16 results on '"Lee, Mi Kyeong"'
Number of results to display per page
Search Results
2. Additional file 1 of Epigenome-wide association study of kidney function identifies trans-ethnic and ethnic-specific loci
- Author
-
Breeze, Charles E., Batorsky, Anna, Lee, Mi Kyeong, Szeto, Mindy D., Xiaoguang Xu, McCartney, Daniel L., Jiang, Rong, Patki, Amit, Kramer, Holly J., Eales, James M., Raffield, Laura, Lange, Leslie, Lange, Ethan, Durda, Peter, Yongmei Liu, Tracy, Russ P., Van Den Berg, David, Evans, Kathryn L., Kraus, William E., Svati Shah, Hermant K. Tiwari, Lifang Hou, Whitsel, Eric A., Jiang, Xiao, Charchar, Fadi J., Baccarelli, Andrea A., Rich, Stephen S., Morris, Andrew P., Irvin, Marguerite R., Arnett, Donna K., Hauser, Elizabeth R., Rotter, Jerome I., Correa, Adolfo, Hayward, Caroline, Horvath, Steve, Marioni, Riccardo E., Tomaszewski, Maciej, Beck, Stephan, Berndt, Sonja I., London, Stephanie J., Josyf C. Mychaleckyj, and Franceschini, Nora
- Abstract
Additional file 1: Supplementary Figures. Figure S1 to S7. Study design, QQ plots, Manhattan plots, forest plots and eFORGE/FORGE2 analyses.
- Published
- 2021
- Full Text
- View/download PDF
3. Higher Criticism Tuned Regression For Weak And Sparse Signals
- Author
-
Jiang, Tao, London, Stephanie J., Lee, Mi Kyeong, Mychaleckyj, Josyf C., and Motsinger-Reif, Alison A.
- Subjects
Methodology (stat.ME) ,FOS: Computer and information sciences ,FOS: Biological sciences ,Quantitative Biology - Quantitative Methods ,Statistics - Methodology ,Quantitative Methods (q-bio.QM) - Abstract
Here we propose a novel searching scheme for a tuning parameter in high-dimensional penalized regression methods to address variable selection and modeling when sample sizes are limited compared to the data dimensions. Our method is motivated by high-throughput biological data such as genome-wide association studies (GWAS) and epigenome-wide association studies (EWAS). We propose a new estimate of the regularization parameter $\lambda$ in penalized regression methods based on an estimated lower bound of the proportion of false null hypotheses with confidence $(1 - \alpha)$. The bound is estimated by applying the empirical null distribution of the higher criticism statistic, a second-level significance test constructed by dependent $p$-values using a multi-split regression and aggregation method. A tuning parameter estimate in penalized regression, $\lambda$, corresponds with the lower bound of the proportion of false null hypotheses. Different penalized regression methods with varied signal sparsity and strength are compared in the multi-split method setting. We demonstrate the performance of our method using both simulation experiments and the applications of real data on (1) lipid-trait genetics from the Action to Control Cardiovascular Risk in Diabetes (ACCORD) clinical trial and (2) epigenetic analysis evaluating smoking's influence in differential methylation in the Agricultural Lung Health Study. The proposed algorithm is included in the HCTR package, available at https://cran.r-project.org/web/packages/HCTR/index.html.
- Published
- 2020
- Full Text
- View/download PDF
4. Genetic landscape of chronic obstructive pulmonary disease identifies heterogeneous cell type and phenotype associations
- Author
-
Sakornsakolpat, Phuwanat, Prokopenko, Dmitry, Lamontagne, Maxime, Reeve, Nicola F., Guyatt, Anna L., Jackson, Victoria E., Shrine, Nick, Qiao, Dandi, Bartz, Traci M., Kim, Deog Kyeom, Lee, Mi Kyeong, Latourelle, Jeanne C., Li, Xingnan, Morrow, Jarrett D., Obeidat, Ma'en, Wyss, Annah B., Bakke, Per, Graham Barr, R., Beaty, Terri H., Belinsky, Steven A., Brusselle, Guy G., Crapo, James D., de Jong, Kim, DeMeo, Dawn L., Fingerlin, Tasha L., Gharib, Sina A., Gulsvik, Amund, Hall, Ian P., Hokanson, John E., Jin Kim, Woo, Lomas, David A., London, Stephanie J., Meyers, Deborah A., O'Connor, George T., Rennard, Stephen I., Schwartz, David A., Sliwinski, Pawel, Sparrow, David, Strachan, David P., Tal-Singer, Ruth, Tesfaigzi, Yohannes, Vonk, Judith M., Yim, Jae-Joon, Zhou, Xiaobo, Bosse, Yohan, Manichaikul, Ani, Lahousse, Lies, Silverman, Edwin K., Marike Boezen, H., Wain, Louise V., Tobin, Martin D., Hobbs, Brian D., and Cho, Michael H.
- Subjects
respiratory tract diseases - Abstract
Chronic obstructive pulmonary disease (COPD) is the leading cause of respiratory mortality worldwide. Genetic risk loci provide novel insights into disease pathogenesis. We performed a genome-wide association study in 35,735 cases and 222,076 controls from the UK Biobank and additional studies from the International COPD Genetics Consortium. We identified 82 loci with P-value [less than] 5 × 10-8; 47 were previously described in association with either COPD or population-based lung function. Of the remaining 35 novel loci, 13 were associated with lung function in 79,055 individuals from the SpiroMeta consortium. Using gene expression and regulation data, we identified enrichment for loci in lung tissue, smooth muscle and several lung cell types. We found 14 COPD loci shared with either asthma or pulmonary fibrosis. COPD genetic risk loci clustered into groups of quantitative imaging features and comorbidity associations. Our analyses provide further support to the genetic susceptibility and heterogeneity of COPD.
- Published
- 2019
5. Genetic landscape of chronic obstructive pulmonary disease identifies heterogeneous cell-type and phenotype associations
- Author
-
Sakornsakolpat, Phuwanat, Prokopenko, Dmitry, Lamontagne, Maxime, Reeve, Nicola F, Guyatt, Anna L, Jackson, Victoria E, Shrine, Nick, Qiao, Dandi, Bartz, Traci M, Kim, Deog Kyeom, Lee, Mi Kyeong, Latourelle, Jeanne C, Li, Xingnan, Morrow, Jarrett D, Obeidat, Ma'en, Wyss, Annah B, Bakke, Per, Barr, R Graham, Beaty, Terri H, Belinsky, Steven A, Brusselle, Guy G, Crapo, James D, de Jong, Kim, DeMeo, Dawn L, Fingerlin, Tasha E, Gharib, Sina A, Gulsvik, Amund, Hall, Ian P, Hokanson, John E, Kim, Woo Jin, Lomas, David A, London, Stephanie J, Meyers, Deborah A, O'Connor, George T, Rennard, Stephen I, Schwartz, David A, Sliwinski, Pawel, Sparrow, David, Strachan, David P, Tal-Singer, Ruth, Tesfaigzi, Yohannes, Vestbo, Jørgen, Vonk, Judith M, Yim, Jae-Joon, Zhou, Xiaobo, Bossé, Yohan, Manichaikul, Ani, Lahousse, Lies, Silverman, Edwin K, Boezen, H Marike, Wain, Louise V, Tobin, Martin D, Hobbs, Brian D, Cho, Michael H, SpiroMeta Consortium, International COPD Genetics Consortium, and Apollo - University of Cambridge Repository
- Subjects
Adult ,Male ,Pulmonary Fibrosis ,Smoking ,Gene Expression ,Middle Aged ,Polymorphism, Single Nucleotide ,Asthma ,respiratory tract diseases ,Pulmonary Disease, Chronic Obstructive ,Phenotype ,Genetic Loci ,Case-Control Studies ,Humans ,Female ,Genetic Predisposition to Disease ,Lung ,Aged ,Genome-Wide Association Study - Abstract
Chronic obstructive pulmonary disease (COPD) is the leading cause of respiratory mortality worldwide. Genetic risk loci provide new insights into disease pathogenesis. We performed a genome-wide association study in 35,735 cases and 222,076 controls from the UK Biobank and additional studies from the International COPD Genetics Consortium. We identified 82 loci associated with P < 5 × 10-8; 47 of these were previously described in association with either COPD or population-based measures of lung function. Of the remaining 35 new loci, 13 were associated with lung function in 79,055 individuals from the SpiroMeta consortium. Using gene expression and regulation data, we identified functional enrichment of COPD risk loci in lung tissue, smooth muscle, and several lung cell types. We found 14 COPD loci shared with either asthma or pulmonary fibrosis. COPD genetic risk loci clustered into groups based on associations with quantitative imaging features and comorbidities. Our analyses provide further support for the genetic susceptibility and heterogeneity of COPD.
- Published
- 2019
6. Genetic landscape of chronic obstructive pulmonary disease identifies heterogeneous cell-type and phenotype associations
- Author
-
Sakornsakolpat, Phuwanat, Prokopenko, Dmitry, Lamontagne, Maxime, Reeve, Nicola F., Guyatt, Anna L., Jackson, Victoria E., Shrine, Nick, Qiao, Dandi, Bartz, Traci M., Kim, Deog Kyeom, Lee, Mi Kyeong, Latourelle, Jeanne C., Li, Xingnan, Morrow, Jarrett D., Obeidat, Ma’en, Wyss, Annah B., Bakke, Per, Barr, R. Graham, Beaty, Terri H., Belinsky, Steven A., Brusselle, Guy G., Crapo, James D., de Jong, Kim, DeMeo, Dawn L., Fingerlin, Tasha E., Gharib, Sina A., Gulsvik, Amund, Hall, Ian P., Hokanson, John E., Kim, Woo Jin, Lomas, David A., London, Stephanie J., Meyers, Deborah A., O’Connor, George T., Rennard, Stephen I., Schwartz, David A., Sliwinski, Pawel, Sparrow, David, Strachan, David P., Tal-Singer, Ruth, Tesfaigzi, Yohannes, Vestbo, Jørgen, Vonk, Judith M., Yim, Jae-Joon, Zhou, Xiaobo, Bossé, Yohan, Manichaikul, Ani, Lahousse, Lies, Silverman, Edwin K., Boezen, H. Marike, Wain, Louise V., Tobin, Martin D., Hobbs, Brian D., Cho, Michael H., Batini, Chiara, Zhao, Jing Hua, Wielscher, Matthias, Weiss, Stefan, Kentistou, Katherine A., Cook, James P., Hui, Jennie, Karrasch, Stefan, Imboden, Medea, Harris, Sarah E., Marten, Jonathan, Enroth, Stefan, Kerr, Shona M., Surakka, Ida, Vitart, Veronique, Lehtimäki, Terho, Ewert, Ralf, Gieger, Christian, Homuth, Georg, Joshi, Peter K., Langenberg, Claudia, Lind, Lars, Luan, Jian’an, Mahajan, Anubha, Murray, Alison, Porteous, David J., Rawal, Rajesh, Smith, Blair H., Timmers, Paul R. H. J., Raitakari, Olli T., Kähönen, Mika, Polasek, Ozren, Gyllensten, Ulf, Rudan, Igor, Deary, Ian J., Probst-Hensch, Nicole M., Schulz, Holger, James, Alan L., Wilson, James F., Stubbe, Beate, Zeggini, Eleftheria, Jarvelin, Marjo-Riitta, Wareham, Nick, Hayward, Caroline, Morris, Andrew P., Agusti, Alvar, Anderson, Wayne, Bakerly, Nawar, Bals, Robert, Barnes, Kathleen C., Bleecker, Eugene R., Bowler, Russell, Brightling, Christopher, de Bruijne, Marleen, Castaldi, Peter J., Celli, Bartolome, Coxson, Harvey O., Crystal, Ron, de Jong, Pim, Dirksen, Asger, Dy, Jennifer, Foreman, Marilyn, Garcia-Aymerich, Judith, Gevenois, Pierre, Ghosh, Soumitra, Gietema, Hester, Hansel, Nadia, Hersh, Craig P., Hoffman, Eric, Kalsheker, Noor, Kauczor, Hans-Ulrich, Laitinen, Tarja, Lambrechts, Diether, Lee, Sang-Do, Litonjua, Augusto A., Loth, Daan W., Lutz, Sharon M., Lynch, David, MacNee, William, McDonald, Merry-Lynn, Newell, John D., Nordestgaard, Borge G., Oh, Yeon-Mok, Paré, Peter D., Pistolesi, Massimo, Postma, Dirkje S., Puhan, Milo, Regan, Elizabeth, Rich, Stephen S., Seo, Joon Beom, Short, Andrea, Stoel, Berend, Sverzellati, Nicola, ter Riet, Gerben, Van Beek, Edwin J. R., van Ginneken, Bram, Vogelmeier, Claus F., Wanner, Adam, Washko, George, Wauters, Els, Wouters, Emiel F. M., Young, Robert P., Zeigler-Heitbrock, Loems, SpiroMeta Consortium, Understanding Society Scientific Group, International COPD Genetics Consortium, Institute for Molecular Medicine Finland, Groningen Research Institute for Asthma and COPD (GRIAC), Life Course Epidemiology (LCE), Beeldvorming, MUMC+: DA BV Medisch Specialisten Radiologie (9), MUMC+: MA Longziekten (3), RS: NUTRIM - R3 - Respiratory & Age-related Health, Pulmonologie, General practice, APH - Aging & Later Life, APH - Personalized Medicine, ACS - Diabetes & metabolism, Epidemiology, Pulmonary Medicine, Medical Informatics, and Radiology & Nuclear Medicine
- Subjects
Male ,Lydia Becker Institute ,Pulmonary Fibrosis ,LD SCORE REGRESSION ,Gene Expression ,Genome-wide association study ,Pulmonary Disease, Chronic Obstructive ,0302 clinical medicine ,Pulmonary fibrosis ,GWAS ,Lung ,GENOME-WIDE ASSOCIATION ,ACIDIC-MAMMALIAN-CHITINASE ,LUNG-FUNCTION ,EXTRACELLULAR-MATRIX ,PREDOMINANT EMPHYSEMA ,CONNECTIVITY MAP ,ATOPIC ASTHMA ,RISK LOCI ,0303 health sciences ,COPD ,education.field_of_study ,Smoking ,1184 Genetics, developmental biology, physiology ,Middle Aged ,3. Good health ,Phenotype ,medicine.anatomical_structure ,Medical genetics ,Female ,Rare cancers Radboud Institute for Health Sciences [Radboudumc 9] ,Adult ,medicine.medical_specialty ,Population ,Biology ,Polymorphism, Single Nucleotide ,Article ,03 medical and health sciences ,All institutes and research themes of the Radboud University Medical Center ,ResearchInstitutes_Networks_Beacons/lydia_becker_institute_of_immunology_and_inflammation ,Genetics ,medicine ,Genetic predisposition ,Humans ,Genetic Predisposition to Disease ,education ,Aged ,030304 developmental biology ,Asthma ,medicine.disease ,respiratory tract diseases ,Genetic Loci ,Case-Control Studies ,Immunology ,3111 Biomedicine ,030217 neurology & neurosurgery ,Genome-Wide Association Study - Abstract
Chronic obstructive pulmonary disease (COPD) is the leading cause of respiratory mortality worldwide. Genetic risk loci provide novel insights into disease pathogenesis. We performed a genome-wide association study in 35,735 cases and 222,076 controls from the UK Biobank and additional studies from the International COPD Genetics Consortium. We identified 82 loci with P-value < 5 × 10−8; 47 were previously described in association with either COPD or population-based lung function. Of the remaining 35 novel loci, 13 were associated with lung function in 79,055 individuals from the SpiroMeta consortium. Using gene expression and regulation data, we identified enrichment for loci in lung tissue, smooth muscle and several lung cell types. We found 14 COPD loci shared with either asthma or pulmonary fibrosis. COPD genetic risk loci clustered into groups of quantitative imaging features and comorbidity associations. Our analyses provide further support to the genetic susceptibility and heterogeneity of COPD., Editorial summary Genome-wide analysis of chronic obstructive pulmonary disease identifies 82 loci, 35 of which are new. Integration of gene expression and genomic annotation data shows enrichment of signals in lung tissue, smooth muscle and several lung cell types.
- Published
- 2019
7. Multiethnic meta-analysis identifies ancestry-specific and cross-ancestry loci for pulmonary function
- Author
-
Wyss, Annah B, Sofer, Tamar, Lee, Mi Kyeong, Terzikhan, Natalie, Nguyen, Jennifer N, Lahousse, Lies, Latourelle, Jeanne C, Smith, Albert Vernon, Bartz, Traci M, Feitosa, Mary F, Gao, Wei, Ahluwalia, Tarunveer S, Tang, Wenbo, Oldmeadow, Christopher, Duan, Qing, de Jong, Kim, Wojczynski, Mary K, Wang, Xin-Qun, Noordam, Raymond, Hartwig, Fernando Pires, Jackson, Victoria E, Wang, Tianyuan, Obeidat, Ma'en, Hobbs, Brian D, Huan, Tianxiao, Gui, Hongsheng, Parker, Margaret M, Hu, Donglei, Mogil, Lauren S, Kichaev, Gleb, Jin, Jianping, Graff, Mariaelisa, Harris, Tamara B, Kalhan, Ravi, Heckbert, Susan R, Paternoster, Lavinia, Burkart, Kristin M, Liu, Yongmei, Holliday, Elizabeth G, Wilson, James G, Vonk, Judith M, Sanders, Jason L, Barr, R Graham, de Mutsert, Renée, Menezes, Ana Maria Baptista, Adams, Hieab HH, van den Berge, Maarten, Joehanes, Roby, Levin, Albert M, Liberto, Jennifer, Launer, Lenore J, Morrison, Alanna C, Sitlani, Colleen M, Celedón, Juan C, Kritchevsky, Stephen B, Scott, Rodney J, Christensen, Kaare, Rotter, Jerome I, Bonten, Tobias N, Wehrmeister, Fernando César, Bossé, Yohan, Xiao, Shujie, Oh, Sam, Franceschini, Nora, Brody, Jennifer A, Kaplan, Robert C, Lohman, Kurt, McEvoy, Mark, Province, Michael A, Rosendaal, Frits R, Taylor, Kent D, Nickle, David C, Williams, L Keoki, Burchard, Esteban G, Wheeler, Heather E, Sin, Don D, Gudnason, Vilmundur, North, Kari E, Fornage, Myriam, Psaty, Bruce M, Myers, Richard H, O'Connor, George, Hansen, Torben, Laurie, Cathy C, Cassano, Patricia A, Sung, Joohon, Kim, Woo Jin, Attia, John R, Lange, Leslie, Boezen, H Marike, Thyagarajan, Bharat, Rich, Stephen S, Mook-Kanamori, Dennis O, Horta, Bernardo Lessa, Uitterlinden, André G, Im, Hae Kyung, Cho, Michael H, Brusselle, Guy G, and Gharib, Sina A
- Subjects
Lung Diseases ,Male ,Chronic Obstructive ,Vital Capacity ,Quantitative Trait Loci ,European Continental Ancestry Group ,Black People ,White People ,Linkage Disequilibrium ,Pulmonary Disease ,Forced Expiratory Volume ,Genetics ,Humans ,Genetic Predisposition to Disease ,Polymorphism ,Lung ,African Continental Ancestry Group ,Asian ,Human Genome ,Smoking ,Hispanic or Latino ,Genomics ,Single Nucleotide ,Asian Americans ,Sample Size ,Regression Analysis ,Female ,Hispanic Americans ,Biotechnology ,Genome-Wide Association Study - Abstract
Nearly 100 loci have been identified for pulmonary function, almost exclusively in studies of European ancestry populations. We extend previous research by meta-analyzing genome-wide association studies of 1000 Genomes imputed variants in relation to pulmonary function in a multiethnic population of 90,715 individuals of European (N = 60,552), African (N = 8429), Asian (N = 9959), and Hispanic/Latino (N = 11,775) ethnicities. We identify over 50 additional loci at genome-wide significance in ancestry-specific or multiethnic meta-analyses. Using recent fine-mapping methods incorporating functional annotation, gene expression, and differences in linkage disequilibrium between ethnicities, we further shed light on potential causal variants and genes at known and newly identified loci. Several of the novel genes encode proteins with predicted or established drug targets, including KCNK2 and CDK12. Our study highlights the utility of multiethnic and integrative genomics approaches to extend existing knowledge of the genetics of lung function and clinical relevance of implicated loci.
- Published
- 2018
8. Genetic loci associated with chronic obstructive pulmonary disease overlap with loci for lung function and pulmonary fibrosis
- Author
-
Hobbs, Brian D, de Jong, Kim, Lamontagne, Maxime, Bossé, Yohan, Shrine, Nick, Artigas, María Soler, Wain, Louise V, Hall, Ian P, Jackson, Victoria E, Wyss, Annah B, London, Stephanie J, North, Kari E, Franceschini, Nora, Strachan, David P, Beaty, Terri H, Hokanson, John E, Crapo, James D, Castaldi, Peter J, Chase, Robert P, Bartz, Traci M, Heckbert, Susan R, Psaty, Bruce M, Gharib, Sina A, Zanen, Pieter, Lammers, Jan W, Oudkerk, Matthijs, Groen, H J, Locantore, Nicholas, Tal-Singer, Ruth, Rennard, Stephen I, Vestbo, Jørgen, Timens, Wim, Paré, Peter D, Latourelle, Jeanne C, Dupuis, Josée, O'Connor, George T, Wilk, Jemma B, Kim, Woo Jin, Lee, Mi Kyeong, Oh, Yeon-Mok, Vonk, Judith M, de Koning, Harry J, Leng, Shuguang, Belinsky, Steven A, Tesfaigzi, Yohannes, Manichaikul, Ani, Wang, Xin-Qun, Rich, Stephen S, Barr, R Graham, Sparrow, David, and COPDGene Investigators
- Subjects
Respiratory tract diseases ,Journal Article ,Genome-wide association studies - Abstract
Chronic obstructive pulmonary disease (COPD) is a leading cause of mortality worldwide. We performed a genetic association study in 15,256 cases and 47,936 controls, with replication of select top results (P < 5 × 10(-6)) in 9,498 cases and 9,748 controls. In the combined meta-analysis, we identified 22 loci associated at genome-wide significance, including 13 new associations with COPD. Nine of these 13 loci have been associated with lung function in general population samples, while 4 (EEFSEC, DSP, MTCL1, and SFTPD) are new. We noted two loci shared with pulmonary fibrosis (FAM13A and DSP) but that had opposite risk alleles for COPD. None of our loci overlapped with genome-wide associations for asthma, although one locus has been implicated in joint susceptibility to asthma and obesity. We also identified genetic correlation between COPD and asthma. Our findings highlight new loci associated with COPD, demonstrate the importance of specific loci associated with lung function to COPD, and identify potential regions of genetic overlap between COPD and other respiratory diseases.
- Published
- 2017
9. Genome-wide association analysis identifies six new loci associated with forced vital capacity
- Author
-
Loth, Daan W., Gharib, Sina A., Wain, Louise V., Franceschini, Nora, Koch, Beate, Pottinger, Tess D., Smith, Albert Vernon, Duan, Qing, Oldmeadow, Chris, Lee, Mi Kyeong, Strachan, David P., James, Alan L., Huffman, Jennifer E., Vitart, Veronique, Ramasamy, Adaikalavan, Wareham, Nicholas J., Kaprio, Jaakko, Wang, Xin-Qun, Trochet, Holly, Flexeder, Claudia, Albrecht, Eva, Lopez, Lorna M., de Jong, Kim, Thyagarajan, Bharat, Alves, Alexessander Couto, Enroth, Stefan, Omenaas, Ernst, Joshi, Peter K., Fall, Tove, Launer, Lenore J., Loehr, Laura R., Fornage, Myriam, Li, Guo, Wilk, Jemma B., Tang, Wenbo, Manichaikul, Ani, Lahousse, Lies, Harris, Tamara B., North, Kari E., Rudnicka, Alicja R., Hui, Jennie, Gu, Xiangjun, Lumley, Thomas, Wright, Alan F., Hastie, Nicholas D., Campbell, Susan, Kumar, Rajesh, Pin, Isabelle, Scott, Robert A., Surakka, Ida, Liu, Yongmei, Holliday, Elizabeth G., Schulz, Holger, Heinrich, Joachim, Davies, Gail, Vonk, Judith M., Wojczynski, Mary, Pouta, Anneli, Wild, Sarah H., Ingelsson, Erik, Rivadeneira, Fernando, Hysi, Pirro G., Eiriksdottir, Gudny, Morrison, Alanna C., Rotter, Jerome I., Gao, Wei, Postma, Dirkje S., White, Wendy B., Rich, Stephen S., Hofman, Albert, Aspelund, Thor, Couper, David, Smith, Lewis J., Psaty, Bruce M., Lohman, Kurt, Burchard, Esteban G., Garcia, Melissa, Joubert, Bonnie R., McArdle, Wendy L., Musk, A Bill, Hansel, Nadia, Heckbert, Susan R., Zgaga, Lina, van Meurs, Joyce B.J., Navarro, Pau, Rudan, Igor, Oh, Yeon-Mok, Redline, Susan, Jarvis, Deborah L., Zhao, Jing Hua, Rantanen, Taina, O'Connor, George T., Ripatti, Samuli, Scott, Rodney J., Karrasch, Stefan, Grallert, Harald, Gaddis, Nathan C., Starr, John M., Wijmenga, Cisca, Minster, Ryan L., Lederer, David J., Pekkanen, Juha, Gyllensten, Ulf, Campbell, Harry, Morris, Andrew P., Hammond, Christopher J., Burkart, Kristin M, Beilby, John, Kritchevsky, Stephen B., Gudnason, Vilmundur, Hancock, Dana B., Williams, O Dale, Polasek, Ozren, Zemunik, Tatijana, Kolcic, Ivana, Petrini, Marcy F., Wjst, Matthias, Kim, Woo Jin, Porteous, David J., Smith, Blair H., Viljanen, Anne, Attia, John R., Sayers, Ian, Hampel, Regina, Gieger, Christian, Deary, Ian J, Boezen, H. Marike, Newman, Anne, Jarvelin, Marjo-Riitta, Wilson, James F, Lind, Lars, Stricker, Bruno H., Teumer, Alexander, Spector, Timothy D., Peters, Marjolein J., Lange, Leslie A., Barr, R. Graham, Bracke, Ken R., Verhamme, Fien M., Sung, Joohon, Hiemstra, Pieter S., Cassano, Patricia A., Sood, Akshay, Hayward, Caroline, Hall, Ian P., Brusselle, Guy G., Tobin, Martin D., and London, Stephanie J.
- Subjects
respiratory system ,Genetics research, Genome-wide association studies, Population genetics, Respiratory tract diseases ,respiratory tract diseases - Abstract
Forced vital capacity (FVC), a spirometric measure of pulmonary function, reflects lung volume and is used to diagnose and monitor lung diseases. We performed genome-wide association study meta-analysis of FVC in 52,253 individuals from 26 studies and followed up the top associations in 32,917 additional individuals of European ancestry. We found six new regions associated at genome-wide significance (P < 5 × 10-8) with FVC in or near EFEMP1, BMP6, MIR129-2-HSD17B12, PRDM11, WWOX and KCNJ2. Two loci previously associated with spirometric measures (GSTCD and PTCH1) were related to FVC. Newly implicated regions were followed up in samples from African-American, Korean, Chinese and Hispanic individuals. We detected transcripts for all six newly implicated genes in human lung tissue. The new loci may inform mechanisms involved in lung development and the pathogenesis of restrictive lung disease.© 2014 Nature America, Inc. All rights reserved.
- Published
- 2014
10. Genome-wide association analysis identifies six new loci associated with forced vital capacity
- Author
-
Loth, Daan W, Artigas, María Soler, Gharib, Sina A, Wain, Louise V, Franceschini, Nora, Koch, Beate, Pottinger, Tess D, Smith, Albert Vernon, Duan, Qing, Oldmeadow, Chris, Lee, Mi Kyeong, Strachan, David P, James, Alan L, Huffman, Jennifer E, Vitart, Veronique, Ramasamy, Adaikalavan, Wareham, Nicholas J, Kaprio, Jaakko, Wang, Xin-Qun, Trochet, Holly, Kähönen, Mika, Flexeder, Claudia, Albrecht, Eva, Lopez, Lorna M, Jong, Kim de, and Rantanen, Taina
- Subjects
idiopathic pulmonary-fibrosis ,lung-function, gene-expression ,respiratory system ,respiratory tract diseases - Abstract
Forced vital capacity (FVC), a spirometric measure of pulmonary function, reflects lung volume and is used to diagnose and monitor lung diseases. We performed genome-wide association study meta-analysis of FVC in 52,253 individuals from 26 studies and followed up the top associations in 32,917 additional individuals of European ancestry. We found six new regions associated at genome-wide significance (P < 5 × 10−8) with FVC in or near EFEMP1, BMP6, MIR129-2–HSD17B12, PRDM11, WWOX and KCNJ2. Two loci previously associated with spirometric measures (GSTCD and PTCH1) were related to FVC. Newly implicated regions were followed up in samples from African-American, Korean, Chinese and Hispanic individuals. We detected transcripts for all six newly implicated genes in human lung tissue. The new loci may inform mechanisms involved in lung development and the pathogenesis of restrictive lung disease. peerReviewed
- Published
- 2014
11. Additional file 1: of Genome-wide DNA methylation and long-term ambient air pollution exposure in Korean adults
- Author
-
Lee, Mi Kyeong, Xu, Cheng-Jian, Carnes, Megan, Nichols, Cody, Ward, James, Kwon, Sung Ok, Kim, Sun-Young, Kim, Woo Jin, and London, Stephanie
- Subjects
13. Climate action - Abstract
Figure S1. Workflow of the epigenome-wide association study of long-term ambient air pollution exposure. Figure S2. Manhattan and quantile-quantile plots. Figure S3. Regional visualization of the association of air pollution exposure (PM10 and NO2) with blood DNA methylation. Figure S4. Visualization of pathway analysis results. Figure S5. Tissue- and cell-type specific enrichment pattern in CpGs significantly associated (FDR
12. Additional file 2 of Epigenome-wide association study of kidney function identifies trans-ethnic and ethnic-specific loci
- Author
-
Breeze, Charles E., Batorsky, Anna, Lee, Mi Kyeong, Szeto, Mindy D., Xiaoguang Xu, McCartney, Daniel L., Jiang, Rong, Patki, Amit, Kramer, Holly J., Eales, James M., Raffield, Laura, Lange, Leslie, Lange, Ethan, Durda, Peter, Yongmei Liu, Tracy, Russ P., Van Den Berg, David, Evans, Kathryn L., Kraus, William E., Svati Shah, Hermant K. Tiwari, Lifang Hou, Whitsel, Eric A., Jiang, Xiao, Charchar, Fadi J., Baccarelli, Andrea A., Rich, Stephen S., Morris, Andrew P., Irvin, Marguerite R., Arnett, Donna K., Hauser, Elizabeth R., Rotter, Jerome I., Correa, Adolfo, Hayward, Caroline, Horvath, Steve, Marioni, Riccardo E., Tomaszewski, Maciej, Beck, Stephan, Berndt, Sonja I., London, Stephanie J., Josyf C. Mychaleckyj, and Franceschini, Nora
- Subjects
10. No inequality - Abstract
Additional file 2: Supplementary Methods. Description of different constituent cohorts and studies, in addition to power analyses.
13. Additional file 2 of Epigenome-wide association study of kidney function identifies trans-ethnic and ethnic-specific loci
- Author
-
Breeze, Charles E., Batorsky, Anna, Lee, Mi Kyeong, Szeto, Mindy D., Xiaoguang Xu, McCartney, Daniel L., Jiang, Rong, Patki, Amit, Kramer, Holly J., Eales, James M., Raffield, Laura, Lange, Leslie, Lange, Ethan, Durda, Peter, Yongmei Liu, Tracy, Russ P., Van Den Berg, David, Evans, Kathryn L., Kraus, William E., Svati Shah, Hermant K. Tiwari, Lifang Hou, Whitsel, Eric A., Jiang, Xiao, Charchar, Fadi J., Baccarelli, Andrea A., Rich, Stephen S., Morris, Andrew P., Irvin, Marguerite R., Arnett, Donna K., Hauser, Elizabeth R., Rotter, Jerome I., Correa, Adolfo, Hayward, Caroline, Horvath, Steve, Marioni, Riccardo E., Tomaszewski, Maciej, Beck, Stephan, Berndt, Sonja I., London, Stephanie J., Josyf C. Mychaleckyj, and Franceschini, Nora
- Subjects
10. No inequality - Abstract
Additional file 2: Supplementary Methods. Description of different constituent cohorts and studies, in addition to power analyses.
14. Genetic loci associated with chronic obstructive pulmonary disease overlap with loci for lung function and pulmonary fibrosis
- Author
-
Hobbs, Brian D., de Jong, Kim, Lamontagne, Maxime, Shrine, Nick, Wain, Louise V., Hall, Ian P., Jackson, Victoria E., Wyss, Annah B., London, Stephanie J., North, Kari E., Franceschini, Nora, Strachan, David P., Beaty, Terri H., Hokanson, John E., Crapo, James D., Castaldi, Peter J., Chase, Robert P., Bartz, Traci M., Heckbert, Susan R., Psaty, Bruce M., Gharib, Sina A., Zanen, Pieter, Lammers, Jan W., Oudkerk, Matthijs, Groen, H.J., Locantore, Nicholas, Tal-Singer, Ruth, Rennard, Stephen I., Timens, Wim, Latourelle, Jeanne C., O'Connor, George T., Wilk, Jemma B., Kim, Woo Jin, Lee, Mi Kyeong, Oh, Yeon-Mok, Vonk, Judith M., de Koning, Harry J., Leng, Shuguang, Belinsky, Steven A., Tesfaigzi, Yohannes, Manichaikul, Ani, Wang, Xin-Qun, Rich, Stephen S., Barr, R. Graham, Sparrow, David, Litonjua, Augusto A., Bakke, Per, Gulsvik, Amund, Lahousse, Lies, Brusselle, Guy G., Stricker, Bruno H., Ampleford, Elizabeth J., Bleecker, Eugene R., Woodruff, Prescott G., Meyers, Deborah A., Qiao, Dandi, Lomas, David A., Yim, Jae-Joon, Kim, Deog Kyeom, Hawrylkiewicz, Iwona, Sliwinski, Pawel, Hardin, Megan, Fingerlin, Tasha E., Schwartz, David A., Postma, Dirkje S., MacNee, William, Tobin, Martin D., Silverman, Edwin K., Boezen, H. Marike, and Cho, Michael H.
- Subjects
respiratory tract diseases - Abstract
Chronic obstructive pulmonary disease (COPD) is a leading cause of mortality worldwide. We performed a genetic association study in 15,256 cases and 47,936 controls, with replication of select top results (P < 5 × 10(-6)) in 9,498 cases and 9,748 controls. In the combined meta-analysis, we identified 22 loci associated at genome-wide significance, including 13 new associations with COPD. Nine of these 13 loci have been associated with lung function in general population samples, while 4 (EEFSEC, DSP, MTCL1, and SFTPD) are new. We noted two loci shared with pulmonary fibrosis (FAM13A and DSP) but that had opposite risk alleles for COPD. None of our loci overlapped with genome-wide associations for asthma, although one locus has been implicated in joint susceptibility to asthma and obesity. We also identified genetic correlation between COPD and asthma. Our findings highlight new loci associated with COPD, demonstrate the importance of specific loci associated with lung function to COPD, and identify potential regions of genetic overlap between COPD and other respiratory diseases.
15. Genetic landscape of chronic obstructive pulmonary disease identifies heterogeneous cell-type and phenotype associations
- Author
-
Sakornsakolpat, Phuwanat, Prokopenko, Dmitry, Lamontagne, Maxime, Reeve, Nicola F, Guyatt, Anna L, Jackson, Victoria E, Shrine, Nick, Qiao, Dandi, Bartz, Traci M, Kim, Deog Kyeom, Lee, Mi Kyeong, Latourelle, Jeanne C, Li, Xingnan, Morrow, Jarrett D, Obeidat, Ma'en, Wyss, Annah B, Bakke, Per, Barr, R Graham, Beaty, Terri H, Belinsky, Steven A, Brusselle, Guy G, Crapo, James D, De Jong, Kim, DeMeo, Dawn L, Fingerlin, Tasha E, Gharib, Sina A, Gulsvik, Amund, Hall, Ian P, Hokanson, John E, Kim, Woo Jin, Lomas, David A, London, Stephanie J, Meyers, Deborah A, O'Connor, George T, Rennard, Stephen I, Schwartz, David A, Sliwinski, Pawel, Sparrow, David, Strachan, David P, Tal-Singer, Ruth, Tesfaigzi, Yohannes, Vestbo, Jørgen, Vonk, Judith M, Yim, Jae-Joon, Zhou, Xiaobo, Bossé, Yohan, Manichaikul, Ani, Lahousse, Lies, Silverman, Edwin K, Boezen, H Marike, Wain, Louise V, Tobin, Martin D, Hobbs, Brian D, Cho, Michael H, SpiroMeta Consortium, and International COPD Genetics Consortium
- Subjects
Adult ,Male ,Pulmonary Fibrosis ,Smoking ,Gene Expression ,Middle Aged ,Polymorphism, Single Nucleotide ,Asthma ,respiratory tract diseases ,3. Good health ,Pulmonary Disease, Chronic Obstructive ,Phenotype ,Genetic Loci ,Case-Control Studies ,Humans ,Female ,Genetic Predisposition to Disease ,Lung ,Aged ,Genome-Wide Association Study - Abstract
Chronic obstructive pulmonary disease (COPD) is the leading cause of respiratory mortality worldwide. Genetic risk loci provide new insights into disease pathogenesis. We performed a genome-wide association study in 35,735 cases and 222,076 controls from the UK Biobank and additional studies from the International COPD Genetics Consortium. We identified 82 loci associated with P < 5 × 10-8; 47 of these were previously described in association with either COPD or population-based measures of lung function. Of the remaining 35 new loci, 13 were associated with lung function in 79,055 individuals from the SpiroMeta consortium. Using gene expression and regulation data, we identified functional enrichment of COPD risk loci in lung tissue, smooth muscle, and several lung cell types. We found 14 COPD loci shared with either asthma or pulmonary fibrosis. COPD genetic risk loci clustered into groups based on associations with quantitative imaging features and comorbidities. Our analyses provide further support for the genetic susceptibility and heterogeneity of COPD.
16. Additional file 1: of Genome-wide DNA methylation and long-term ambient air pollution exposure in Korean adults
- Author
-
Lee, Mi Kyeong, Xu, Cheng-Jian, Carnes, Megan, Nichols, Cody, Ward, James, Kwon, Sung Ok, Kim, Sun-Young, Kim, Woo Jin, and London, Stephanie
- Subjects
13. Climate action - Abstract
Figure S1. Workflow of the epigenome-wide association study of long-term ambient air pollution exposure. Figure S2. Manhattan and quantile-quantile plots. Figure S3. Regional visualization of the association of air pollution exposure (PM10 and NO2) with blood DNA methylation. Figure S4. Visualization of pathway analysis results. Figure S5. Tissue- and cell-type specific enrichment pattern in CpGs significantly associated (FDR
Catalog
Books, media, physical & digital resources
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.