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291 results on '"Croteau-Chonka, Damien"'

1. Proteomic signatures improve risk prediction for common and rare diseases

Author

Carrasco-Zanini, Julia, Pietzner, Maik, Davitte, Jonathan, Surendran, Praveen, Croteau-Chonka, Damien C., Robins, Chloe, Torralbo, Ana, Tomlinson, Christopher, Grünschläger, Florian, Fitzpatrick, Natalie, Ytsma, Cai, Kanno, Tokuwa, Gade, Stephan, Freitag, Daniel, Ziebell, Frederik, Haas, Simon, Denaxas, Spiros, Betts, Joanna C., Wareham, Nicholas J., Hemingway, Harry, Scott, Robert A., and Langenberg, Claudia

Published
2024
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3. Expression of SMARCD1 interacts with age in association with asthma control on inhaled corticosteroid therapy

Author

McGeachie, Michael J, Sordillo, Joanne E, Dahlin, Amber, Wang, Alberta L, Lutz, Sharon M, Tantisira, Kelan G, Panganiban, Ronald, Lu, Quan, Sajuthi, Satria, Urbanek, Cydney, Kelly, Rachel, Saef, Benjamin, Eng, Celeste, Oh, Sam S, Kho, Alvin T, Croteau-Chonka, Damien C, Weiss, Scott T, Raby, Benjamin A, Mak, Angel CY, Rodriguez-Santana, Jose R, Burchard, Esteban G, Seibold, Max A, and Wu, Ann Chen

Subjects
Biomedical and Clinical Sciences, Cardiovascular Medicine and Haematology, Clinical Sciences, Asthma, Biotechnology, Genetics, Clinical Research, Human Genome, Lung, Aetiology, 2.1 Biological and endogenous factors, Respiratory, Administration, Inhalation, Adolescent, Adrenal Cortex Hormones, Adult, Age Factors, Child, Chromosomal Proteins, Non-Histone, Cohort Studies, Female, Gene Expression, Hispanic or Latino, Humans, Male, Middle Aged, Treatment Outcome, Young Adult, Cardiorespiratory Medicine and Haematology, Respiratory System, Cardiovascular medicine and haematology, Clinical sciences
Abstract

BackgroundGlobal gene expression levels are known to be highly dependent upon gross demographic features including age, yet identification of age-related genomic indicators has yet to be comprehensively undertaken in a disease and treatment-specific context.MethodsWe used gene expression data from CD4+ lymphocytes in the Asthma BioRepository for Integrative Genomic Exploration (Asthma BRIDGE), an open-access collection of subjects participating in genetic studies of asthma with available gene expression data. Replication population participants were Puerto Rico islanders recruited as part of the ongoing Genes environments & Admixture in Latino Americans (GALA II), who provided nasal brushings for transcript sequencing. The main outcome measure was chronic asthma control as derived by questionnaires. Genomic associations were performed using regression of chronic asthma control score on gene expression with age in years as a covariate, including a multiplicative interaction term for gene expression times age.ResultsThe SMARCD1 gene (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1) interacted with age to influence chronic asthma control on inhaled corticosteroids, with a doubling of expression leading to an increase of 1.3 units of chronic asthma control per year (95% CI [0.86, 1.74], p = 6 × 10- 9), suggesting worsening asthma control with increasing age. This result replicated in GALA II (p = 3.8 × 10- 8). Cellular assays confirmed the role of SMARCD1 in glucocorticoid response in airway epithelial cells.ConclusionFocusing on age-dependent factors may help identify novel indicators of asthma medication response. Age appears to modulate the effect of SMARCD1 on asthma control with inhaled corticosteroids.

Published
2020

5. Stress and Bronchodilator Response in Children with Asthma

Author

Brehm, John M, Ramratnam, Sima K, Tse, Sze Man, Croteau-Chonka, Damien C, Pino-Yanes, Maria, Rosas-Salazar, Christian, Litonjua, Augusto A, Raby, Benjamin A, Boutaoui, Nadia, Han, Yueh-Ying, Chen, Wei, Forno, Erick, Marsland, Anna L, Nugent, Nicole R, Eng, Celeste, Colón-Semidey, Angel, Alvarez, María, Acosta-Pérez, Edna, Spear, Melissa L, Martinez, Fernando D, Avila, Lydiana, Weiss, Scott T, Soto-Quiros, Manuel, Ober, Carole, Nicolae, Dan L, Barnes, Kathleen C, Lemanske, Robert F, Strunk, Robert C, Liu, Andrew, London, Stephanie J, Gilliland, Frank, Sleiman, Patrick, March, Michael, Hakonarson, Hakon, Duan, Qing Ling, Kolls, Jay K, Fritz, Gregory K, Hu, Donglei, Fani, Negar, Stevens, Jennifer S, Almli, Lynn M, Burchard, Esteban G, Shin, Jaemin, McQuaid, Elizabeth L, Ressler, Kerry, Canino, Glorisa, and Celedón, Juan C

Subjects
Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, Pediatric, Asthma, Behavioral and Social Science, Clinical Research, Mental Health, Lung, Genetics, Aetiology, 2.3 Psychological, social and economic factors, Respiratory, Good Health and Well Being, Adolescent, Anxiety, Bronchodilator Agents, Case-Control Studies, Child, Cross-Sectional Studies, Down-Regulation, Female, Genetic Markers, Genotype, Humans, Linear Models, Male, Multivariate Analysis, Polymorphism, Single Nucleotide, Puerto Rico, Receptors, Adrenergic, beta-2, Receptors, Pituitary Adenylate Cyclase-Activating Polypeptide, Type I, Rhode Island, Risk Factors, Stress, Psychological, Treatment Outcome, asthma, Puerto Ricans, bronchodilator response, stress, Medical and Health Sciences, Respiratory System, Cardiovascular medicine and haematology, Clinical sciences
Abstract

RationaleStress is associated with asthma morbidity in Puerto Ricans (PRs), who have reduced bronchodilator response (BDR).ObjectivesTo examine whether stress and/or a gene regulating anxiety (ADCYAP1R1) is associated with BDR in PR and non-PR children with asthma.MethodsThis was a cross-sectional study of stress and BDR (percent change in FEV1 after BD) in 234 PRs ages 9-14 years with asthma. We assessed child stress using the Checklist of Children's Distress Symptoms, and maternal stress using the Perceived Stress Scale. Replication analyses were conducted in two cohorts. Polymorphisms in ADCYAP1R1 were genotyped in our study and six replication studies. Multivariable models of stress and BDR were adjusted for age, sex, income, environmental tobacco smoke, and use of inhaled corticosteroids.Measurements and main resultsHigh child stress was associated with reduced BDR in three cohorts. PR children who were highly stressed (upper quartile, Checklist of Children's Distress Symptoms) and whose mothers had high stress (upper quartile, Perceived Stress Scale) had a BDR that was 10.2% (95% confidence interval, 6.1-14.2%) lower than children who had neither high stress nor a highly stressed mother. A polymorphism in ADCYAP1R1 (rs34548976) was associated with reduced BDR. This single-nucleotide polymorphism is associated with reduced expression of the gene for the β2-adrenergic receptor (ADRB2) in CD4(+) lymphocytes of subjects with asthma, and it affects brain connectivity of the amygdala and the insula (a biomarker of anxiety).ConclusionsHigh child stress and an ADCYAP1R1 single-nucleotide polymorphism are associated with reduced BDR in children with asthma. This is likely caused by down-regulation of ADRB2 in highly stressed children.

Published
2015

6. New genetic loci link adipose and insulin biology to body fat distribution

Author

Shungin, Dmitry, Winkler, Thomas W, Croteau-Chonka, Damien C, Ferreira, Teresa, Locke, Adam E, Mägi, Reedik, Strawbridge, Rona J, Pers, Tune H, Fischer, Krista, Justice, Anne E, Workalemahu, Tsegaselassie, Wu, Joseph MW, Buchkovich, Martin L, Heard-Costa, Nancy L, Roman, Tamara S, Drong, Alexander W, Song, Ci, Gustafsson, Stefan, Day, Felix R, Esko, Tonu, Fall, Tove, Kutalik, Zoltán, Luan, Jian’an, Randall, Joshua C, Scherag, André, Vedantam, Sailaja, Wood, Andrew R, Chen, Jin, Fehrmann, Rudolf, Karjalainen, Juha, Kahali, Bratati, Liu, Ching-Ti, Schmidt, Ellen M, Absher, Devin, Amin, Najaf, Anderson, Denise, Beekman, Marian, Bragg-Gresham, Jennifer L, Buyske, Steven, Demirkan, Ayse, Ehret, Georg B, Feitosa, Mary F, Goel, Anuj, Jackson, Anne U, Johnson, Toby, Kleber, Marcus E, Kristiansson, Kati, Mangino, Massimo, Mateo Leach, Irene, Medina-Gomez, Carolina, Palmer, Cameron D, Pasko, Dorota, Pechlivanis, Sonali, Peters, Marjolein J, Prokopenko, Inga, Stančáková, Alena, Ju Sung, Yun, Tanaka, Toshiko, Teumer, Alexander, Van Vliet-Ostaptchouk, Jana V, Yengo, Loïc, Zhang, Weihua, Albrecht, Eva, Ärnlöv, Johan, Arscott, Gillian M, Bandinelli, Stefania, Barrett, Amy, Bellis, Claire, Bennett, Amanda J, Berne, Christian, Blüher, Matthias, Böhringer, Stefan, Bonnet, Fabrice, Böttcher, Yvonne, Bruinenberg, Marcel, Carba, Delia B, Caspersen, Ida H, Clarke, Robert, Warwick Daw, E, Deelen, Joris, Deelman, Ewa, Delgado, Graciela, Doney, Alex SF, Eklund, Niina, Erdos, Michael R, Estrada, Karol, Eury, Elodie, Friedrich, Nele, Garcia, Melissa E, Giedraitis, Vilmantas, Gigante, Bruna, Go, Alan S, Golay, Alain, Grallert, Harald, Grammer, Tanja B, Gräßler, Jürgen, Grewal, Jagvir, Groves, Christopher J, Haller, Toomas, and Hallmans, Goran

Subjects
Genetics, Human Genome, Diabetes, Obesity, Nutrition, 2.1 Biological and endogenous factors, Aetiology, Metabolic and endocrine, Cardiovascular, Stroke, Adipocytes, Adipogenesis, Adipose Tissue, Age Factors, Body Fat Distribution, Body Mass Index, Epigenesis, Genetic, Europe, Female, Genome, Human, Genome-Wide Association Study, Humans, Insulin, Insulin Resistance, Male, Models, Biological, Neovascularization, Physiologic, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Racial Groups, Sex Characteristics, Transcription, Genetic, Waist-Hip Ratio, ADIPOGen Consortium, CARDIOGRAMplusC4D Consortium, CKDGen Consortium, GEFOS Consortium, GENIE Consortium, GLGC, ICBP, International Endogene Consortium, LifeLines Cohort Study, MAGIC Investigators, MuTHER Consortium, PAGE Consortium, ReproGen Consortium, General Science & Technology
Abstract

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P

Published
2015

7. Genetic studies of body mass index yield new insights for obesity biology

Author

Locke, Adam E, Kahali, Bratati, Berndt, Sonja I, Justice, Anne E, Pers, Tune H, Day, Felix R, Powell, Corey, Vedantam, Sailaja, Buchkovich, Martin L, Yang, Jian, Croteau-Chonka, Damien C, Esko, Tonu, Fall, Tove, Ferreira, Teresa, Gustafsson, Stefan, Kutalik, Zoltán, Luan, Jian’an, Mägi, Reedik, Randall, Joshua C, Winkler, Thomas W, Wood, Andrew R, Workalemahu, Tsegaselassie, Faul, Jessica D, Smith, Jennifer A, Hua Zhao, Jing, Zhao, Wei, Chen, Jin, Fehrmann, Rudolf, Hedman, Åsa K, Karjalainen, Juha, Schmidt, Ellen M, Absher, Devin, Amin, Najaf, Anderson, Denise, Beekman, Marian, Bolton, Jennifer L, Bragg-Gresham, Jennifer L, Buyske, Steven, Demirkan, Ayse, Deng, Guohong, Ehret, Georg B, Feenstra, Bjarke, Feitosa, Mary F, Fischer, Krista, Goel, Anuj, Gong, Jian, Jackson, Anne U, Kanoni, Stavroula, Kleber, Marcus E, Kristiansson, Kati, Lim, Unhee, Lotay, Vaneet, Mangino, Massimo, Mateo Leach, Irene, Medina-Gomez, Carolina, Medland, Sarah E, Nalls, Michael A, Palmer, Cameron D, Pasko, Dorota, Pechlivanis, Sonali, Peters, Marjolein J, Prokopenko, Inga, Shungin, Dmitry, Stančáková, Alena, Strawbridge, Rona J, Ju Sung, Yun, Tanaka, Toshiko, Teumer, Alexander, Trompet, Stella, van der Laan, Sander W, van Setten, Jessica, Van Vliet-Ostaptchouk, Jana V, Wang, Zhaoming, Yengo, Loïc, Zhang, Weihua, Isaacs, Aaron, Albrecht, Eva, Ärnlöv, Johan, Arscott, Gillian M, Attwood, Antony P, Bandinelli, Stefania, Barrett, Amy, Bas, Isabelita N, Bellis, Claire, Bennett, Amanda J, Berne, Christian, Blagieva, Roza, Blüher, Matthias, Böhringer, Stefan, Bonnycastle, Lori L, Böttcher, Yvonne, Boyd, Heather A, Bruinenberg, Marcel, Caspersen, Ida H, Ida Chen, Yii-Der, Clarke, Robert, Warwick Daw, E, de Craen, Anton JM, Delgado, Graciela, and Dimitriou, Maria

Subjects
Epidemiology, Biological Sciences, Health Sciences, Genetics, Human Genome, Nutrition, Obesity, Prevention, Aetiology, 2.1 Biological and endogenous factors, Stroke, Cardiovascular, Metabolic and endocrine, Oral and gastrointestinal, Cancer, Adipogenesis, Adiposity, Age Factors, Body Mass Index, Energy Metabolism, Europe, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Glutamic Acid, Humans, Insulin, Insulin Secretion, Male, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Racial Groups, Synapses, LifeLines Cohort Study, ADIPOGen Consortium, AGEN-BMI Working Group, CARDIOGRAMplusC4D Consortium, CKDGen Consortium, GLGC, ICBP, MAGIC Investigators, MuTHER Consortium, MIGen Consortium, PAGE Consortium, ReproGen Consortium, GENIE Consortium, International Endogene Consortium, General Science & Technology
Abstract

Obesity is heritable and predisposes to many diseases. To understand the genetic basis of obesity better, here we conduct a genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals. This analysis identifies 97 BMI-associated loci (P 20% of BMI variation. Pathway analyses provide strong support for a role of the central nervous system in obesity susceptibility and implicate new genes and pathways, including those related to synaptic function, glutamate signalling, insulin secretion/action, energy metabolism, lipid biology and adipogenesis.

Published
2015

8. Defining the role of common variation in the genomic and biological architecture of adult human height

Author

Wood, Andrew R, Esko, Tonu, Yang, Jian, Vedantam, Sailaja, Pers, Tune H, Gustafsson, Stefan, Chu, Audrey Y, Estrada, Karol, Luan, Jian'an, Kutalik, Zoltán, Amin, Najaf, Buchkovich, Martin L, Croteau-Chonka, Damien C, Day, Felix R, Duan, Yanan, Fall, Tove, Fehrmann, Rudolf, Ferreira, Teresa, Jackson, Anne U, Karjalainen, Juha, Lo, Ken Sin, Locke, Adam E, Mägi, Reedik, Mihailov, Evelin, Porcu, Eleonora, Randall, Joshua C, Scherag, André, Vinkhuyzen, Anna AE, Westra, Harm-Jan, Winkler, Thomas W, Workalemahu, Tsegaselassie, Zhao, Jing Hua, Absher, Devin, Albrecht, Eva, Anderson, Denise, Baron, Jeffrey, Beekman, Marian, Demirkan, Ayse, Ehret, Georg B, Feenstra, Bjarke, Feitosa, Mary F, Fischer, Krista, Fraser, Ross M, Goel, Anuj, Gong, Jian, Justice, Anne E, Kanoni, Stavroula, Kleber, Marcus E, Kristiansson, Kati, Lim, Unhee, Lotay, Vaneet, Lui, Julian C, Mangino, Massimo, Leach, Irene Mateo, Medina-Gomez, Carolina, Nalls, Michael A, Nyholt, Dale R, Palmer, Cameron D, Pasko, Dorota, Pechlivanis, Sonali, Prokopenko, Inga, Ried, Janina S, Ripke, Stephan, Shungin, Dmitry, Stancáková, Alena, Strawbridge, Rona J, Sung, Yun Ju, Tanaka, Toshiko, Teumer, Alexander, Trompet, Stella, van der Laan, Sander W, van Setten, Jessica, Van Vliet-Ostaptchouk, Jana V, Wang, Zhaoming, Yengo, Loïc, Zhang, Weihua, Afzal, Uzma, Ärnlöv, Johan, Arscott, Gillian M, Bandinelli, Stefania, Barrett, Amy, Bellis, Claire, Bennett, Amanda J, Berne, Christian, Blüher, Matthias, Bolton, Jennifer L, Böttcher, Yvonne, Boyd, Heather A, Bruinenberg, Marcel, Buckley, Brendan M, Buyske, Steven, Caspersen, Ida H, Chines, Peter S, Clarke, Robert, Claudi-Boehm, Simone, Cooper, Matthew, Daw, E Warwick, De Jong, Pim A, Deelen, Joris, and Delgado, Graciela

Subjects
Biological Sciences, Genetics, Biotechnology, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Adult, Analysis of Variance, Body Height, Genetic Variation, Genetics, Population, Genome-Wide Association Study, Humans, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, White People, Electronic Medical Records and Genomics (eMEMERGEGE) Consortium, MIGen Consortium, PAGEGE Consortium, LifeLines Cohort Study, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Using genome-wide data from 253,288 individuals, we identified 697 variants at genome-wide significance that together explained one-fifth of the heritability for adult height. By testing different numbers of variants in independent studies, we show that the most strongly associated ∼2,000, ∼3,700 and ∼9,500 SNPs explained ∼21%, ∼24% and ∼29% of phenotypic variance. Furthermore, all common variants together captured 60% of heritability. The 697 variants clustered in 423 loci were enriched for genes, pathways and tissue types known to be involved in growth and together implicated genes and pathways not highlighted in earlier efforts, such as signaling by fibroblast growth factors, WNT/β-catenin and chondroitin sulfate-related genes. We identified several genes and pathways not previously connected with human skeletal growth, including mTOR, osteoglycin and binding of hyaluronic acid. Our results indicate a genetic architecture for human height that is characterized by a very large but finite number (thousands) of causal variants.

Published
2014

9. Genome-wide interaction studies reveal sex-specific asthma risk alleles

Author

Myers, Rachel A, Scott, Nicole M, Gauderman, W James, Qiu, Weiliang, Mathias, Rasika A, Romieu, Isabelle, Levin, Albert M, Pino-Yanes, Maria, Graves, Penelope E, Villarreal, Albino Barraza, Beaty, Terri H, Carey, Vincent J, Croteau-Chonka, Damien C, del Rio Navarro, Blanca, Edlund, Christopher, Hernandez-Cadena, Leticia, Navarro-Olivos, Efrain, Padhukasahasram, Badri, Salam, Muhammad T, Torgerson, Dara G, Van den Berg, David J, Vora, Hita, Bleecker, Eugene R, Meyers, Deborah A, Williams, L Keoki, Martinez, Fernando D, Burchard, Esteban G, Barnes, Kathleen C, Gilliland, Frank D, Weiss, Scott T, London, Stephanie J, Raby, Benjamin A, Ober, Carole, Nicolae, Dan L, Santana, Jose Rodriguez, Cintron, William Rodriguez, Chapela, Rocio, Ford, Jean, Thyne, Shannon, Avila, Pedro C, Monge, Juan Jose Sienra, Boorgula, Meher, Cheadle, Chris, Eng, Celeste S, Kiley, J, Banks-Schlegel, S, and Gan, W

Subjects
Biological Sciences, Genetics, Clinical Research, Human Genome, Lung, Prevention, Asthma, Aetiology, 2.1 Biological and endogenous factors, Inflammatory and immune system, Respiratory, Alleles, Chromosome Mapping, Female, Gene Expression Regulation, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Humans, Male, Odds Ratio, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Racial Groups, Reproducibility of Results, Sex Factors, GRAAD, Continental Population Groups, Medical and Health Sciences, Genetics & Heredity
Abstract

Asthma is a complex disease with sex-specific differences in prevalence. Candidate gene studies have suggested that genotype-by-sex interaction effects on asthma risk exist, but this has not yet been explored at a genome-wide level. We aimed to identify sex-specific asthma risk alleles by performing a genome-wide scan for genotype-by-sex interactions in the ethnically diverse participants in the EVE Asthma Genetics Consortium. We performed male- and female-specific genome-wide association studies in 2653 male asthma cases, 2566 female asthma cases and 3830 non-asthma controls from European American, African American, African Caribbean and Latino populations. Association tests were conducted in each study sample, and the results were combined in ancestry-specific and cross-ancestry meta-analyses. Six sex-specific asthma risk loci had P-values < 1 × 10(-6), of which two were male specific and four were female specific; all were ancestry specific. The most significant sex-specific association in European Americans was at the interferon regulatory factor 1 (IRF1) locus on 5q31.1. We also identify a Latino female-specific association in RAP1GAP2. Both of these loci included single-nucleotide polymorphisms that are known expression quantitative trait loci and have been associated with asthma in independent studies. The IRF1 locus is a strong candidate region for male-specific asthma susceptibility due to the association and validation we demonstrate here, the known role of IRF1 in asthma-relevant immune pathways and prior reports of sex-specific differences in interferon responses.

Published
2014

11. Biological, clinical and population relevance of 95 loci for blood lipids

Author

Teslovich, Tanya M, Musunuru, Kiran, Smith, Albert V, Edmondson, Andrew C, Stylianou, Ioannis M, Koseki, Masahiro, Pirruccello, James P, Ripatti, Samuli, Chasman, Daniel I, Willer, Cristen J, Johansen, Christopher T, Fouchier, Sigrid W, Isaacs, Aaron, Peloso, Gina M, Barbalic, Maja, Ricketts, Sally L, Bis, Joshua C, Aulchenko, Yurii S, Thorleifsson, Gudmar, Feitosa, Mary F, Chambers, John, Orho-Melander, Marju, Melander, Olle, Johnson, Toby, Li, Xiaohui, Guo, Xiuqing, Li, Mingyao, Shin Cho, Yoon, Jin Go, Min, Jin Kim, Young, Lee, Jong-Young, Park, Taesung, Kim, Kyunga, Sim, Xueling, Twee-Hee Ong, Rick, Croteau-Chonka, Damien C, Lange, Leslie A, Smith, Joshua D, Song, Kijoung, Hua Zhao, Jing, Yuan, Xin, Luan, Jian’an, Lamina, Claudia, Ziegler, Andreas, Zhang, Weihua, Zee, Robert YL, Wright, Alan F, Witteman, Jacqueline CM, Wilson, James F, Willemsen, Gonneke, Wichmann, H-Erich, Whitfield, John B, Waterworth, Dawn M, Wareham, Nicholas J, Waeber, Gérard, Vollenweider, Peter, Voight, Benjamin F, Vitart, Veronique, Uitterlinden, Andre G, Uda, Manuela, Tuomilehto, Jaakko, Thompson, John R, Tanaka, Toshiko, Surakka, Ida, Stringham, Heather M, Spector, Tim D, Soranzo, Nicole, Smit, Johannes H, Sinisalo, Juha, Silander, Kaisa, Sijbrands, Eric JG, Scuteri, Angelo, Scott, James, Schlessinger, David, Sanna, Serena, Salomaa, Veikko, Saharinen, Juha, Sabatti, Chiara, Ruokonen, Aimo, Rudan, Igor, Rose, Lynda M, Roberts, Robert, Rieder, Mark, Psaty, Bruce M, Pramstaller, Peter P, Pichler, Irene, Perola, Markus, Penninx, Brenda WJH, Pedersen, Nancy L, Pattaro, Cristian, Parker, Alex N, Pare, Guillaume, Oostra, Ben A, O’Donnell, Christopher J, Nieminen, Markku S, Nickerson, Deborah A, Montgomery, Grant W, Meitinger, Thomas, McPherson, Ruth, and McCarthy, Mark I

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Heart Disease, Human Genome, Cardiovascular, Prevention, Atherosclerosis, Heart Disease - Coronary Heart Disease, 2.1 Biological and endogenous factors, Aetiology, Black or African American, Animals, Asian People, Cholesterol, HDL, Cholesterol, LDL, Coronary Artery Disease, Europe, Female, Genetic Loci, Genome-Wide Association Study, Genotype, Humans, Lipid Metabolism, Lipids, Liver, Male, Mice, N-Acetylgalactosaminyltransferases, Phenotype, Polymorphism, Single Nucleotide, Protein Phosphatase 1, Reproducibility of Results, Triglycerides, White People, Polypeptide N-acetylgalactosaminyltransferase, General Science & Technology
Abstract

Plasma concentrations of total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides are among the most important risk factors for coronary artery disease (CAD) and are targets for therapeutic intervention. We screened the genome for common variants associated with plasma lipids in >100,000 individuals of European ancestry. Here we report 95 significantly associated loci (P < 5 x 10(-8)), with 59 showing genome-wide significant association with lipid traits for the first time. The newly reported associations include single nucleotide polymorphisms (SNPs) near known lipid regulators (for example, CYP7A1, NPC1L1 and SCARB1) as well as in scores of loci not previously implicated in lipoprotein metabolism. The 95 loci contribute not only to normal variation in lipid traits but also to extreme lipid phenotypes and have an impact on lipid traits in three non-European populations (East Asians, South Asians and African Americans). Our results identify several novel loci associated with plasma lipids that are also associated with CAD. Finally, we validated three of the novel genes-GALNT2, PPP1R3B and TTC39B-with experiments in mouse models. Taken together, our findings provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD.

Published
2010

12. Proteomic prediction of common and rare diseases

Author

Carrasco-Zanini, Julia, primary, Pietzner, Maik, additional, Davitte, Jonathan, additional, Surendran, Praveen, additional, Croteau-Chonka, Damien C., additional, Robins, Chloe, additional, Torralbo, Ana, additional, Tomlinson, Christopher, additional, Fitzpatrick, Natalie, additional, Ytsma, Cai, additional, Kanno, Tokuwa, additional, Gade, Stephan, additional, Freitag, Daniel, additional, Ziebell, Frederik, additional, Denaxas, Spiros, additional, Betts, Joanna C., additional, Wareham, Nicholas J., additional, Hemingway, Harry, additional, Scott, Robert A., additional, and Langenberg, Claudia, additional

Published
2023
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14. Integration of metabolomic and transcriptomic networks in pregnant women reveals biological pathways and predictive signatures associated with preeclampsia

Author

Kelly, Rachel S., Croteau-Chonka, Damien C., Dahlin, Amber, Mirzakhani, Hooman, Wu, Ann C., Wan, Emily S., McGeachie, Michael J., Qiu, Weiliang, Sordillo, Joanne E., Al-Garawi, Amal, Gray, Kathryn J., McElrath, Thomas F., Carey, Vincent J., Clish, Clary B., Litonjua, Augusto A., Weiss, Scott T., and Lasky-Su, Jessica A.

Published
2017
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15. List of Contributors

Author

Assimes, Themistocles L., primary, Billatos, Ehab, additional, Bregendahl, Maria Esperanza, additional, Chahrour, Maria, additional, Conran, Carly, additional, Croteau-Chonka, Damien C., additional, Florez, Jose C., additional, Gesthalter, Yaron B., additional, Haga, Susanne B., additional, Hegele, Robert A., additional, Hicks, J. Kevin, additional, Jenkins, Jean, additional, Johnson, Samuel G., additional, Kathuria, Hasmeena, additional, Kuiper, Roland P., additional, Lanktree, Matthew B., additional, Liu, Wennuan, additional, Marcom, Paul K., additional, McGeachie, Michael J., additional, McLeod, Howard L., additional, Morgan, Thomas, additional, Munroe, Patricia B., additional, Na, Rong, additional, Orlando, Lori A., additional, Palaniappan, Latha, additional, Patel, Keyur, additional, Rodriguez, Laura Lyman, additional, Saxena, Akanksha, additional, Shackel, Nicholas A., additional, Tu, Thomas, additional, Udler, Miriam S., additional, van Kessel, Ad Geurts, additional, Warren, Helen R., additional, Weiss, Scott T., additional, Weren, Robbert D.A., additional, and Xu, Jianfeng, additional

Published
2017
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16. Asthma

Author

McGeachie, Michael J., primary, Croteau-Chonka, Damien C., additional, and Weiss, Scott T., additional

Published
2017
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17. A saturated map of common genetic variants associated with human height

Author

Yengo, Loïc, Vedantam, Sailaja, Marouli, Eirini, Sidorenko, Julia, Bartell, Eric, Sakaue, Saori, Graff, Marielisa, Eliasen, Anders U., Jiang, Yunxuan, Raghavan, Sridharan, Miao, Jenkai, Arias, Joshua D., Graham, Sarah E., Mukamel, Ronen E., Spracklen, Cassandra N., Yin, Xianyong, Chen, Shyh-Huei, Ferreira, Teresa, Highland, Heather H., Ji, Yingjie, Karaderi, Tugce, Lin, Kuang, Lüll, Kreete, Malden, Deborah E., Medina-Gomez, Carolina, Machado, Moara, Moore, Amy, Rüeger, Sina, Sim, Xueling, Vrieze, Scott, Ahluwalia, Tarunveer S., Akiyama, Masato, Allison, Matthew A., Alvarez, Marcus, Andersen, Mette K., Ani, Alireza, Appadurai, Vivek, Arbeeva, Liubov, Bhaskar, Seema, Bielak, Lawrence F., Bollepalli, Sailalitha, Bonnycastle, Lori L., Bork-Jensen, Jette, Bradfield, Jonathan P., Bradford, Yuki, Braund, Peter S., Brody, Jennifer A., Burgdorf, Kristoffer S., Cade, Brian E., Cai, Hui, Cai, Qiuyin, Campbell, Archie, Cañadas-Garre, Marisa, Catamo, Eulalia, Chai, Jin-Fang, Chai, Xiaoran, Chang, Li-Ching, Chang, Yi-Cheng, Chen, Chien-Hsiun, Chesi, Alessandra, Choi, Seung Hoan, Chung, Ren-Hua, Cocca, Massimiliano, Concas, Maria Pina, Couture, Christian, Cuellar-Partida, Gabriel, Danning, Rebecca, Daw, E. Warwick, Degenhard, Frauke, Delgado, Graciela E., Delitala, Alessandro, Demirkan, Ayse, Deng, Xuan, Devineni, Poornima, Dietl, Alexander, Dimitriou, Maria, Dimitrov, Latchezar, Dorajoo, Rajkumar, Ekici, Arif B., Engmann, Jorgen E., Fairhurst-Hunter, Zammy, Farmaki, Aliki-Eleni, Faul, Jessica D., Fernandez-Lopez, Juan-Carlos, Forer, Lukas, Francescatto, Margherita, Freitag-Wolf, Sandra, Fuchsberger, Christian, Galesloot, Tessel E., Gao, Yan, Gao, Zishan, Geller, Frank, Giannakopoulou, Olga, Giulianini, Franco, Gjesing, Anette P., Goel, Anuj, Gordon, Scott D., Gorski, Mathias, Grove, Jakob, Guo, Xiuqing, Gustafsson, Stefan, Haessler, Jeffrey, Hansen, Thomas F., Havulinna, Aki S., Haworth, Simon J., He, Jing, Heard-Costa, Nancy, Hebbar, Prashantha, Hindy, George, Ho, Yuk-Lam A., Hofer, Edith, Holliday, Elizabeth, Horn, Katrin, Hornsby, Whitney E., Hottenga, Jouke-Jan, Huang, Hongyan, Huang, Jie, Huerta-Chagoya, Alicia, Huffman, Jennifer E., Hung, Yi-Jen, Huo, Shaofeng, Hwang, Mi Yeong, Iha, Hiroyuki, Ikeda, Daisuke D., Isono, Masato, Jackson, Anne U., Jäger, Susanne, Jansen, Iris E., Johansson, Ingegerd, Jonas, Jost B., Jonsson, Anna, Jørgensen, Torben, Kalafati, Ioanna-Panagiota, Kanai, Masahiro, Kanoni, Stavroula, Kårhus, Line L., Kasturiratne, Anuradhani, Katsuya, Tomohiro, Kawaguchi, Takahisa, Kember, Rachel L., Kentistou, Katherine A., Kim, Han-Na, Kim, Young Jin, Kleber, Marcus E., Knol, Maria J., Kurbasic, Azra, Lauzon, Marie, Le, Phuong, Lea, Rodney, Lee, Jong-Young, Leonard, Hampton L., Li, Shengchao A., Li, Xiaohui, Li, Xiaoyin, Liang, Jingjing, Lin, Honghuang, Lin, Shih-Yi, Liu, Jun, Liu, Xueping, Lo, Ken Sin, Long, Jirong, Lores-Motta, Laura, Luan, Jian’an, Lyssenko, Valeriya, Lyytikäinen, Leo-Pekka, Mahajan, Anubha, Mamakou, Vasiliki, Mangino, Massimo, Manichaikul, Ani, Marten, Jonathan, Mattheisen, Manuel, Mavarani, Laven, McDaid, Aaron F., Meidtner, Karina, Melendez, Tori L., Mercader, Josep M., Milaneschi, Yuri, Miller, Jason E., Millwood, Iona Y., Mishra, Pashupati P., Mitchell, Ruth E., Møllehave, Line T., Morgan, Anna, Mucha, Soeren, Munz, Matthias, Nakatochi, Masahiro, Nelson, Christopher P., Nethander, Maria, Nho, Chu Won, Nielsen, Aneta A., Nolte, Ilja M., Nongmaithem, Suraj S., Noordam, Raymond, Ntalla, Ioanna, Nutile, Teresa, Pandit, Anita, Christofidou, Paraskevi, Pärna, Katri, Pauper, Marc, Petersen, Eva R. B., Petersen, Liselotte V., Pitkänen, Niina, Polašek, Ozren, Poveda, Alaitz, Preuss, Michael H., Pyarajan, Saiju, Raffield, Laura M., Rakugi, Hiromi, Ramirez, Julia, Rasheed, Asif, Raven, Dennis, Rayner, Nigel W., Riveros, Carlos, Rohde, Rebecca, Ruggiero, Daniela, Ruotsalainen, Sanni E., Ryan, Kathleen A., Sabater-Lleal, Maria, Saxena, Richa, Scholz, Markus, Sendamarai, Anoop, Shen, Botong, Shi, Jingchunzi, Shin, Jae Hun, Sidore, Carlo, Sitlani, Colleen M., Slieker, Roderick C., Smit, Roelof A. J., Smith, Albert V., Smith, Jennifer A., Smyth, Laura J., Southam, Lorraine, Steinthorsdottir, Valgerdur, Sun, Liang, Takeuchi, Fumihiko, Tallapragada, Divya Sri Priyanka, Taylor, Kent D., Tayo, Bamidele O., Tcheandjieu, Catherine, Terzikhan, Natalie, Tesolin, Paola, Teumer, Alexander, Theusch, Elizabeth, Thompson, Deborah J., Thorleifsson, Gudmar, Timmers, Paul R. H. J., Trompet, Stella, Turman, Constance, Vaccargiu, Simona, van der Laan, Sander W., van der Most, Peter J., van Klinken, Jan B., van Setten, Jessica, Verma, Shefali S., Verweij, Niek, Veturi, Yogasudha, Wang, Carol A., Wang, Chaolong, Wang, Lihua, Wang, Zhe, Warren, Helen R., Bin Wei, Wen, Wickremasinghe, Ananda R., Wielscher, Matthias, Wiggins, Kerri L., Winsvold, Bendik S., Wong, Andrew, Wu, Yang, Wuttke, Matthias, Xia, Rui, Xie, Tian, Yamamoto, Ken, Yang, Jingyun, Yao, Jie, Young, Hannah, Yousri, Noha A., Yu, Lei, Zeng, Lingyao, Zhang, Weihua, Zhang, Xinyuan, Zhao, Jing-Hua, Zhao, Wei, Zhou, Wei, Zimmermann, Martina E., Zoledziewska, Magdalena, Adair, Linda S., Adams, Hieab H. H., Aguilar-Salinas, Carlos A., Al-Mulla, Fahd, Arnett, Donna K., Asselbergs, Folkert W., Åsvold, Bjørn Olav, Attia, John, Banas, Bernhard, Bandinelli, Stefania, Bennett, David A., Bergler, Tobias, Bharadwaj, Dwaipayan, Biino, Ginevra, Bisgaard, Hans, Boerwinkle, Eric, Böger, Carsten A., Bønnelykke, Klaus, Boomsma, Dorret I., Børglum, Anders D., Borja, Judith B., Bouchard, Claude, Bowden, Donald W., Brandslund, Ivan, Brumpton, Ben, Buring, Julie E., Caulfield, Mark J., Chambers, John C., Chandak, Giriraj R., Chanock, Stephen J., Chaturvedi, Nish, Chen, Yii-Der Ida, Chen, Zhengming, Cheng, Ching-Yu, Christophersen, Ingrid E., Ciullo, Marina, Cole, John W., Collins, Francis S., Cooper, Richard S., Cruz, Miguel, Cucca, Francesco, Cupples, L. Adrienne, Cutler, Michael J., Damrauer, Scott M., Dantoft, Thomas M., de Borst, Gert J., de Groot, Lisette C. P. G. M., De Jager, Philip L., de Kleijn, Dominique P. V., Janaka de Silva, H., Dedoussis, George V., den Hollander, Anneke I., Du, Shufa, Easton, Douglas F., Elders, Petra J. M., Eliassen, A. Heather, Ellinor, Patrick T., Elmståhl, Sölve, Erdmann, Jeanette, Evans, Michele K., Fatkin, Diane, Feenstra, Bjarke, Feitosa, Mary F., Ferrucci, Luigi, Ford, Ian, Fornage, Myriam, Franke, Andre, Franks, Paul W., Freedman, Barry I., Gasparini, Paolo, Gieger, Christian, Girotto, Giorgia, Goddard, Michael E., Golightly, Yvonne M., Gonzalez-Villalpando, Clicerio, Gordon-Larsen, Penny, Grallert, Harald, Grant, Struan F. A., Grarup, Niels, Griffiths, Lyn, Gudnason, Vilmundur, Haiman, Christopher, Hakonarson, Hakon, Hansen, Torben, Hartman, Catharina A., Hattersley, Andrew T., Hayward, Caroline, Heckbert, Susan R., Heng, Chew-Kiat, Hengstenberg, Christian, Hewitt, Alex W., Hishigaki, Haretsugu, Hoyng, Carel B., Huang, Paul L., Huang, Wei, Hunt, Steven C., Hveem, Kristian, Hyppönen, Elina, Iacono, William G., Ichihara, Sahoko, Ikram, M. Arfan, Isasi, Carmen R., Jackson, Rebecca D., Jarvelin, Marjo-Riitta, Jin, Zi-Bing, Jöckel, Karl-Heinz, Joshi, Peter K., Jousilahti, Pekka, Jukema, J. Wouter, Kähönen, Mika, Kamatani, Yoichiro, Kang, Kui Dong, Kaprio, Jaakko, Kardia, Sharon L. R., Karpe, Fredrik, Kato, Norihiro, Kee, Frank, Kessler, Thorsten, Khera, Amit V., Khor, Chiea Chuen, Kiemeney, Lambertus A. L. M., Kim, Bong-Jo, Kim, Eung Kweon, Kim, Hyung-Lae, Kirchhof, Paulus, Kivimaki, Mika, Koh, Woon-Puay, Koistinen, Heikki A., Kolovou, Genovefa D., Kooner, Jaspal S., Kooperberg, Charles, Köttgen, Anna, Kovacs, Peter, Kraaijeveld, Adriaan, Kraft, Peter, Krauss, Ronald M., Kumari, Meena, Kutalik, Zoltan, Laakso, Markku, Lange, Leslie A., Langenberg, Claudia, Launer, Lenore J., Le Marchand, Loic, Lee, Hyejin, Lee, Nanette R., Lehtimäki, Terho, Li, Huaixing, Li, Liming, Lieb, Wolfgang, Lin, Xu, Lind, Lars, Linneberg, Allan, Liu, Ching-Ti, Liu, Jianjun, Loeffler, Markus, London, Barry, Lubitz, Steven A., Lye, Stephen J., Mackey, David A., Mägi, Reedik, Magnusson, Patrik K. E., Marcus, Gregory M., Vidal, Pedro Marques, Martin, Nicholas G., März, Winfried, Matsuda, Fumihiko, McGarrah, Robert W., McGue, Matt, McKnight, Amy Jayne, Medland, Sarah E., Mellström, Dan, Metspalu, Andres, Mitchell, Braxton D., Mitchell, Paul, Mook-Kanamori, Dennis O., Morris, Andrew D., Mucci, Lorelei A., Munroe, Patricia B., Nalls, Mike A., Nazarian, Saman, Nelson, Amanda E., Neville, Matt J., Newton-Cheh, Christopher, Nielsen, Christopher S., Nöthen, Markus M., Ohlsson, Claes, Oldehinkel, Albertine J., Orozco, Lorena, Pahkala, Katja, Pajukanta, Päivi, Palmer, Colin N. A., Parra, Esteban J., Pattaro, Cristian, Pedersen, Oluf, Pennell, Craig E., Penninx, Brenda W. J. H., Perusse, Louis, Peters, Annette, Peyser, Patricia A., Porteous, David J., Posthuma, Danielle, Power, Chris, Pramstaller, Peter P., Province, Michael A., Qi, Qibin, Qu, Jia, Rader, Daniel J., Raitakari, Olli T., Ralhan, Sarju, Rallidis, Loukianos S., Rao, Dabeeru C., Redline, Susan, Reilly, Dermot F., Reiner, Alexander P., Rhee, Sang Youl, Ridker, Paul M., Rienstra, Michiel, Ripatti, Samuli, Ritchie, Marylyn D., Roden, Dan M., Rosendaal, Frits R., Rotter, Jerome I., Rudan, Igor, Rutters, Femke, Sabanayagam, Charumathi, Saleheen, Danish, Salomaa, Veikko, Samani, Nilesh J., Sanghera, Dharambir K., Sattar, Naveed, Schmidt, Börge, Schmidt, Helena, Schmidt, Reinhold, Schulze, Matthias B., Schunkert, Heribert, Scott, Laura J., Scott, Rodney J., Sever, Peter, Shiroma, Eric J., Shoemaker, M. Benjamin, Shu, Xiao-Ou, Simonsick, Eleanor M., Sims, Mario, Singh, Jai Rup, Singleton, Andrew B., Sinner, Moritz F., Smith, J. Gustav, Snieder, Harold, Spector, Tim D., Stampfer, Meir J., Stark, Klaus J., Strachan, David P., ‘t Hart, Leen M., Tabara, Yasuharu, Tang, Hua, Tardif, Jean-Claude, Thanaraj, Thangavel A., Timpson, Nicholas J., Tönjes, Anke, Tremblay, Angelo, Tuomi, Tiinamaija, Tuomilehto, Jaakko, Tusié-Luna, Maria-Teresa, Uitterlinden, Andre G., van Dam, Rob M., van der Harst, Pim, Van der Velde, Nathalie, van Duijn, Cornelia M., van Schoor, Natasja M., Vitart, Veronique, Völker, Uwe, Vollenweider, Peter, Völzke, Henry, Wacher-Rodarte, Niels H., Walker, Mark, Wang, Ya Xing, Wareham, Nicholas J., Watanabe, Richard M., Watkins, Hugh, Weir, David R., Werge, Thomas M., Widen, Elisabeth, Wilkens, Lynne R., Willemsen, Gonneke, Willett, Walter C., Wilson, James F., Wong, Tien-Yin, Woo, Jeong-Taek, Wright, Alan F., Wu, Jer-Yuarn, Xu, Huichun, Yajnik, Chittaranjan S., Yokota, Mitsuhiro, Yuan, Jian-Min, Zeggini, Eleftheria, Zemel, Babette S., Zheng, Wei, Zhu, Xiaofeng, Zmuda, Joseph M., Zonderman, Alan B., Zwart, John-Anker, Partida, Gabriel Cuellar, Sun, Yan, Croteau-Chonka, Damien, Vonk, Judith M., Chanock, Stephen, Chasman, Daniel I., Cho, Yoon Shin, Heid, Iris M., McCarthy, Mark I., Ng, Maggie C. Y., O’Donnell, Christopher J., Rivadeneira, Fernando, Thorsteinsdottir, Unnur, Sun, Yan V., Tai, E. Shyong, Boehnke, Michael, Deloukas, Panos, Justice, Anne E., Lindgren, Cecilia M., Loos, Ruth J. F., Mohlke, Karen L., North, Kari E., Stefansson, Kari, Walters, Robin G., Winkler, Thomas W., Young, Kristin L., Loh, Po-Ru, Yang, Jian, Esko, Tõnu, Assimes, Themistocles L., Auton, Adam, Abecasis, Goncalo R., Willer, Cristen J., Locke, Adam E., Berndt, Sonja I., Lettre, Guillaume, Frayling, Timothy M., Okada, Yukinori, Wood, Andrew R., Visscher, Peter M., Hirschhorn, Joel N., Yengo, Loïc, Vedantam, Sailaja, Marouli, Eirini, Sidorenko, Julia, Bartell, Eric, Sakaue, Saori, Graff, Marielisa, Eliasen, Anders U., Jiang, Yunxuan, Raghavan, Sridharan, Miao, Jenkai, Arias, Joshua D., Graham, Sarah E., Mukamel, Ronen E., Spracklen, Cassandra N., Yin, Xianyong, Chen, Shyh-Huei, Ferreira, Teresa, Highland, Heather H., Ji, Yingjie, Karaderi, Tugce, Lin, Kuang, Lüll, Kreete, Malden, Deborah E., Medina-Gomez, Carolina, Machado, Moara, Moore, Amy, Rüeger, Sina, Sim, Xueling, Vrieze, Scott, Ahluwalia, Tarunveer S., Akiyama, Masato, Allison, Matthew A., Alvarez, Marcus, Andersen, Mette K., Ani, Alireza, Appadurai, Vivek, Arbeeva, Liubov, Bhaskar, Seema, Bielak, Lawrence F., Bollepalli, Sailalitha, Bonnycastle, Lori L., Bork-Jensen, Jette, Bradfield, Jonathan P., Bradford, Yuki, Braund, Peter S., Brody, Jennifer A., Burgdorf, Kristoffer S., Cade, Brian E., Cai, Hui, Cai, Qiuyin, Campbell, Archie, Cañadas-Garre, Marisa, Catamo, Eulalia, Chai, Jin-Fang, Chai, Xiaoran, Chang, Li-Ching, Chang, Yi-Cheng, Chen, Chien-Hsiun, Chesi, Alessandra, Choi, Seung Hoan, Chung, Ren-Hua, Cocca, Massimiliano, Concas, Maria Pina, Couture, Christian, Cuellar-Partida, Gabriel, Danning, Rebecca, Daw, E. Warwick, Degenhard, Frauke, Delgado, Graciela E., Delitala, Alessandro, Demirkan, Ayse, Deng, Xuan, Devineni, Poornima, Dietl, Alexander, Dimitriou, Maria, Dimitrov, Latchezar, Dorajoo, Rajkumar, Ekici, Arif B., Engmann, Jorgen E., Fairhurst-Hunter, Zammy, Farmaki, Aliki-Eleni, Faul, Jessica D., Fernandez-Lopez, Juan-Carlos, Forer, Lukas, Francescatto, Margherita, Freitag-Wolf, Sandra, Fuchsberger, Christian, Galesloot, Tessel E., Gao, Yan, Gao, Zishan, Geller, Frank, Giannakopoulou, Olga, Giulianini, Franco, Gjesing, Anette P., Goel, Anuj, Gordon, Scott D., Gorski, Mathias, Grove, Jakob, Guo, Xiuqing, Gustafsson, Stefan, Haessler, Jeffrey, Hansen, Thomas F., Havulinna, Aki S., Haworth, Simon J., He, Jing, Heard-Costa, Nancy, Hebbar, Prashantha, Hindy, George, Ho, Yuk-Lam A., Hofer, Edith, Holliday, Elizabeth, Horn, Katrin, Hornsby, Whitney E., Hottenga, Jouke-Jan, Huang, Hongyan, Huang, Jie, Huerta-Chagoya, Alicia, Huffman, Jennifer E., Hung, Yi-Jen, Huo, Shaofeng, Hwang, Mi Yeong, Iha, Hiroyuki, Ikeda, Daisuke D., Isono, Masato, Jackson, Anne U., Jäger, Susanne, Jansen, Iris E., Johansson, Ingegerd, Jonas, Jost B., Jonsson, Anna, Jørgensen, Torben, Kalafati, Ioanna-Panagiota, Kanai, Masahiro, Kanoni, Stavroula, Kårhus, Line L., Kasturiratne, Anuradhani, Katsuya, Tomohiro, Kawaguchi, Takahisa, Kember, Rachel L., Kentistou, Katherine A., Kim, Han-Na, Kim, Young Jin, Kleber, Marcus E., Knol, Maria J., Kurbasic, Azra, Lauzon, Marie, Le, Phuong, Lea, Rodney, Lee, Jong-Young, Leonard, Hampton L., Li, Shengchao A., Li, Xiaohui, Li, Xiaoyin, Liang, Jingjing, Lin, Honghuang, Lin, Shih-Yi, Liu, Jun, Liu, Xueping, Lo, Ken Sin, Long, Jirong, Lores-Motta, Laura, Luan, Jian’an, Lyssenko, Valeriya, Lyytikäinen, Leo-Pekka, Mahajan, Anubha, Mamakou, Vasiliki, Mangino, Massimo, Manichaikul, Ani, Marten, Jonathan, Mattheisen, Manuel, Mavarani, Laven, McDaid, Aaron F., Meidtner, Karina, Melendez, Tori L., Mercader, Josep M., Milaneschi, Yuri, Miller, Jason E., Millwood, Iona Y., Mishra, Pashupati P., Mitchell, Ruth E., Møllehave, Line T., Morgan, Anna, Mucha, Soeren, Munz, Matthias, Nakatochi, Masahiro, Nelson, Christopher P., Nethander, Maria, Nho, Chu Won, Nielsen, Aneta A., Nolte, Ilja M., Nongmaithem, Suraj S., Noordam, Raymond, Ntalla, Ioanna, Nutile, Teresa, Pandit, Anita, Christofidou, Paraskevi, Pärna, Katri, Pauper, Marc, Petersen, Eva R. B., Petersen, Liselotte V., Pitkänen, Niina, Polašek, Ozren, Poveda, Alaitz, Preuss, Michael H., Pyarajan, Saiju, Raffield, Laura M., Rakugi, Hiromi, Ramirez, Julia, Rasheed, Asif, Raven, Dennis, Rayner, Nigel W., Riveros, Carlos, Rohde, Rebecca, Ruggiero, Daniela, Ruotsalainen, Sanni E., Ryan, Kathleen A., Sabater-Lleal, Maria, Saxena, Richa, Scholz, Markus, Sendamarai, Anoop, Shen, Botong, Shi, Jingchunzi, Shin, Jae Hun, Sidore, Carlo, Sitlani, Colleen M., Slieker, Roderick C., Smit, Roelof A. J., Smith, Albert V., Smith, Jennifer A., Smyth, Laura J., Southam, Lorraine, Steinthorsdottir, Valgerdur, Sun, Liang, Takeuchi, Fumihiko, Tallapragada, Divya Sri Priyanka, Taylor, Kent D., Tayo, Bamidele O., Tcheandjieu, Catherine, Terzikhan, Natalie, Tesolin, Paola, Teumer, Alexander, Theusch, Elizabeth, Thompson, Deborah J., Thorleifsson, Gudmar, Timmers, Paul R. H. J., Trompet, Stella, Turman, Constance, Vaccargiu, Simona, van der Laan, Sander W., van der Most, Peter J., van Klinken, Jan B., van Setten, Jessica, Verma, Shefali S., Verweij, Niek, Veturi, Yogasudha, Wang, Carol A., Wang, Chaolong, Wang, Lihua, Wang, Zhe, Warren, Helen R., Bin Wei, Wen, Wickremasinghe, Ananda R., Wielscher, Matthias, Wiggins, Kerri L., Winsvold, Bendik S., Wong, Andrew, Wu, Yang, Wuttke, Matthias, Xia, Rui, Xie, Tian, Yamamoto, Ken, Yang, Jingyun, Yao, Jie, Young, Hannah, Yousri, Noha A., Yu, Lei, Zeng, Lingyao, Zhang, Weihua, Zhang, Xinyuan, Zhao, Jing-Hua, Zhao, Wei, Zhou, Wei, Zimmermann, Martina E., Zoledziewska, Magdalena, Adair, Linda S., Adams, Hieab H. H., Aguilar-Salinas, Carlos A., Al-Mulla, Fahd, Arnett, Donna K., Asselbergs, Folkert W., Åsvold, Bjørn Olav, Attia, John, Banas, Bernhard, Bandinelli, Stefania, Bennett, David A., Bergler, Tobias, Bharadwaj, Dwaipayan, Biino, Ginevra, Bisgaard, Hans, Boerwinkle, Eric, Böger, Carsten A., Bønnelykke, Klaus, Boomsma, Dorret I., Børglum, Anders D., Borja, Judith B., Bouchard, Claude, Bowden, Donald W., Brandslund, Ivan, Brumpton, Ben, Buring, Julie E., Caulfield, Mark J., Chambers, John C., Chandak, Giriraj R., Chanock, Stephen J., Chaturvedi, Nish, Chen, Yii-Der Ida, Chen, Zhengming, Cheng, Ching-Yu, Christophersen, Ingrid E., Ciullo, Marina, Cole, John W., Collins, Francis S., Cooper, Richard S., Cruz, Miguel, Cucca, Francesco, Cupples, L. Adrienne, Cutler, Michael J., Damrauer, Scott M., Dantoft, Thomas M., de Borst, Gert J., de Groot, Lisette C. P. G. M., De Jager, Philip L., de Kleijn, Dominique P. V., Janaka de Silva, H., Dedoussis, George V., den Hollander, Anneke I., Du, Shufa, Easton, Douglas F., Elders, Petra J. M., Eliassen, A. Heather, Ellinor, Patrick T., Elmståhl, Sölve, Erdmann, Jeanette, Evans, Michele K., Fatkin, Diane, Feenstra, Bjarke, Feitosa, Mary F., Ferrucci, Luigi, Ford, Ian, Fornage, Myriam, Franke, Andre, Franks, Paul W., Freedman, Barry I., Gasparini, Paolo, Gieger, Christian, Girotto, Giorgia, Goddard, Michael E., Golightly, Yvonne M., Gonzalez-Villalpando, Clicerio, Gordon-Larsen, Penny, Grallert, Harald, Grant, Struan F. A., Grarup, Niels, Griffiths, Lyn, Gudnason, Vilmundur, Haiman, Christopher, Hakonarson, Hakon, Hansen, Torben, Hartman, Catharina A., Hattersley, Andrew T., Hayward, Caroline, Heckbert, Susan R., Heng, Chew-Kiat, Hengstenberg, Christian, Hewitt, Alex W., Hishigaki, Haretsugu, Hoyng, Carel B., Huang, Paul L., Huang, Wei, Hunt, Steven C., Hveem, Kristian, Hyppönen, Elina, Iacono, William G., Ichihara, Sahoko, Ikram, M. Arfan, Isasi, Carmen R., Jackson, Rebecca D., Jarvelin, Marjo-Riitta, Jin, Zi-Bing, Jöckel, Karl-Heinz, Joshi, Peter K., Jousilahti, Pekka, Jukema, J. Wouter, Kähönen, Mika, Kamatani, Yoichiro, Kang, Kui Dong, Kaprio, Jaakko, Kardia, Sharon L. R., Karpe, Fredrik, Kato, Norihiro, Kee, Frank, Kessler, Thorsten, Khera, Amit V., Khor, Chiea Chuen, Kiemeney, Lambertus A. L. M., Kim, Bong-Jo, Kim, Eung Kweon, Kim, Hyung-Lae, Kirchhof, Paulus, Kivimaki, Mika, Koh, Woon-Puay, Koistinen, Heikki A., Kolovou, Genovefa D., Kooner, Jaspal S., Kooperberg, Charles, Köttgen, Anna, Kovacs, Peter, Kraaijeveld, Adriaan, Kraft, Peter, Krauss, Ronald M., Kumari, Meena, Kutalik, Zoltan, Laakso, Markku, Lange, Leslie A., Langenberg, Claudia, Launer, Lenore J., Le Marchand, Loic, Lee, Hyejin, Lee, Nanette R., Lehtimäki, Terho, Li, Huaixing, Li, Liming, Lieb, Wolfgang, Lin, Xu, Lind, Lars, Linneberg, Allan, Liu, Ching-Ti, Liu, Jianjun, Loeffler, Markus, London, Barry, Lubitz, Steven A., Lye, Stephen J., Mackey, David A., Mägi, Reedik, Magnusson, Patrik K. E., Marcus, Gregory M., Vidal, Pedro Marques, Martin, Nicholas G., März, Winfried, Matsuda, Fumihiko, McGarrah, Robert W., McGue, Matt, McKnight, Amy Jayne, Medland, Sarah E., Mellström, Dan, Metspalu, Andres, Mitchell, Braxton D., Mitchell, Paul, Mook-Kanamori, Dennis O., Morris, Andrew D., Mucci, Lorelei A., Munroe, Patricia B., Nalls, Mike A., Nazarian, Saman, Nelson, Amanda E., Neville, Matt J., Newton-Cheh, Christopher, Nielsen, Christopher S., Nöthen, Markus M., Ohlsson, Claes, Oldehinkel, Albertine J., Orozco, Lorena, Pahkala, Katja, Pajukanta, Päivi, Palmer, Colin N. A., Parra, Esteban J., Pattaro, Cristian, Pedersen, Oluf, Pennell, Craig E., Penninx, Brenda W. J. H., Perusse, Louis, Peters, Annette, Peyser, Patricia A., Porteous, David J., Posthuma, Danielle, Power, Chris, Pramstaller, Peter P., Province, Michael A., Qi, Qibin, Qu, Jia, Rader, Daniel J., Raitakari, Olli T., Ralhan, Sarju, Rallidis, Loukianos S., Rao, Dabeeru C., Redline, Susan, Reilly, Dermot F., Reiner, Alexander P., Rhee, Sang Youl, Ridker, Paul M., Rienstra, Michiel, Ripatti, Samuli, Ritchie, Marylyn D., Roden, Dan M., Rosendaal, Frits R., Rotter, Jerome I., Rudan, Igor, Rutters, Femke, Sabanayagam, Charumathi, Saleheen, Danish, Salomaa, Veikko, Samani, Nilesh J., Sanghera, Dharambir K., Sattar, Naveed, Schmidt, Börge, Schmidt, Helena, Schmidt, Reinhold, Schulze, Matthias B., Schunkert, Heribert, Scott, Laura J., Scott, Rodney J., Sever, Peter, Shiroma, Eric J., Shoemaker, M. Benjamin, Shu, Xiao-Ou, Simonsick, Eleanor M., Sims, Mario, Singh, Jai Rup, Singleton, Andrew B., Sinner, Moritz F., Smith, J. Gustav, Snieder, Harold, Spector, Tim D., Stampfer, Meir J., Stark, Klaus J., Strachan, David P., ‘t Hart, Leen M., Tabara, Yasuharu, Tang, Hua, Tardif, Jean-Claude, Thanaraj, Thangavel A., Timpson, Nicholas J., Tönjes, Anke, Tremblay, Angelo, Tuomi, Tiinamaija, Tuomilehto, Jaakko, Tusié-Luna, Maria-Teresa, Uitterlinden, Andre G., van Dam, Rob M., van der Harst, Pim, Van der Velde, Nathalie, van Duijn, Cornelia M., van Schoor, Natasja M., Vitart, Veronique, Völker, Uwe, Vollenweider, Peter, Völzke, Henry, Wacher-Rodarte, Niels H., Walker, Mark, Wang, Ya Xing, Wareham, Nicholas J., Watanabe, Richard M., Watkins, Hugh, Weir, David R., Werge, Thomas M., Widen, Elisabeth, Wilkens, Lynne R., Willemsen, Gonneke, Willett, Walter C., Wilson, James F., Wong, Tien-Yin, Woo, Jeong-Taek, Wright, Alan F., Wu, Jer-Yuarn, Xu, Huichun, Yajnik, Chittaranjan S., Yokota, Mitsuhiro, Yuan, Jian-Min, Zeggini, Eleftheria, Zemel, Babette S., Zheng, Wei, Zhu, Xiaofeng, Zmuda, Joseph M., Zonderman, Alan B., Zwart, John-Anker, Partida, Gabriel Cuellar, Sun, Yan, Croteau-Chonka, Damien, Vonk, Judith M., Chanock, Stephen, Chasman, Daniel I., Cho, Yoon Shin, Heid, Iris M., McCarthy, Mark I., Ng, Maggie C. Y., O’Donnell, Christopher J., Rivadeneira, Fernando, Thorsteinsdottir, Unnur, Sun, Yan V., Tai, E. Shyong, Boehnke, Michael, Deloukas, Panos, Justice, Anne E., Lindgren, Cecilia M., Loos, Ruth J. F., Mohlke, Karen L., North, Kari E., Stefansson, Kari, Walters, Robin G., Winkler, Thomas W., Young, Kristin L., Loh, Po-Ru, Yang, Jian, Esko, Tõnu, Assimes, Themistocles L., Auton, Adam, Abecasis, Goncalo R., Willer, Cristen J., Locke, Adam E., Berndt, Sonja I., Lettre, Guillaume, Frayling, Timothy M., Okada, Yukinori, Wood, Andrew R., Visscher, Peter M., and Hirschhorn, Joel N.

Abstract

Common single-nucleotide polymorphisms (SNPs) are predicted to collectively explain 40–50% of phenotypic variation in human height, but identifying the specific variants and associated regions requires huge sample sizes1. Here, using data from a genome-wide association study of 5.4 million individuals of diverse ancestries, we show that 12,111 independent SNPs that are significantly associated with height account for nearly all of the common SNP-based heritability. These SNPs are clustered within 7,209 non-overlapping genomic segments with a mean size of around 90 kb, covering about 21% of the genome. The density of independent associations varies across the genome and the regions of increased density are enriched for biologically relevant genes. In out-of-sample estimation and prediction, the 12,111 SNPs (or all SNPs in the HapMap 3 panel2) account for 40% (45%) of phenotypic variance in populations of European ancestry but only around 10–20% (14–24%) in populations of other ancestries. Effect sizes, associated regions and gene prioritization are similar across ancestries, indicating that reduced prediction accuracy is likely to be explained by linkage disequilibrium and differences in allele frequency within associated regions. Finally, we show that the relevant biological pathways are detectable with smaller sample sizes than are needed to implicate causal genes and variants. Overall, this study provides a comprehensive map of specific genomic regions that contain the vast majority of common height-associated variants. Although this map is saturated for populations of European ancestry, further research is needed to achieve equivalent saturation in other ancestries.

Published
2022
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18. Gene Expression Profiling in Blood Provides Reproducible Molecular Insights into Asthma Control

Author

Croteau-Chonka, Damien C., Qiu, Weiliang, Martinez, Fernando D., Strunk, Robert C., Lemanske, Robert F., Jr., Liu, Andrew H., Gilliland, Frank D., Millstein, Joshua, Gauderman, James W., Ober, Carole, Krishnan, Jerry A., White, Steven R., Naureckas, Edward T., Nicolae, Dan L., Barnes, Kathleen C., London, Stephanie J., Barraza-Villarreal, Albino, Carey, Vincent J., Weiss, Scott T., and Raby, Benjamin A.

Published
2017
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20. Patterns of Growth and Decline in Lung Function in Persistent Childhood Asthma

Author

McGeachie, Michael J., Yates, Katherine P., Zhou, Xiaobo, Guo, Feng, Sternberg, Alice L., Van Natta, Mark L., Wise, Robert A., Szefler, Stanley J., Sharma, Sunita, Kho, Alvin T., Cho, Michael H., Croteau-Chonka, Damien C., Castaldi, Peter J., Jain, Gaurav, Sanyal, Amartya, Zhan, Ye, Lajoie, Bryan R., Dekker, Job, Stamatoyannopoulos, John, Covar, Ronina A., Zeiger, Robert S., Adkinson, N. Franklin, Williams, Paul V., Kelly, H. William, Grasemann, Hartmut, Vonk, Judith M., Koppelman, Gerard H., Postma, Dirkje S., Raby, Benjamin A., Houston, Isaac, Lu, Quan, Fuhlbrigge, Anne L., Tantisira, Kelan G., Silverman, Edwin K., Tonascia, James, Weiss, Scott T., and Strunk, Robert C.

Published
2016
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21. Early Changes in Immune Cell Count, Metabolism, and Function Following Sleeve Gastrectomy: A Prospective Human Study

Author

Lo, Tammy, primary, Haridas, Renuka S, additional, Rudge, Eleanor J M, additional, Chase, Robert P, additional, Heshmati, Keyvan, additional, Lucey, Elizabeth M, additional, Weigl, Alison M, additional, Iyoha-Bello, Otatade J, additional, Ituah, Chelsea O, additional, Benjamin, Emily J, additional, McNutt, Seth W, additional, Sathe, Leena, additional, Farnam, Leanna, additional, Raby, Benjamin A, additional, Tavakkoli, Ali, additional, Croteau-Chonka, Damien C, additional, and Sheu, Eric G, additional

Published
2021
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22. A Genome-Wide Association Study of Post-bronchodilator Lung Function in Children with Asthma

Author

Brehm, John M., Man Tse, Sze, Croteau-Chonka, Damien C., Forno, Erick, Litonjua, Augusto A., Raby, Benjamin A., Chen, Wei, Yan, Qi, Boutaoui, Nadia, Acosta-Pérez, Edna, Avila, Lydiana, Weiss, Scott T., Soto-Quiros, Manuel, Cloutier, Michelle M., Hu, Donglei, Pino-Yanes, Maria, Wenzel, Sally E., Spear, Melissa L., Kolls, Jay K., Burchard, Esteban G., Canino, Glorisa, and Celedón, Juan C.

Published
2015
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23. A meta-analysis of genome-wide association studies for adiponectin levels in East Asians identifies a novel locus near WDR11-FGFR2

Author

Wu, Ying, Gao, He, Li, Huaixing, Tabara, Yasuharu, Nakatochi, Masahiro, Chiu, Yen-Feng, Park, Eun Jung, Wen, Wanqing, Adair, Linda S., Borja, Judith B., Cai, Qiuyin, Chang, Yi-Cheng, Chen, Peng, Croteau-Chonka, Damien C., Fogarty, Marie P., Gan, Wei, He, Chih-Tsueng, Hsiung, Chao A., Hwu, Chii-Min, Ichihara, Sahoko, Igase, Michiya, Jo, Jaeseong, Kato, Norihiro, Kawamoto, Ryuichi, Kuzawa, Christophor W., Lee, Jeannette J.M., Liu, Jianjun, Lu, Ling, Mcdade, Thomas W., Osawa, Haruhiko, Sheu, Wayne H-H., Teo, Yvonne, Vadlamudi, Swarooparani, Van Dam, Rob M., Wang, Yiqin, Xiang, Yong-Bing, Yamamoto, Ken, Ye, Xingwang, Young, Terri L., Zheng, Wei, Zhu, Jingwen, Shu, Xiao-Ou, Shin, Chol, Jee, Sun Ha, Chuang, Lee-Ming, Miki, Tetsuro, Yokota, Mitsuhiro, Lin, Xu, Mohlke, Karen L, and Tai, E Shyong

Published
2014
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24. Asthma Susceptibility Gene ORMDL3 Promotes Autophagy in Human Bronchial Epithelium.

Author

Feng Guo, Yuan Hao, Li Zhang, Croteau-Chonka, Damien C., Thibault, Derek, Kothari, Parul, Lijia Li, Levy, Bruce D., Xiaobo Zhou, and Raby, Benjamin A.

Subjects
LUNGS, EPITHELIUM, AUTOPHAGY, GENOME-wide association studies, ELECTRON detection, INTRACELLULAR calcium, WESTERN immunoblotting, EPITHELIAL cells
Abstract

The genome-wide association study (GWAS)-identified asthma susceptibility risk alleles on chromosome 17q21 increase the expression of ORMDL3 (ORMDL sphingolipid biosynthesis regulator 3) in lung tissue. Given the importance of epithelial integrity in asthma, we hypothesized that ORMDL3 directly impacted bronchial epithelial function. To determine whether and how ORMDL3 expression impacts the bronchial epithelium, in studies using both primary human bronchial epithelial cells and human bronchial epithelial cell line, 16HBE (16HBE14o-), we assessed the impact of ORMDL3 on autophagy. Studies included: autophagosome detection by electron microscopy, RFP-GFP-LC3B to assess autophagic activity, and Western blot analysis of autophagy-related proteins. Mechanistic assessments included immunoprecipitation assays, intracellular calcium mobilization assessments, and cell viability assays. Coexpression of ORMDL3 and autophagy-related genes was measured in primary human bronchial epithelial cells derived from 44 subjects. Overexpressing ORMDL3 demonstrated increased numbers of autophagosomes and increased levels of autophagy-related proteins LC3B, ATG3, ATG7, and ATG16L1. ORMDL3 overexpression promotes autophagy and subsequent cell death by impairing intracellular calcium mobilization through interacting with SERCA2. Strong correlation was observed between expression of ORMDL3 and autophagy-related genes in patient-derived bronchial epithelial cells. Increased ORMDL3 expression induces autophagy, possibly through interacting with SERCA2, thereby inhibiting intracellular calcium influx, and induces cell death, impairing bronchial epithelial function in asthma. [ABSTRACT FROM AUTHOR]

Published
2022
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25. The eMERGE genotype set of 83,717 subjects imputed to ~40 million variants genome wide and association with the herpes zoster medical record phenotype

Author

Stanaway, Ian B., Hall, Taryn O., Rosenthal, Elisabeth A., Palmer, Melody, Naranbhai, Vivek, Knevel, Rachel, Namjou‐Khales, Bahram, Carroll, Robert J., Kiryluk, Krzysztof, Gordon, Adam S., Linder, Jodell, Howell, Kayla Marie, Mapes, Brandy M., Lin, Frederick T.J., Joo, Yoonjung Yoonie, Hayes, M. Geoffrey, Gharavi, Ali G., Pendergrass, Sarah A., Ritchie, Marylyn D., de Andrade, Mariza, Croteau‐Chonka, Damien C., Raychaudhuri, Soumya, Weiss, Scott T., Lebo, Matt, Amr, Sami S., Carrell, David, Larson, Eric B., Chute, Christopher G., Rasmussen‐Torvik, Laura Jarmila, Roy‐Puckelwartz, Megan J., Sleiman, Patrick, Hakonarson, Hakon, Li, Rongling, Karlson, Elizabeth W., Peterson, Josh F., Kullo, Iftikhar J., Chisholm, Rex, Denny, Joshua Charles, Jarvik, Gail P., and Crosslin, David R.

Subjects
Male, variants, Principal Component Analysis, Homozygote, Black People, herpes zoster, Polymorphism, Single Nucleotide, White People, Phenotype, Haplotypes, genotypes, electronic medical records, GWAS, Chromosomes, Human, Electronic Health Records, Humans, Female, Genetic Predisposition to Disease, Research Articles, Algorithms, Research Article, Genome-Wide Association Study
Abstract

The Electronic Medical Records and Genomics (eMERGE) network is a network of medical centers with electronic medical records linked to existing biorepository samples for genomic discovery and genomic medicine research. The network sought to unify the genetic results from 78 Illumina and Affymetrix genotype array batches from 12 contributing medical centers for joint association analysis of 83,717 human participants. In this report, we describe the imputation of eMERGE results and methods to create the unified imputed merged set of genome‐wide variant genotype data. We imputed the data using the Michigan Imputation Server, which provides a missing single‐nucleotide variant genotype imputation service using the minimac3 imputation algorithm with the Haplotype Reference Consortium genotype reference set. We describe the quality control and filtering steps used in the generation of this data set and suggest generalizable quality thresholds for imputation and phenotype association studies. To test the merged imputed genotype set, we replicated a previously reported chromosome 6 HLA‐B herpes zoster (shingles) association and discovered a novel zoster‐associated loci in an epigenetic binding site near the terminus of chromosome 3 (3p29).

Published
2018

28. Early changes in immune cell metabolism and function are a hallmark of sleeve gastrectomy: a prospective human study

Author

Lo, Tammy, primary, Rudge, Eleanor J.M., additional, Chase, Robert P., additional, Subramaniam, Renuka, additional, Heshmati, Keyvan, additional, Lucey, Elizabeth M., additional, Weigl, Alison M., additional, Iyoha-Bello, Otatade J., additional, Ituah, Chelsea O., additional, Benjamin, Emily J., additional, McNutt, Seth T., additional, Sathe, Leena, additional, Farnam, Leanna, additional, Raby, Benjamin A., additional, Tavakkoli, Ali, additional, Croteau-Chonka, Damien C., additional, and Sheu, Eric G., additional

Published
2020
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31. Early Changes in Immune Cell Count, Metabolism, and Function Following Sleeve Gastrectomy: A Prospective Human Study.

Author

Lo, Tammy, Haridas, Renuka S., Rudge, Eleanor J. M., Chase, Robert P., Heshmati, Keyvan, Lucey, Elizabeth M., Weigl, Alison M., Iyoha-Bello, Otatade J., Ituah, Chelsea O., Benjamin, Emily J., McNutt, Seth W., Sathe, Leena, Farnam, Leanna, Raby, Benjamin A., Tavakkoli, Ali, Croteau-Chonka, Damien C., and Sheu, Eric G.

Subjects
SLEEVE gastrectomy, OBESITY, BIOMARKERS
Abstract

Objective: To characterize longitudinal changes in blood biomarkers, leukocyte composition, and gene expression following laparoscopic sleeve gastrectomy (LSG). Background. LSG is an effective treatment for obesity, leading to sustainable weight loss and improvements in obesity-related comorbidities and inflammatory profiles. However, the effects of LSG on immune function and metabolism remain uncertain. Methods. Prospective data were collected from 23 enrolled human subjects from a single institution. Parameters of weight, comorbidities, and trends in blood biomarkers and leukocyte subsets were observed from preoperative baseline to 1 year postsurgery in 3-month follow-up intervals. RNA sequencing was performed on pairs of whole blood samples from the first 6 subjects of the study (baseline and 3 months postsurgery) to identify genome-wide gene expression changes associated with undergoing LSG. Results. LSG led to a significant decrease in mean total body weight loss (18.1%) at 3 months and among diabetic subjects a reduction in hemoglobin A1c. Improvements in clinical inflammatory and hormonal biomarkers were demonstrated as early as 3 months after LSG. A reduction in neutrophil-lymphocyte ratio was observed, driven by a reduction in absolute neutrophil counts. Gene set enrichment analyses of differential whole blood gene expression demonstrated that after 3 months LSG induced transcriptomic changes not only in inflammatory cytokine pathways but also in several key metabolic pathways related to energy metabolism. Conclusions. LSG induces significant changes in the composition and metabolism of immune cells as early as 3 months postoperatively. Further evaluation is required of bariatric surgery’s effects on immunometabolism and the consequences for host defense and metabolic disease. [ABSTRACT FROM AUTHOR]

Published
2022
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32. The role of local CpG DNA methylation in mediating the 17q21 asthma-susceptibility GSDMB/ORMDL3 expression quantitative trait locus

Author

Kothari, Parul H., Qiu, Weiliang, Croteau-Chonka, Damien C., Martinez, Fernando D., Liu, Andrew H., Lemanske, Robert F., Ober, Carole, Krishnan, Jerry A., Nicolae, Dan L., Barnes, Kathleen C., London, Stephanie J., Barraza-Villarreal, Albino, White, Steven R., Naureckas, Edward T., Millstein, Joshua, Gauderman, W. James, Gilliland, Frank D., Carey, Vincent J., Weiss, Scott T., and Raby, Benjamin A.

Subjects
Gene Expression Regulation, Genotype, Quantitative Trait Loci, Humans, Membrane Proteins, CpG Islands, Genetic Predisposition to Disease, DNA Methylation, Polymorphism, Single Nucleotide, Article, Asthma, Chromosomes, Human, Pair 17, Neoplasm Proteins
Published
2018

35. Gene Coexpression Networks in Whole Blood Implicate Multiple Interrelated Molecular Pathways in Obesity in People with Asthma.

Author

Croteau‐Chonka, Damien C., Chen, Zhanghua, Barnes, Kathleen C., Barraza‐Villarreal, Albino, Celedón, Juan C., Gauderman, W. James, Gilliland, Frank D., Krishnan, Jerry A., Liu, Andrew H., London, Stephanie J., Martinez, Fernando D., Millstein, Joshua, Naureckas, Edward T., Nicolae, Dan L., White, Steven R., Ober, Carole, Weiss, Scott T., Raby, Benjamin A., Croteau-Chonka, Damien C, and Barraza-Villarreal, Albino

Subjects
ASTHMA in children, ASTHMATICS, OBESITY, ADOLESCENCE, GENE expression, ASTHMA, LONGITUDINAL method
Abstract

Objective: Asthmatic children who develop obesity through adolescence have poorer disease outcomes compared with those who do not. This study aimed to characterize the biology of childhood asthma complicated by adult obesity.Methods: Gene expression networks are powerful statistical tools for characterizing human disease that leverage the putative coregulatory relationships of genes to infer relevant biological pathways. Weighted gene coexpression network analysis of gene expression data was performed in whole blood from 514 adult asthmatic subjects. Then, module preservation and association replication analyses were performed in 418 subjects from two independent asthma cohorts (one pediatric and one adult).Results: A multivariate model was identified in which three gene coexpression network modules were associated with incident obesity in the discovery cohort (each P < 0.05). Two module memberships were enriched for genes in pathways related to platelets, integrins, extracellular matrix, smooth muscle, NF-κB signaling, and Hedgehog signaling. The network structures of each of the obesity modules were significantly preserved in both replication cohorts (permutation P = 9.999E-05). The corresponding module gene sets were significantly enriched for differential expression in subjects with obesity in both replication cohorts (each P < 0.05).Conclusions: The gene coexpression network profiles thus implicate multiple interrelated pathways in the biology of an important endotype of asthma with obesity. [ABSTRACT FROM AUTHOR]

Published
2018
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37. An Integrative Transcriptomic and Metabolomic Study of Lung Function in Children With Asthma

Author

Kelly, Rachel S, Chawes, Bo L, Blighe, Kevin, Virkud, Yamini V, Croteau-Chonka, Damien C, McGeachie, Michael J, Clish, Clary B, Bullock, Kevin, Celedón, Juan C, Weiss, Scott T, Lasky-Su, Jessica A, Kelly, Rachel S, Chawes, Bo L, Blighe, Kevin, Virkud, Yamini V, Croteau-Chonka, Damien C, McGeachie, Michael J, Clish, Clary B, Bullock, Kevin, Celedón, Juan C, Weiss, Scott T, and Lasky-Su, Jessica A

Abstract

BACKGROUND: Single omic analyses have provided some insight into the basis of lung function in children with asthma, but the underlying biologic pathways are still poorly understood.METHODS: Weighted gene coexpression network analysis (WGCNA) was used to identify modules of coregulated gene transcripts and metabolites in blood among 325 children with asthma from the Genetic Epidemiology of Asthma in Costa Rica study. The biology of modules associated with lung function as measured by FEV1, the FEV1/FVC ratio, bronchodilator response, and airway responsiveness to methacholine was explored. Significantly correlated gene-metabolite module pairs were then identified, and their constituent features were analyzed for biologic pathway enrichments.RESULTS: WGCNA clustered 25,060 gene probes and 8,185 metabolite features into eight gene modules and eight metabolite modules, where four and six, respectively, were associated with lung function (P ≤ .05). The gene modules were enriched for immune, mitotic, and metabolic processes and asthma-associated microRNA targets. The metabolite modules were enriched for lipid and amino acid metabolism. Integration of correlated gene-metabolite modules expanded the single omic findings, linking the FEV1/FVC ratio with ORMDL3 and dysregulated lipid metabolism. This finding was replicated in an independent population.CONCLUSIONS: The results of this hypothesis-generating study suggest a mechanistic basis for multiple asthma genes, including ORMDL3, and a role for lipid metabolism. They demonstrate that integrating multiple omic technologies may provide a more informative picture of asthmatic lung function biology than single omic analyses.

Published
2018

38. Across-cohort QC analyses of GWAS summary statistics from complex traits

Author

Trzaskowski, Maciej, Yang, Jian, Robinson, Matthew R, Lee, Sang Hong, Visscher, Peter M., Chen, Guo-Bo, Loos, Ruth J F, Zhu, Zhi-Xiang, Wray, Naomi R, Locke, Adam E, Winkler, Thomas W, Frayling, Timothy M, Hirschhorn, Joel N, Day, Felix R, Croteau-Chonka, Damien C, Wood, Andrew R, and Kutalik, Zoltán

Abstract

Genome-wide association studies (GWASs) have been successful in discovering SNP trait associations for many quantitative traits and common diseases. Typically, the effect sizes of SNP alleles are very small and this requires large genome-wide association meta-analyses (GWAMAs) to maximize statistical power. A trend towards ever-larger GWAMA is likely to continue, yet dealing with summary statistics from hundreds of cohorts increases logistical and quality control problems, including unknown sample overlap, and these can lead to both false positive and false negative findings. In this study, we propose four metrics and visualization tools for GWAMA, using summary statistics from cohort-level GWASs. We propose methods to examine the concordance between demographic information, and summary statistics and methods to investigate sample overlap. (I) We use the population genetics Fst statistic to verify the genetic origin of each cohort and their geographic location, and demonstrate using GWAMA data from the GIANT Consortium that geographic locations of cohorts can be recovered and outlier cohorts can be detected. (II) We conduct principal component analysis based on reported allele frequencies, and are able to recover the ancestral information for each cohort. (III) We propose a new statistic that uses the reported allelic effect sizes and their standard errors to identify significant sample overlap or heterogeneity between pairs of cohorts. (IV) To quantify unknown sample overlap across all pairs of cohorts, we propose a method that uses randomly generated genetic predictors that does not require the sharing of individual-level genotype data and does not breach individual privacy.

Published
2017
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43. Role of local CpG DNA methylation in mediating the 17q21 asthma susceptibility gasdermin B (GSDMB)/ORMDL sphingolipid biosynthesis regulator 3 (ORMDL3) expression quantitative trait locus

Author

Kothari, Parul H., primary, Qiu, Weiliang, additional, Croteau-Chonka, Damien C., additional, Martinez, Fernando D., additional, Liu, Andrew H., additional, Lemanske, Robert F., additional, Ober, Carole, additional, Krishnan, Jerry A., additional, Nicolae, Dan L., additional, Barnes, Kathleen C., additional, London, Stephanie J., additional, Barraza-Villarreal, Albino, additional, White, Steven R., additional, Naureckas, Edward T., additional, Millstein, Joshua, additional, Gauderman, W. James, additional, Gilliland, Frank D., additional, Carey, Vincent J., additional, Weiss, Scott T., additional, and Raby, Benjamin A., additional

Published
2018
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44. Meta-analysis of genome-wide association studies for body fat distribution in 694,649 individuals of European ancestry

Author

Pulit, Sara L., primary, Stoneman, Charli, additional, Morris, Andrew P., additional, Wood, Andrew R., additional, Glastonbury, Craig A., additional, Tyrrell, Jessica, additional, Yengo, Loïc, additional, Ferreira, Teresa, additional, Marouli, Eirini, additional, Ji, Yingjie, additional, Yang, Jian, additional, Jones, Samuel, additional, Beaumont, Robin, additional, Croteau-Chonka, Damien C., additional, Winkler, Thomas W., additional, Consortium, Giant, additional, Hattersley, Andrew. T., additional, Loos, Ruth J. F., additional, Hirschhorn, Joel N., additional, Visscher, Peter M., additional, Frayling, Timothy M., additional, Yaghootkar, Hanieh, additional, and Lindgren, Cecilia M., additional

Published
2018
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45. Across-cohort QC analyses of GWAS summary statistics from complex traits

Author

Chen, Guo-Bo, Lee, Sang Hong, Robinson, Matthew R, Trzaskowski, Maciej, Zhu, Zhi-Xiang, Winkler, Thomas W, Day, Felix R, Croteau-Chonka, Damien C, Wood, Andrew R, Locke, Adam E, Kutalik, Zoltán, Loos, Ruth JF, Frayling, Timothy M, Hirschhorn, Joel N, Yang, Jian, Wray, Naomi R, Genetic Investigation Of Anthropometric Traits (GIANT) Consortium, Visscher, Peter M, Chen, Guo-Bo [0000-0001-5475-8237], Day, Felix R [0000-0003-3789-7651], Yang, Jian [0000-0003-2001-2474], Wray, Naomi R [0000-0001-7421-3357], Visscher, Peter M [0000-0002-2143-8760], and Apollo - University of Cambridge Repository

Subjects
Cohort Studies, Genetic Heterogeneity, Phenotype, Genotype, Meta-Analysis as Topic, Quantitative Trait Loci, Humans, Polymorphism, Single Nucleotide, Alleles, Software, Genome-Wide Association Study
Abstract

Genome-wide association studies (GWASs) have been successful in discovering SNP trait associations for many quantitative traits and common diseases. Typically, the effect sizes of SNP alleles are very small and this requires large genome-wide association meta-analyses (GWAMAs) to maximize statistical power. A trend towards ever-larger GWAMA is likely to continue, yet dealing with summary statistics from hundreds of cohorts increases logistical and quality control problems, including unknown sample overlap, and these can lead to both false positive and false negative findings. In this study, we propose four metrics and visualization tools for GWAMA, using summary statistics from cohort-level GWASs. We propose methods to examine the concordance between demographic information, and summary statistics and methods to investigate sample overlap. (I) We use the population genetics Fst statistic to verify the genetic origin of each cohort and their geographic location, and demonstrate using GWAMA data from the GIANT Consortium that geographic locations of cohorts can be recovered and outlier cohorts can be detected. (II) We conduct principal component analysis based on reported allele frequencies, and are able to recover the ancestral information for each cohort. (III) We propose a new statistic that uses the reported allelic effect sizes and their standard errors to identify significant sample overlap or heterogeneity between pairs of cohorts. (IV) To quantify unknown sample overlap across all pairs of cohorts, we propose a method that uses randomly generated genetic predictors that does not require the sharing of individual-level genotype data and does not breach individual privacy.

Published
2016

46. Gene co-expression networks in whole blood implicate multiple interrelated molecular pathways in obese asthma

Author

Croteau-Chonka, Damien C., primary, Chen, Zhanghua, additional, Barnes, Kathleen C., additional, Barraza-Villarreal, Albino, additional, Celedón, Juan C., additional, James Gauderman, W., additional, Gilliland, Frank D., additional, Krishnan, Jerry A., additional, Liu, Andrew H., additional, London, Stephanie J., additional, Martinez, Fernando D., additional, Millstein, Joshua, additional, Naureckas, Edward T., additional, Nicolae, Dan L., additional, White, Steven R., additional, Ober, Carole, additional, Weiss, Scott T., additional, and Raby, Benjamin A., additional

Published
2017
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49. Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma

Author

McGeachie, Michael J., primary, Yates, Katherine P., additional, Zhou, Xiaobo, additional, Guo, Feng, additional, Sternberg, Alice L., additional, Van Natta, Mark L., additional, Wise, Robert A., additional, Szefler, Stanley J., additional, Sharma, Sunita, additional, Kho, Alvin T., additional, Cho, Michael H., additional, Croteau-Chonka, Damien C., additional, Castaldi, Peter J., additional, Jain, Gaurav, additional, Sanyal, Amartya, additional, Zhan, Ye, additional, Lajoie, Bryan R., additional, Dekker, Job, additional, Stamatoyannopoulos, John, additional, Covar, Ronina A., additional, Zeiger, Robert S., additional, Adkinson, N. Franklin, additional, Williams, Paul V., additional, Kelly, H. William, additional, Grasemann, Hartmut, additional, Vonk, Judith M., additional, Koppelman, Gerard H., additional, Postma, Dirkje S., additional, Raby, Benjamin A., additional, Houston, Isaac, additional, Lu, Quan, additional, Fuhlbrigge, Anne L., additional, Tantisira, Kelan G., additional, Silverman, Edwin K., additional, Tonascia, James, additional, Strunk, Robert C., additional, and Weiss, Scott T., additional

Published
2016
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50. Integration of metabolomic and transcriptomic networks in pregnant women reveals biological pathways and predictive signatures associated with preeclampsia

Author

Kelly, Rachel S., primary, Croteau-Chonka, Damien C., additional, Dahlin, Amber, additional, Mirzakhani, Hooman, additional, Wu, Ann C., additional, Wan, Emily S., additional, McGeachie, Michael J., additional, Qiu, Weiliang, additional, Sordillo, Joanne E., additional, Al-Garawi, Amal, additional, Gray, Kathryn J., additional, McElrath, Thomas F., additional, Carey, Vincent J., additional, Clish, Clary B., additional, Litonjua, Augusto A., additional, Weiss, Scott T., additional, and Lasky-Su, Jessica A., additional

Published
2016
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