confirmed previously reported loci, providing further insight into the genetic architecture of VCDR.
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- 2017
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170. Steroid-induced ocular hypertension/glaucoma: Focus on pharmacogenomics and implications for precision medicine.
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Fini ME, Schwartz SG, Gao X, Jeong S, Patel N, Itakura T, Price MO, Price FW Jr, Varma R, and Stamer WD
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- Disease Management, Glaucoma therapy, Humans, Ocular Hypertension therapy, Genome-Wide Association Study, Glaucoma chemically induced, Glucocorticoids adverse effects, Intraocular Pressure drug effects, Ocular Hypertension chemically induced, Pharmacogenetics methods, Precision Medicine methods
- Abstract
Elevation of intraocular pressure (IOP) due to therapeutic use of glucocorticoids is called steroid-induced ocular hypertension (SIOH); this can lead to steroid-induced glaucoma (SIG). Glucocorticoids initiate signaling cascades ultimately affecting expression of hundreds of genes; this provides the potential for a highly personalized pharmacological response. Studies attempting to define genetic risk factors were undertaken early in the history of glucocorticoid use, however scientific tools available at that time were limited and progress stalled. In contrast, significant advances were made over the ensuing years in defining disease pathophysiology. As the genomics age emerged, it appeared the time was right to renew investigation into genetics. Pharmacogenomics is an unbiased discovery approach, not requiring an underlying hypothesis, and provides a way to pinpoint clinically significant genes and pathways that could not have been discovered any other way. Results of the first genome-wide association study to identify polymorphisms associated with SIOH, and follow-up on two novel genes linked to the disorder, GPR158 and HCG22, is discussed in the second half of the article. However, knowledge of genetic variants determining response to steroids in the eye also has value in its own right as a predictive and diagnostic tool. This article concludes with a discussion of how the Precision Medicine Initiative
® , announced by U.S. President Obama in his 2015 State of the Union address, is beginning to touch the practice of ophthalmology. It is argued that SIOH/SIG may provide one of the next opportunities for effective application of precision medicine., (Copyright © 2016 Elsevier Ltd. All rights reserved.)- Published
- 2017
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171. Genome-wide association study identifies WNT7B as a novel locus for central corneal thickness in Latinos.
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Gao X, Nannini DR, Corrao K, Torres M, Chen YI, Fan BJ, Wiggs JL, Taylor KD, Gauderman WJ, Rotter JI, and Varma R
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- Adult, Aged, Cornea physiology, Corneal Pachymetry methods, Female, Genetic Loci, Genome-Wide Association Study methods, Genotype, Glaucoma genetics, Glaucoma, Open-Angle genetics, Humans, Keratoconus genetics, Los Angeles, Male, Middle Aged, Polymorphism, Single Nucleotide, Wnt Proteins metabolism, Cornea pathology, Hispanic or Latino genetics, Wnt Proteins genetics
- Abstract
The cornea is the outermost layer of the eye and is a vital component of focusing incoming light on the retina. Central corneal thickness (CCT) is now recognized to have a significant role in ocular health and is a risk factor for various ocular diseases, such as keratoconus and primary open angle glaucoma. Most previous genetic studies utilized European and Asian subjects to identify genetic loci associated with CCT. Minority populations, such as Latinos, may aid in identifying additional loci and improve our understanding of the genetic architecture of CCT. In this study, we conducted a genome-wide association study (GWAS) in Latinos, a traditionally understudied population in genetic research, to further identify loci contributing to CCT. Study participants were genotyped using either the Illumina OmniExpress BeadChip (∼730K markers) or the Illumina Hispanic/SOL BeadChip (∼2.5 million markers). All study participants were 40 years of age and older. We assessed the association between individual single nucleotide polymorphisms (SNPs) and CCT using linear regression, adjusting for age, gender and principal components of genetic ancestry. To expand genomic coverage and to interrogate additional SNPs, we imputed SNPs from the 1000 Genomes Project reference panels. We identified a novel SNP, rs10453441 (P = 6.01E-09), in an intron of WNT7B that is associated with CCT. Furthermore, WNT7B is expressed in the human cornea. We also replicated 11 previously reported loci, including IBTK, RXRA-COL5A1, COL5A1, FOXO1, LRRK1 and ZNF469 (P < 1.25E-3). These findings provide further insight into the genetic architecture of CCT and illustrate that the use of minority groups in GWAS will help identify additional loci.
- Published
- 2016
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172. Genetic Variants Associated With Quantitative Glucose Homeostasis Traits Translate to Type 2 Diabetes in Mexican Americans: The GUARDIAN (Genetics Underlying Diabetes in Hispanics) Consortium.
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Palmer ND, Goodarzi MO, Langefeld CD, Wang N, Guo X, Taylor KD, Fingerlin TE, Norris JM, Buchanan TA, Xiang AH, Haritunians T, Ziegler JT, Williams AH, Stefanovski D, Cui J, Mackay AW, Henkin LF, Bergman RN, Gao X, Gauderman J, Varma R, Hanis CL, Cox NJ, Highland HM, Below JE, Williams AL, Burtt NP, Aguilar-Salinas CA, Huerta-Chagoya A, Gonzalez-Villalpando C, Orozco L, Haiman CA, Tsai MY, Johnson WC, Yao J, Rasmussen-Torvik L, Pankow J, Snively B, Jackson RD, Liu S, Nadler JL, Kandeel F, Chen YD, Bowden DW, Rich SS, Raffel LJ, Rotter JI, Watanabe RM, and Wagenknecht LE
- Subjects
- Blood Glucose metabolism, Databases, Factual, Diabetes Mellitus, Type 2 ethnology, Gene Expression Regulation physiology, Genome, Genome-Wide Association Study, Genotype, Hispanic or Latino, Homeostasis genetics, Humans, Blood Glucose genetics, Diabetes Mellitus, Type 2 metabolism, Genetic Variation, Homeostasis physiology
- Abstract
Insulin sensitivity, insulin secretion, insulin clearance, and glucose effectiveness exhibit strong genetic components, although few studies have examined their genetic architecture or influence on type 2 diabetes (T2D) risk. We hypothesized that loci affecting variation in these quantitative traits influence T2D. We completed a multicohort genome-wide association study to search for loci influencing T2D-related quantitative traits in 4,176 Mexican Americans. Quantitative traits were measured by the frequently sampled intravenous glucose tolerance test (four cohorts) or euglycemic clamp (three cohorts), and random-effects models were used to test the association between loci and quantitative traits, adjusting for age, sex, and admixture proportions (Discovery). Analysis revealed a significant (P < 5.00 × 10(-8)) association at 11q14.3 (MTNR1B) with acute insulin response. Loci with P < 0.0001 among the quantitative traits were examined for translation to T2D risk in 6,463 T2D case and 9,232 control subjects of Mexican ancestry (Translation). Nonparametric meta-analysis of the Discovery and Translation cohorts identified significant associations at 6p24 (SLC35B3/TFAP2A) with glucose effectiveness/T2D, 11p15 (KCNQ1) with disposition index/T2D, and 6p22 (CDKAL1) and 11q14 (MTNR1B) with acute insulin response/T2D. These results suggest that T2D and insulin secretion and sensitivity have both shared and distinct genetic factors, potentially delineating genomic components of these quantitative traits that drive the risk for T2D., (© 2015 by the American Diabetes Association. Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered.)
- Published
- 2015
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173. Identification of a Novel Mucin Gene HCG22 Associated With Steroid-Induced Ocular Hypertension.
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Jeong S, Patel N, Edlund CK, Hartiala J, Hazelett DJ, Itakura T, Wu PC, Avery RL, Davis JL, Flynn HW, Lalwani G, Puliafito CA, Wafapoor H, Hijikata M, Keicho N, Gao X, Argüeso P, Allayee H, Coetzee GA, Pletcher MT, Conti DV, Schwartz SG, Eaton AM, and Fini ME
- Subjects
- Adult, Female, Follow-Up Studies, Genome-Wide Association Study, Genotype, Glucocorticoids adverse effects, Humans, Male, Middle Aged, Mucins biosynthesis, Ocular Hypertension chemically induced, Ocular Hypertension metabolism, Trabecular Meshwork metabolism, Gene Expression Regulation, Intraocular Pressure drug effects, Mucins genetics, Ocular Hypertension genetics, RNA, Messenger genetics, Triamcinolone adverse effects
- Abstract
Purpose: The pathophysiology of ocular hypertension (OH) leading to primary open-angle glaucoma shares many features with a secondary form of OH caused by treatment with glucocorticoids, but also exhibits distinct differences. In this study, a pharmacogenomics approach was taken to discover candidate genes for this disorder., Methods: A genome-wide association study was performed, followed by an independent candidate gene study, using a cohort enrolled from patients treated with off-label intravitreal triamcinolone, and handling change in IOP as a quantitative trait., Results: An intergenic quantitative trait locus (QTL) was identified at chromosome 6p21.33 near the 5' end of HCG22 that attained the accepted statistical threshold for genome-level significance. The HCG22 transcript, encoding a novel mucin protein, was expressed in trabecular meshwork cells, and expression was stimulated by IL-1, and inhibited by triamcinolone acetate and TGF-β. Bioinformatic analysis defined the QTL as an approximately 4 kilobase (kb) linkage disequilibrium block containing 10 common single nucleotide polymorphisms (SNPs). Four of these SNPs were identified in the National Center for Biotechnology Information (NCBI) GTEx eQTL browser as modifiers of HCG22 expression. Most are predicted to disrupt or improve motifs for transcription factor binding, the most relevant being disruption of the glucocorticoid receptor binding motif. A second QTL was identified within the predicted signal peptide of the HCG22 encoded protein that could affect its secretion. Translation, O-glycosylation, and secretion of the predicted HCG22 protein was verified in cultured trabecular meshwork cells., Conclusions: Identification of two independent QTLs that could affect expression of the HCG22 mucin gene product via two different mechanisms (transcription or secretion) is highly suggestive of a role in steroid-induced OH.
- Published
- 2015
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174. Native American ancestry is associated with severe diabetic retinopathy in Latinos.
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Gao X, Gauderman WJ, Marjoram P, Torres M, Chen YD, Taylor KD, Rotter JI, and Varma R
- Subjects
- Aged, Case-Control Studies, Diabetes Mellitus, Type 2 ethnology, Diabetes Mellitus, Type 2 genetics, Female, Genotype, Humans, Los Angeles epidemiology, Male, Middle Aged, Multivariate Analysis, Prevalence, Risk Factors, Severity of Illness Index, Diabetic Retinopathy ethnology, Diabetic Retinopathy genetics, Hispanic or Latino genetics, Hispanic or Latino statistics & numerical data, Indians, North American genetics, Indians, North American statistics & numerical data
- Abstract
Purpose: Diabetic retinopathy (DR) is a leading cause of blindness in working age adults. Studies have observed that Latinos have a higher prevalence of DR than whites. The purpose of this study is to test the association between genetic admixture and severe DR in Latinos with type 2 diabetes mellitus (T2DM)., Methods: We conducted a case-control study using 944 T2DM subjects from the Los Angeles Latino Eye Study. Cases (n = 135) were defined as proliferative or severe nonproliferative DR subjects. Controls (n = 809) were other diabetic subjects in the cohort. Genotyping was performed on the Illumina OmniExpress BeadChip. We estimated genetic ancestry in Latinos using STRUCTURE with the HapMap reference panels. Univariate and multivariate logistic regression analyses were used to test the relationship between the proportions of genetic ancestry and severe DR., Results: Native American ancestry (NAA) in Latino T2DM subjects is associated significantly with severe DR (P = 0.002). The association remained significant (P = 0.005) after adjusting for age, sex, duration of diabetes, hemoglobin A1c, body mass index, systolic blood pressure, education, and income. We also validated the NAA estimates in Latinos using ADMIXTURE with the 1000 Genomes Project reference panels and obtained consistent results., Conclusions: Our results demonstrate for the first time to our knowledge that NAA is a significant risk factor for severe DR in Latinos., (Copyright 2014 The Association for Research in Vision and Ophthalmology, Inc.)
- Published
- 2014
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175. Harmonizing the classification of age-related macular degeneration in the three-continent AMD consortium.
- Author
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Klein R, Meuer SM, Myers CE, Buitendijk GH, Rochtchina E, Choudhury F, de Jong PT, McKean-Cowdin R, Iyengar SK, Gao X, Lee KE, Vingerling JR, Mitchell P, Klaver CC, Wang JJ, and Klein BE
- Subjects
- Aged, Aged, 80 and over, Australia epidemiology, Cohort Studies, Female, Humans, Macular Degeneration epidemiology, Macular Degeneration pathology, Male, Middle Aged, Netherlands epidemiology, Prevalence, Severity of Illness Index, United States epidemiology, Macular Degeneration classification
- Abstract
Purpose: To describe methods to harmonize the classification of age-related macular degeneration (AMD) phenotypes across four population-based cohort studies: the Beaver Dam Eye Study (BDES), the Blue Mountains Eye Study (BMES), the Los Angeles Latino Eye Study (LALES), and the Rotterdam Study (RS)., Methods: AMD grading protocols, definitions of categories, and grading forms from each study were compared to determine whether there were systematic differences in AMD severity definitions and lesion categorization among the three grading centers. Each center graded the same set of 60 images using their respective systems to determine presence and severity of AMD lesions. A common 5-step AMD severity scale and definitions of lesion measurement cutpoints and early and late AMD were developed from this exercise., Results: Applying this severity scale changed the age-sex adjusted prevalence of early AMD from 18.7% to 20.3% in BDES, from 4.7% to 14.4% in BMES, from 14.1% to 15.8% in LALES, and from 7.5% to 17.1% in RS. Age-sex adjusted prevalences of late AMD remained unchanged. Comparison of each center's grades of the 60 images converted to the consortium scale showed that exact agreement of AMD severity among centers varied from 61.0-81.4%, and one-step agreement varied from 84.7-98.3%., Conclusion: Harmonization of AMD classification reduced categorical differences in phenotypic definitions across the studies, resulted in a new 5-step AMD severity scale, and enhanced similarity of AMD prevalence among the four cohorts. Despite harmonization it may still be difficult to remove systematic differences in grading, if present.
- Published
- 2014
- Full Text
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