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Author: Mariza de Andrade (220)


Nov
2017

Evidence show that stress hormones can influence cancer progression, but its role in carcinogenesis is poorly understood. In this study, we used a new method based on oral carcinogenesis model in rats to test the hypothesis that physiological levels of stress hormones in the normal tissue microenvironment would have significant predictive value for chemically induced cancer occurrence. Male Wistar rats were submitted to a tongue biopsy for measuring not-stress induced levels of norepinephrine, corticosterone, adrenocorticotropic hormone (ACTH) and brain-derived neurotrophic factor (BDNF) in the tissue before carcinogenic induction.

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Oct
2017

Certain diseases can occur with and without a trigger. We use Venous Thromboembolism (VTE) as our example to identify genetic interaction with pregnancy in women with VTE during pre- or postpartum. Pregnancy is one of the major risk factors for VTE as it accounts for 10% of maternal deaths.

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Sep
2017

Gene-environment (GE) interaction has important implications in the etiology of complex diseases that are caused by a combination of genetic factors and environment variables. Several authors have developed GE analysis in the context of independent subjects or longitudinal data using a gene-set. In this paper, we propose to analyze GE interaction for discrete and continuous phenotypes in family studies by incorporating the relatedness among the relatives for each family into a generalized linear mixed model (GLMM) and by using a gene-based variance component test.

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Dec
1969

One of four American cancer patients dies of lung cancer. Environmental factors such as tobacco smoking are known to affect lung cancer risk. However, there is a genetic factor to lung cancer risk as well.

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Aug
2017

To determine if hepatocyte growth factor (HGF), a promising biomarker of coronary heart disease (CHD) given its release into circulation in response to endothelial damage, is associated with subclinical and clinical CHD in a racial/ethnic diverse population.
HGF was measured in 6738 participants of the Multi-Ethnic Study of Atherosclerosis (MESA). Highest mean HGF values (pg/mL) were observed in Hispanic, followed by African, non-Hispanic white, then Chinese Americans.

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Jul
2017

Observational studies have shown an association between obesity and venous thromboembolism (VTE) but it is not known if observed associations are causal, due to reverse causation or confounding bias. We conducted a Mendelian Randomization study of body mass index (BMI) and VTE. We identified 95 single nucleotide polymorphisms (SNPs) that have been previously associated with BMI and assessed the association between genetically predicted high BMI and VTE leveraging data from a previously conducted GWAS within the INVENT consortium comprising a total of 7507 VTE cases and 52,632 controls of European ancestry.

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Apr
2017

Achaete-scute homolog 1 (ASCL1) is a neuroendocrine transcription factor specifically expressed in 10-20% of lung adenocarcinomas (AD) with neuroendocrine (NE) differentiation (NED). ASCL1 functions as an upstream regulator of the RET oncogene in AD with high ASCL1 expression (A+AD). RET is a receptor tyrosine kinase with two main human isoforms; RET9 (short) and RET51 (long).

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Aug
2017

NFAT5 and SLC4A10 Loci Associate with Plasma Osmolality.

J Am Soc Nephrol 2017 Aug 30;28(8):2311-2321. Epub 2017 Mar 30.
Carsten A Böger, Mathias Gorski, Gearoid M McMahon, Huichun Xu, Yen-Pei C Chang, Peter J van der Most, Gerjan Navis, Ilja M Nolte, Martin H de Borst, Weihua Zhang, Benjamin Lehne, Marie Loh, Sian-Tsung Tan, Eric Boerwinkle, Morgan E Grams, Peggy Sekula, Man Li, Beth Wilmot, James G Moon, Paul Scheet, Francesco Cucca, Xiangjun Xiao, Leo-Pekka Lyytikäinen, Graciela Delgado, Tanja B Grammer, Marcus E Kleber, Sanaz Sedaghat, Fernando Rivadeneira, Tanguy Corre, Zoltan Kutalik, Sven Bergmann, Carrie M Nielson, Priya Srikanth, Alexander Teumer, Martina Müller-Nurasyid, Anne Catharina Brockhaus, Arne Pfeufer, Wolfgang Rathmann, Annette Peters, Martha Matsumoto, Mariza de Andrade, Elizabeth J Atkinson, Cassianne Robinson-Cohen, Ian H de Boer, Shih-Jen Hwang, Iris M Heid, Martin Gögele, Maria Pina Concas, Toshiko Tanaka, Stefania Bandinelli, Mike A Nalls, Andrew Singleton, Salman M Tajuddin, Adebowale Adeyemo, Jie Zhou, Ayo Doumatey, Shannon McWeeney, Joanne Murabito, Nora Franceschini, Michael Flessner, Michael Shlipak, James G Wilson, Guanjie Chen, Charles N Rotimi, Alan B Zonderman, Michele K Evans, Luigi Ferrucci, Olivier Devuyst, Mario Pirastu, Alan Shuldiner, Andrew A Hicks, Peter Paul Pramstaller, Bryan Kestenbaum, Sharon L R Kardia, Stephen T Turner, LifeLines Cohort Study, Tamara Ellefson Briske, Christian Gieger, Konstantin Strauch, Christa Meisinger, Thomas Meitinger, Uwe Völker, Matthias Nauck, Henry Völzke, Peter Vollenweider, Murielle Bochud, Gerard Waeber, Mika Kähönen, Terho Lehtimäki, Winfried März, Abbas Dehghan, Oscar H Franco, Andre G Uitterlinden, Albert Hofman, Herman A Taylor, John C Chambers, Jaspal S Kooner, Caroline S Fox, Robert Hitzemann, Eric S Orwoll, Cristian Pattaro, David Schlessinger, Anna Köttgen, Harold Snieder, Afshin Parsa, David M Cohen
Disorders of water balance, an excess or deficit of total body water relative to body electrolyte content, are common and ascertained by plasma hypo- or hypernatremia, respectively. We performed a two-stage genome-wide association study meta-analysis on plasma sodium concentration in 45,889 individuals of European descent (stage 1 discovery) and 17,637 additional individuals of European descent (stage 2 replication), and a transethnic meta-analysis of replicated single-nucleotide polymorphisms in 79,506 individuals (63,526 individuals of European descent, 8765 individuals of Asian Indian descent, and 7215 individuals of African descent). In stage 1, we identified eight loci associated with plasma sodium concentration at P<5.

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Oct
2017

Primary sclerosing cholangitis (PSC) typically develops in middle-age adults. Little is known about phenotypic differences when PSC is diagnosed at various ages. Therefore, we sought to compare the clinical characteristics of a large PSC cohort based on the age when PSC was diagnosed.

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Dec
1969

Resistant hypertension is defined as high blood pressure that remains above treatment goals in spite of the concurrent use of three antihypertensive agents from different classes. Despite the important health consequences of resistant hypertension, few studies of resistant hypertension have been conducted. To perform a genome-wide association study for resistant hypertension, we defined and identified cases of resistant hypertension and hypertensives with treated, controlled hypertension among >47,500 adults residing in the US linked to electronic health records (EHRs) and genotyped as part of the electronic MEdical Records & GEnomics (eMERGE) Network.

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Apr
2017

To identify novel single nucleotide polymorphisms (SNPs) associated with venous thromboembolism (VTE) in African-Americans (AAs), we performed a genome-wide association study (GWAS) of VTE in AAs using the Electronic Medical Records and Genomics (eMERGE) Network, comprised of seven sites each with DNA biobanks (total ~39,200 unique DNA samples) with genome-wide SNP data (imputed to 1000 Genomes Project cosmopolitan reference panel) and linked to electronic health records (EHRs). Using a validated EHR-driven phenotype extraction algorithm, we identified VTE cases and controls and tested for an association between each SNP and VTE using unconditional logistic regression, adjusted for age, sex, stroke, site-platform combination and sickle cell risk genotype. Among 393 AA VTE cases and 4,941 AA controls, three intragenic SNPs reached genome-wide significance: LEMD3 rs138916004 (OR=3.

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Jan
2017

Lung cancer is the deadliest cancer in the United States, killing roughly one of four cancer patients in 2016. While it is well-established that lung cancer is caused primarily by environmental effects (particularly tobacco smoking), there is evidence for genetic susceptibility. Lung cancer has been shown to aggregate in families, and segregation analyses have hypothesized a major susceptibility locus for the disease.

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Feb
2017

Primary sclerosing cholangitis (PSC) is a rare progressive disorder leading to bile duct destruction; ∼75% of patients have comorbid inflammatory bowel disease (IBD). We undertook the largest genome-wide association study of PSC (4,796 cases and 19,955 population controls) and identified four new genome-wide significant loci. The most associated SNP at one locus affects splicing and expression of UBASH3A, with the protective allele (C) predicted to cause nonstop-mediated mRNA decay and lower expression of UBASH3A.

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Feb
2017

PCSK9 genetic variants and risk of type 2 diabetes: a mendelian randomisation study.

Lancet Diabetes Endocrinol 2017 Feb 29;5(2):97-105. Epub 2016 Nov 29.
Amand F Schmidt, Daniel I Swerdlow, Michael V Holmes, Riyaz S Patel, Zammy Fairhurst-Hunter, Donald M Lyall, Fernando Pires Hartwig, Bernardo Lessa Horta, Elina Hyppönen, Christine Power, Max Moldovan, Erik van Iperen, G Kees Hovingh, Ilja Demuth, Kristina Norman, Elisabeth Steinhagen-Thiessen, Juri Demuth, Lars Bertram, Tian Liu, Stefan Coassin, Johann Willeit, Stefan Kiechl, Karin Willeit, Dan Mason, John Wright, Richard Morris, Goya Wanamethee, Peter Whincup, Yoav Ben-Shlomo, Stela McLachlan, Jackie F Price, Mika Kivimaki, Catherine Welch, Adelaida Sanchez-Galvez, Pedro Marques-Vidal, Andrew Nicolaides, Andrie G Panayiotou, N Charlotte Onland-Moret, Yvonne T van der Schouw, Giuseppe Matullo, Giovanni Fiorito, Simonetta Guarrera, Carlotta Sacerdote, Nicholas J Wareham, Claudia Langenberg, Robert Scott, Jian'an Luan, Martin Bobak, Sofia Malyutina, Andrzej Pająk, Ruzena Kubinova, Abdonas Tamosiunas, Hynek Pikhart, Lise Lotte Nystrup Husemoen, Niels Grarup, Oluf Pedersen, Torben Hansen, Allan Linneberg, Kenneth Starup Simonsen, Jackie Cooper, Steve E Humphries, Murray Brilliant, Terrie Kitchner, Hakon Hakonarson, David S Carrell, Catherine A McCarty, H Lester Kirchner, Eric B Larson, David R Crosslin, Mariza de Andrade, Dan M Roden, Joshua C Denny, Cara Carty, Stephen Hancock, John Attia, Elizabeth Holliday, Martin O'Donnell, Salim Yusuf, Michael Chong, Guillaume Pare, Pim van der Harst, M Abdullah Said, Ruben N Eppinga, Niek Verweij, Harold Snieder, , Tim Christen, Dennis O Mook-Kanamori, Stefan Gustafsson, Lars Lind, Erik Ingelsson, Raha Pazoki, Oscar Franco, Albert Hofman, Andre Uitterlinden, Abbas Dehghan, Alexander Teumer, Sebastian Baumeister, Marcus Dörr, Markus M Lerch, Uwe Völker, Henry Völzke, Joey Ward, Jill P Pell, Daniel J Smith, Tom Meade, Anke H Maitland-van der Zee, Ekaterina V Baranova, Robin Young, Ian Ford, Archie Campbell, Sandosh Padmanabhan, Michiel L Bots, Diederick E Grobbee, Philippe Froguel, Dorothée Thuillier, Beverley Balkau, Amélie Bonnefond, Bertrand Cariou, Melissa Smart, Yanchun Bao, Meena Kumari, Anubha Mahajan, Paul M Ridker, Daniel I Chasman, Alex P Reiner, Leslie A Lange, Marylyn D Ritchie, Folkert W Asselbergs, Juan-Pablo Casas, Brendan J Keating, David Preiss, Aroon D Hingorani, , Naveed Sattar
Statin treatment and variants in the gene encoding HMG-CoA reductase are associated with reductions in both the concentration of LDL cholesterol and the risk of coronary heart disease, but also with modest hyperglycaemia, increased bodyweight, and modestly increased risk of type 2 diabetes, which in no way offsets their substantial benefits. We sought to investigate the associations of LDL cholesterol-lowering PCSK9 variants with type 2 diabetes and related biomarkers to gauge the likely effects of PCSK9 inhibitors on diabetes risk.
In this mendelian randomisation study, we used data from cohort studies, randomised controlled trials, case control studies, and genetic consortia to estimate associations of PCSK9 genetic variants with LDL cholesterol, fasting blood glucose, HbA1c, fasting insulin, bodyweight, waist-to-hip ratio, BMI, and risk of type 2 diabetes, using a standardised analysis plan, meta-analyses, and weighted gene-centric scores.

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Jan
2017

Meta-Analysis of Genome-Wide Association Studies for Abdominal Aortic Aneurysm Identifies Four New Disease-Specific Risk Loci.

Circ Res 2017 Jan 29;120(2):341-353. Epub 2016 Nov 29.
Gregory T Jones, Gerard Tromp, Helena Kuivaniemi, Solveig Gretarsdottir, Annette F Baas, Betti Giusti, Ewa Strauss, Femke N G Van't Hof, Thomas R Webb, Robert Erdman, Marylyn D Ritchie, James R Elmore, Anurag Verma, Sarah Pendergrass, Iftikhar J Kullo, Zi Ye, Peggy L Peissig, Omri Gottesman, Shefali S Verma, Jennifer Malinowski, Laura J Rasmussen-Torvik, Kenneth M Borthwick, Diane T Smelser, David R Crosslin, Mariza de Andrade, Evan J Ryer, Catherine A McCarty, Erwin P Böttinger, Jennifer A Pacheco, Dana C Crawford, David S Carrell, Glenn S Gerhard, David P Franklin, David J Carey, Victoria L Phillips, Michael J A Williams, Wenhua Wei, Ross Blair, Andrew A Hill, Thodor M Vasudevan, David R Lewis, Ian A Thomson, Jo Krysa, Geraldine B Hill, Justin Roake, Tony R Merriman, Grzegorz Oszkinis, Silvia Galora, Claudia Saracini, Rosanna Abbate, Raffaele Pulli, Carlo Pratesi, Athanasios Saratzis, Ana R Verissimo, Suzannah Bumpstead, Stephen A Badger, Rachel E Clough, Gillian Cockerill, Hany Hafez, D Julian A Scott, T Simon Futers, Simon P R Romaine, Katherine Bridge, Kathryn J Griffin, Marc A Bailey, Alberto Smith, Matthew M Thompson, Frank M van Bockxmeer, Stefan E Matthiasson, Gudmar Thorleifsson, Unnur Thorsteinsdottir, Jan D Blankensteijn, Joep A W Teijink, Cisca Wijmenga, Jacqueline de Graaf, Lambertus A Kiemeney, Jes S Lindholt, Anne Hughes, Declan T Bradley, Kathleen Stirrups, Jonathan Golledge, Paul E Norman, Janet T Powell, Steve E Humphries, Stephen E Hamby, Alison H Goodall, Christopher P Nelson, Natzi Sakalihasan, Audrey Courtois, Robert E Ferrell, Per Eriksson, Lasse Folkersen, Anders Franco-Cereceda, John D Eicher, Andrew D Johnson, Christer Betsholtz, Arno Ruusalepp, Oscar Franzén, Eric E Schadt, Johan L M Björkegren, Leonard Lipovich, Anne M Drolet, Eric L Verhoeven, Clark J Zeebregts, Robert H Geelkerken, Marc R van Sambeek, Steven M van Sterkenburg, Jean-Paul de Vries, Kari Stefansson, John R Thompson, Paul I W de Bakker, Panos Deloukas, Robert D Sayers, Seamus C Harrison, Andre M van Rij, Nilesh J Samani, Matthew J Bown
Abdominal aortic aneurysm (AAA) is a complex disease with both genetic and environmental risk factors. Together, 6 previously identified risk loci only explain a small proportion of the heritability of AAA.
To identify additional AAA risk loci using data from all available genome-wide association studies.

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Dec
1969

Cardiovascular disease (CVD) is a major challenge to global health. The same epidemiological transition scenario is replayed as countries develop, but with variations based on environment, culture and ethnic mixture. The Baependi Heart Study was set up in 2005 to develop a longitudinal family-based cohort study that reflects on some of the genetic and lifestyle-related peculiarities of the Brazilian populations, in order to evaluate genetic and environmental influences on CVD risk factor traits.

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Dec
1969

We explored premature stop-gain variants to test the hypothesis that variants, which are likely to have a consequence on protein structure and function, will reveal important insights with respect to the phenotypes associated with them. We performed a phenome-wide association study (PheWAS) exploring the association between a selected list of functional stop-gain genetic variants (variation resulting in truncated proteins or in nonsense-mediated decay) and an extensive group of diagnoses to identify novel associations and uncover potential pleiotropy.
In this study, we selected 25 stop-gain variants: 5 stop-gain variants with previously reported phenotypic associations, and a set of 20 putative stop-gain variants identified using dbSNP.

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Apr
2017

Inflammation plays a pivotal role in peripheral artery disease (PAD). Cellular adhesion proteins mediate the interaction of leukocytes with endothelial cells during inflammation. To determine the association of cellular adhesion molecules with ankle-brachial index (ABI) and ABI category (≤1.

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Jul
2016

Intracranial aneurysms (IAs), abdominal aortic aneurysms (AAAs), and thoracic aortic aneurysms (TAAs) all have a familial predisposition. Given that aneurysm types are known to co-occur, we hypothesized that there may be shared genetic risk factors for IAs, AAAs, and TAAs.
We performed a mega-analysis of 1000 Genomes Project-imputed genome-wide association study (GWAS) data of 4 previously published aneurysm cohorts: 2 IA cohorts (in total 1516 cases, 4305 controls), 1 AAA cohort (818 cases, 3004 controls), and 1 TAA cohort (760 cases, 2212 controls), and observed associations of 4 known IA, AAA, and/or TAA risk loci (9p21, 18q11, 15q21, and 2q33) with consistent effect directions in all 4 cohorts.

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Jul
2016

An important precursor to lung cancer development is chronic obstructive pulmonary disease (COPD), independent of exposure to tobacco smoke. Both diseases are associated with increased host susceptibility, inflammation, and genomic instability. However, validation of the candidate genes and functional confirmation to test shared genetic contribution and cellular mechanisms to the development of lung cancer in patients with COPD remains underexplored.

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Aug
2016

Onset and symptoms of menopause, and response to hormone therapy (HT) show large interindividual variability. SULT1A1 encodes for a highly expressed enzyme that metabolizes estrogens. We evaluated the relationship between genetic variation in SULT1A1, menopause age, symptoms, and response to HT.

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Apr
2016

Endothelial dysfunction is an early stage of atherosclerosis. Single-nucleotide polymorphisms (SNPs) have been associated with vascular dysfunction, cardiac events, and coronary artery remodeling. We aimed to detect SNPs associated with endothelial dysfunction and determine whether these associations are sex specific.

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May
2016

The International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society and 2015 World Health Organization classifications of lung adenocarcinoma recommend designating tumors showing entirely lepidic growth as adenocarcinoma in situ (AIS) and lepidic tumors with invasion less than or equal to 5 mm as minimally invasive adenocarcinoma (MIA), both of which have superior outcome to conventional invasive adenocarcinoma (IA). Data on interobserver variability within this classification are limited, and further validation of the superior survival of AIS and MIA is needed. A total of 296 surgically excised pulmonary adenocarcinomas were reviewed from 254 patients (1997-2009).

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Apr
2016

The goal of this paper is to present an implementation of stochastic search variable selection (SSVS) to multilevel model from item response theory (IRT). As experimental settings get more complex and models are required to integrate multiple (and sometimes massive) sources of information, a model that can jointly summarize and select the most relevant characteristics can provide better interpretation and a deeper insight into the problem. A multilevel IRT model recently proposed in the literature for modeling multifactorial diseases is extended to perform variable selection in the presence of thousands of covariates using SSVS.

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Jan
2016

Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.

Nat Commun 2016 Jan 21;7:10023. Epub 2016 Jan 21.
Cristian Pattaro, Alexander Teumer, Mathias Gorski, Audrey Y Chu, Man Li, Vladan Mijatovic, Maija Garnaas, Adrienne Tin, Rossella Sorice, Yong Li, Daniel Taliun, Matthias Olden, Meredith Foster, Qiong Yang, Ming-Huei Chen, Tune H Pers, Andrew D Johnson, Yi-An Ko, Christian Fuchsberger, Bamidele Tayo, Michael Nalls, Mary F Feitosa, Aaron Isaacs, Abbas Dehghan, Pio d'Adamo, Adebowale Adeyemo, Aida Karina Dieffenbach, Alan B Zonderman, Ilja M Nolte, Peter J van der Most, Alan F Wright, Alan R Shuldiner, Alanna C Morrison, Albert Hofman, Albert V Smith, Albert W Dreisbach, Andre Franke, Andre G Uitterlinden, Andres Metspalu, Anke Tonjes, Antonio Lupo, Antonietta Robino, Åsa Johansson, Ayse Demirkan, Barbara Kollerits, Barry I Freedman, Belen Ponte, Ben A Oostra, Bernhard Paulweber, Bernhard K Krämer, Braxton D Mitchell, Brendan M Buckley, Carmen A Peralta, Caroline Hayward, Catherine Helmer, Charles N Rotimi, Christian M Shaffer, Christian Müller, Cinzia Sala, Cornelia M van Duijn, Aude Saint-Pierre, Daniel Ackermann, Daniel Shriner, Daniela Ruggiero, Daniela Toniolo, Yingchang Lu, Daniele Cusi, Darina Czamara, David Ellinghaus, David S Siscovick, Douglas Ruderfer, Christian Gieger, Harald Grallert, Elena Rochtchina, Elizabeth J Atkinson, Elizabeth G Holliday, Eric Boerwinkle, Erika Salvi, Erwin P Bottinger, Federico Murgia, Fernando Rivadeneira, Florian Ernst, Florian Kronenberg, Frank B Hu, Gerjan J Navis, Gary C Curhan, George B Ehret, Georg Homuth, Stefan Coassin, Gian-Andri Thun, Giorgio Pistis, Giovanni Gambaro, Giovanni Malerba, Grant W Montgomery, Gudny Eiriksdottir, Gunnar Jacobs, Guo Li, H-Erich Wichmann, Harry Campbell, Helena Schmidt, Henri Wallaschofski, Henry Völzke, Hermann Brenner, Heyo K Kroemer, Holly Kramer, Honghuang Lin, I Mateo Leach, Ian Ford, Idris Guessous, Igor Rudan, Inga Prokopenko, Ingrid Borecki, Iris M Heid, Ivana Kolcic, Ivana Persico, J Wouter Jukema, James F Wilson, Janine F Felix, Jasmin Divers, Jean-Charles Lambert, Jeanette M Stafford, Jean-Michel Gaspoz, Jennifer A Smith, Jessica D Faul, Jie Jin Wang, Jingzhong Ding, Joel N Hirschhorn, John Attia, John B Whitfield, John Chalmers, Jorma Viikari, Josef Coresh, Joshua C Denny, Juha Karjalainen, Jyotika K Fernandes, Karlhans Endlich, Katja Butterbach, Keith L Keene, Kurt Lohman, Laura Portas, Lenore J Launer, Leo-Pekka Lyytikäinen, Loic Yengo, Lude Franke, Luigi Ferrucci, Lynda M Rose, Lyudmyla Kedenko, Madhumathi Rao, Maksim Struchalin, Marcus E Kleber, Margherita Cavalieri, Margot Haun, Marilyn C Cornelis, Marina Ciullo, Mario Pirastu, Mariza de Andrade, Mark A McEvoy, Mark Woodward, Martin Adam, Massimiliano Cocca, Matthias Nauck, Medea Imboden, Melanie Waldenberger, Menno Pruijm, Marie Metzger, Michael Stumvoll, Michele K Evans, Michele M Sale, Mika Kähönen, Mladen Boban, Murielle Bochud, Myriam Rheinberger, Niek Verweij, Nabila Bouatia-Naji, Nicholas G Martin, Nick Hastie, Nicole Probst-Hensch, Nicole Soranzo, Olivier Devuyst, Olli Raitakari, Omri Gottesman, Oscar H Franco, Ozren Polasek, Paolo Gasparini, Patricia B Munroe, Paul M Ridker, Paul Mitchell, Paul Muntner, Christa Meisinger, Johannes H Smit, , , , , , Peter Kovacs, Philipp S Wild, Philippe Froguel, Rainer Rettig, Reedik Mägi, Reiner Biffar, Reinhold Schmidt, Rita P S Middelberg, Robert J Carroll, Brenda W Penninx, Rodney J Scott, Ronit Katz, Sanaz Sedaghat, Sarah H Wild, Sharon L R Kardia, Sheila Ulivi, Shih-Jen Hwang, Stefan Enroth, Stefan Kloiber, Stella Trompet, Benedicte Stengel, Stephen J Hancock, Stephen T Turner, Sylvia E Rosas, Sylvia Stracke, Tamara B Harris, Tanja Zeller, Tatijana Zemunik, Terho Lehtimäki, Thomas Illig, Thor Aspelund, Tiit Nikopensius, Tonu Esko, Toshiko Tanaka, Ulf Gyllensten, Uwe Völker, Valur Emilsson, Veronique Vitart, Ville Aalto, Vilmundur Gudnason, Vincent Chouraki, Wei-Min Chen, Wilmar Igl, Winfried März, Wolfgang Koenig, Wolfgang Lieb, Ruth J F Loos, Yongmei Liu, Harold Snieder, Peter P Pramstaller, Afshin Parsa, Jeffrey R O'Connell, Katalin Susztak, Pavel Hamet, Johanne Tremblay, Ian H de Boer, Carsten A Böger, Wolfram Goessling, Daniel I Chasman, Anna Köttgen, W H Linda Kao, Caroline S Fox
Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci.

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Jan
2016

The association between smoking-induced chronic obstructive pulmonary disease (COPD) and lung cancer (LC) is well documented. Recent genome-wide association studies (GWAS) have identified 28 susceptibility loci for LC, 10 for COPD, 32 for smoking behavior, and 63 for pulmonary function, totaling 107 nonoverlapping loci. Given that common variants have been found to be associated with LC in genome-wide association studies, exome sequencing of these high-priority regions has great potential to identify novel rare causal variants.

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Jan
2016

At the cellular level, how excess adiposity promotes atherogenesis is not fully understood. One pathway involves secretion of adipokines that stimulate endothelial dysfunction through increased expression of adhesion molecules. However, the relationship of adiposity to adhesion molecules that promote atherosclerosis is largely unknown.

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Jan
2016

Prior to the initiation of menopausal hormone treatment (MHT), genetic variations in the innate immunity pathway were found to be associated with carotid artery intima-medial thickness (CIMT) and coronary arterial calcification (CAC) in women (n = 606) enrolled in the Kronos Early Estrogen Prevention Study (KEEPS). Whether MHT might affect these associations is unknown. The association of treatment outcomes with variation in the same 764 candidate genes was evaluated in the same KEEPS participants 4 yr after randomization to either oral conjugated equine estrogens (0.

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Oct
2015

A comprehensive 1,000 Genomes-based genome-wide association meta-analysis of coronary artery disease.

Nat Genet 2015 Oct 7;47(10):1121-1130. Epub 2015 Sep 7.
Majid Nikpay, Anuj Goel, Hong-Hee Won, Leanne M Hall, Christina Willenborg, Stavroula Kanoni, Danish Saleheen, Theodosios Kyriakou, Christopher P Nelson, Jemma C Hopewell, Thomas R Webb, Lingyao Zeng, Abbas Dehghan, Maris Alver, Sebastian M Armasu, Kirsi Auro, Andrew Bjonnes, Daniel I Chasman, Shufeng Chen, Ian Ford, Nora Franceschini, Christian Gieger, Christopher Grace, Stefan Gustafsson, Jie Huang, Shih-Jen Hwang, Yun Kyoung Kim, Marcus E Kleber, King Wai Lau, Xiangfeng Lu, Yingchang Lu, Leo-Pekka Lyytikäinen, Evelin Mihailov, Alanna C Morrison, Natalia Pervjakova, Liming Qu, Lynda M Rose, Elias Salfati, Richa Saxena, Markus Scholz, Albert V Smith, Emmi Tikkanen, Andre Uitterlinden, Xueli Yang, Weihua Zhang, Wei Zhao, Mariza de Andrade, Paul S de Vries, Natalie R van Zuydam, Sonia S Anand, Lars Bertram, Frank Beutner, George Dedoussis, Philippe Frossard, Dominique Gauguier, Alison H Goodall, Omri Gottesman, Marc Haber, Bok-Ghee Han, Jianfeng Huang, Shapour Jalilzadeh, Thorsten Kessler, Inke R König, Lars Lannfelt, Wolfgang Lieb, Lars Lind, Cecilia M Lindgren, Marja-Liisa Lokki, Patrik K Magnusson, Nadeem H Mallick, Narinder Mehra, Thomas Meitinger, Fazal-Ur-Rehman Memon, Andrew P Morris, Markku S Nieminen, Nancy L Pedersen, Annette Peters, Loukianos S Rallidis, Asif Rasheed, Maria Samuel, Svati H Shah, Juha Sinisalo, Kathleen E Stirrups, Stella Trompet, Laiyuan Wang, Khan S Zaman, Diego Ardissino, Eric Boerwinkle, Ingrid B Borecki, Erwin P Bottinger, Julie E Buring, John C Chambers, Rory Collins, L Adrienne Cupples, John Danesh, Ilja Demuth, Roberto Elosua, Stephen E Epstein, Tõnu Esko, Mary F Feitosa, Oscar H Franco, Maria Grazia Franzosi, Christopher B Granger, Dongfeng Gu, Vilmundur Gudnason, Alistair S Hall, Anders Hamsten, Tamara B Harris, Stanley L Hazen, Christian Hengstenberg, Albert Hofman, Erik Ingelsson, Carlos Iribarren, J Wouter Jukema, Pekka J Karhunen, Bong-Jo Kim, Jaspal S Kooner, Iftikhar J Kullo, Terho Lehtimäki, Ruth J F Loos, Olle Melander, Andres Metspalu, Winfried März, Colin N Palmer, Markus Perola, Thomas Quertermous, Daniel J Rader, Paul M Ridker, Samuli Ripatti, Robert Roberts, Veikko Salomaa, Dharambir K Sanghera, Stephen M Schwartz, Udo Seedorf, Alexandre F Stewart, David J Stott, Joachim Thiery, Pierre A Zalloua, Christopher J O'Donnell, Muredach P Reilly, Themistocles L Assimes, John R Thompson, Jeanette Erdmann, Robert Clarke, Hugh Watkins, Sekar Kathiresan, Ruth McPherson, Panos Deloukas, Heribert Schunkert, Nilesh J Samani, Martin Farrall
Existing knowledge of genetic variants affecting risk of coronary artery disease (CAD) is largely based on genome-wide association study (GWAS) analysis of common SNPs. Leveraging phased haplotypes from the 1000 Genomes Project, we report a GWAS meta-analysis of ∼185,000 CAD cases and controls, interrogating 6.7 million common (minor allele frequency (MAF) > 0.

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Dec
1969

In an effort to return actionable results from variant data to electronic health records (EHRs), participants in the Electronic Medical Records and Genomics (eMERGE) Network are being sequenced with the targeted Pharmacogenomics Research Network sequence platform (PGRNseq). This cost-effective, highly-scalable, and highly-accurate platform was created to explore rare variation in 84 key pharmacogenetic genes with strong drug phenotype associations.
To return Clinical Laboratory Improvement Amendments (CLIA) results to our participants at the Group Health Cooperative, we sequenced the DNA of 900 participants (61 % female) with non-CLIA biobanked samples.

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Nov
2015

Identifying populations of heart failure (HF) patients is paramount to research efforts aimed at developing strategies to effectively reduce the burden of this disease. The use of electronic medical record (EMR) data for this purpose is challenging given the syndromic nature of HF and the need to distinguish HF with preserved or reduced ejection fraction. Using a gold standard cohort of manually abstracted cases, an EMR-driven phenotype algorithm based on structured and unstructured data was developed to identify all the cases.

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Sep
2015

Hypoplastic left heart syndrome (HLHS) is a severe congenital heart defect (CHD) that necessitates staged, single ventricle surgical palliation. An increased frequency of bicuspid aortic valve (BAV) has been observed among relatives. We postulated number of mutant alleles as a molecular basis for variable CHD expression in an extended family comprised of an HLHS proband and four family members who underwent echocardiography and whole-genome sequencing (WGS).

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Dec
1969

Studies of complex human diseases and traits associated with candidate genes are potentially vulnerable to bias (confounding) due to population stratification and inbreeding, especially in admixed population. In GWAS, the principal components (PCs) method provides a global ancestry value per subject, allowing corrections for population stratification. However, these coefficients are typically estimated assuming unrelated individuals, and if family structure is present and ignored, such substructures may induce artifactual PCs.

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Jul
2015

Percent mammographic density (PD) estimates the proportion of stromal, fat, and epithelial breast tissues on the mammogram image. Adjusted for age and body mass index (BMI), PD is one of the strongest risk factors for breast cancer. Inherited factors are hypothesized to explain between 30 and 60% of the variance in this trait.

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Jul
2015

Hepatocyte growth factor (HGF) is a mesenchyme-derived pleiotropic factor that regulates cell growth, motility, mitogenesis, and morphogenesis in a variety of cells, and increased serum levels of HGF have been linked to a number of clinical and subclinical cardiovascular disease phenotypes. However, little is currently known regarding which genetic factors influence HGF levels, despite evidence of substantial genetic contributions to HGF variation. Based upon ethnicity-stratified single-variant association analysis and trans-ethnic meta-analysis of 6201 participants of the Multi-Ethnic Study of Atherosclerosis (MESA), we discovered five statistically significant common and low-frequency variants: HGF missense polymorphism rs5745687 (p.

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Jul
2015

Bioinformatics approaches to examine gene-gene models provide a means to discover interactions between multiple genes that underlie complex disease. Extensive computational demands and adjusting for multiple testing make uncovering genetic interactions a challenge. Here, we address these issues using our knowledge-driven filtering method, Biofilter, to identify putative single nucleotide polymorphism (SNP) interaction models for cataract susceptibility, thereby reducing the number of models for analysis.

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Jul
2015

Sex differences in incidence and prevalence of and morbidity and mortality from cardiovascular disease are well documented. However, many studies examining the genetic basis for cardiovascular disease fail to consider sex as a variable in the study design, in part, because there is an inherent difficulty in studying the contribution of the sex chromosomes in women due to X chromosome inactivation. This paper will provide general background on the X and Y chromosomes (including gene content, the pseudoautosomal regions, and X chromosome inactivation), discuss how sex chromosomes have been ignored in Genome-wide Association Studies (GWAS) of cardiovascular diseases, and discuss genetics influencing development of cardiovascular risk factors and atherosclerosis with particular attention to carotid intima-medial thickness, and coronary arterial calcification based on sex-specific studies.

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Mar
2015

Characterization of large structural genetic mosaicism in human autosomes.

Am J Hum Genet 2015 Mar;96(3):487-97
Mitchell J Machiela, Weiyin Zhou, Joshua N Sampson, Michael C Dean, Kevin B Jacobs, Amanda Black, Louise A Brinton, I-Shou Chang, Chu Chen, Constance Chen, Kexin Chen, Linda S Cook, Marta Crous Bou, Immaculata De Vivo, Jennifer Doherty, Christine M Friedenreich, Mia M Gaudet, Christopher A Haiman, Susan E Hankinson, Patricia Hartge, Brian E Henderson, Yun-Chul Hong, H Dean Hosgood, Chao A Hsiung, Wei Hu, David J Hunter, Lea Jessop, Hee Nam Kim, Yeul Hong Kim, Young Tae Kim, Robert Klein, Peter Kraft, Qing Lan, Dongxin Lin, Jianjun Liu, Loic Le Marchand, Xiaolin Liang, Jolanta Lissowska, Lingeng Lu, Anthony M Magliocco, Keitaro Matsuo, Sara H Olson, Irene Orlow, Jae Yong Park, Loreall Pooler, Jennifer Prescott, Radhai Rastogi, Harvey A Risch, Fredrick Schumacher, Adeline Seow, Veronica Wendy Setiawan, Hongbing Shen, Xin Sheng, Min-Ho Shin, Xiao-Ou Shu, David VanDen Berg, Jiu-Cun Wang, Nicolas Wentzensen, Maria Pik Wong, Chen Wu, Tangchun Wu, Yi-Long Wu, Lucy Xia, Hannah P Yang, Pan-Chyr Yang, Wei Zheng, Baosen Zhou, Christian C Abnet, Demetrius Albanes, Melinda C Aldrich, Christopher Amos, Laufey T Amundadottir, Sonja I Berndt, William J Blot, Cathryn H Bock, Paige M Bracci, Laurie Burdett, Julie E Buring, Mary A Butler, Tania Carreón, Nilanjan Chatterjee, Charles C Chung, Michael B Cook, Michael Cullen, Faith G Davis, Ti Ding, Eric J Duell, Caroline G Epstein, Jin-Hu Fan, Jonine D Figueroa, Joseph F Fraumeni, Neal D Freedman, Charles S Fuchs, Yu-Tang Gao, Susan M Gapstur, Ana Patiño-Garcia, Montserrat Garcia-Closas, J Michael Gaziano, Graham G Giles, Elizabeth M Gillanders, Edward L Giovannucci, Lynn Goldin, Alisa M Goldstein, Mark H Greene, Goran Hallmans, Curtis C Harris, Roger Henriksson, Elizabeth A Holly, Robert N Hoover, Nan Hu, Amy Hutchinson, Mazda Jenab, Christoffer Johansen, Kay-Tee Khaw, Woon-Puay Koh, Laurence N Kolonel, Charles Kooperberg, Vittorio Krogh, Robert C Kurtz, Andrea LaCroix, Annelie Landgren, Maria Teresa Landi, Donghui Li, Linda M Liao, Nuria Malats, Katherine A McGlynn, Lorna H McNeill, Robert R McWilliams, Beatrice S Melin, Lisa Mirabello, Beata Peplonska, Ulrike Peters, Gloria M Petersen, Ludmila Prokunina-Olsson, Mark Purdue, You-Lin Qiao, Kari G Rabe, Preetha Rajaraman, Francisco X Real, Elio Riboli, Benjamín Rodríguez-Santiago, Nathaniel Rothman, Avima M Ruder, Sharon A Savage, Ann G Schwartz, Kendra L Schwartz, Howard D Sesso, Gianluca Severi, Debra T Silverman, Margaret R Spitz, Victoria L Stevens, Rachael Stolzenberg-Solomon, Daniel Stram, Ze-Zhong Tang, Philip R Taylor, Lauren R Teras, Geoffrey S Tobias, Kala Viswanathan, Sholom Wacholder, Zhaoming Wang, Stephanie J Weinstein, William Wheeler, Emily White, John K Wiencke, Brian M Wolpin, Xifeng Wu, Jay S Wunder, Kai Yu, Krista A Zanetti, Anne Zeleniuch-Jacquotte, Regina G Ziegler, Mariza de Andrade, Kathleen C Barnes, Terri H Beaty, Laura J Bierut, Karl C Desch, Kimberly F Doheny, Bjarke Feenstra, David Ginsburg, John A Heit, Jae H Kang, Cecilia A Laurie, Jun Z Li, William L Lowe, Mary L Marazita, Mads Melbye, Daniel B Mirel, Jeffrey C Murray, Sarah C Nelson, Louis R Pasquale, Kenneth Rice, Janey L Wiggs, Anastasia Wise, Margaret Tucker, Luis A Pérez-Jurado, Cathy C Laurie, Neil E Caporaso, Meredith Yeager, Stephen J Chanock
Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals.

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May
2015

P-selectin is a cellular adhesion molecule that has been shown to be crucial in development of coronary heart disease (CHD). We sought to determine the role of P-selectin on the risk of atherosclerosis in a large multi-ethnic population.
Data from the Multi-Ethnic Study of Atherosclerosis (MESA), including 1628 African, 702 Chinese, 2393 non-Hispanic white, and 1302 Hispanic Americans, were used to investigate the association of plasma P-selectin with CHD risk factors, coronary artery calcium (CAC), intima-media thickness, and CHD.

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Apr
2015

Multiethnic genome-wide association study of cerebral white matter hyperintensities on MRI.

Circ Cardiovasc Genet 2015 Apr 7;8(2):398-409. Epub 2015 Feb 7.
Benjamin F J Verhaaren, Stéphanie Debette, Joshua C Bis, Jennifer A Smith, M Kamran Ikram, Hieab H Adams, Ashley H Beecham, Kumar B Rajan, Lorna M Lopez, Sandra Barral, Mark A van Buchem, Jeroen van der Grond, Albert V Smith, Katrin Hegenscheid, Neelum T Aggarwal, Mariza de Andrade, Elizabeth J Atkinson, Marian Beekman, Alexa S Beiser, Susan H Blanton, Eric Boerwinkle, Adam M Brickman, R Nick Bryan, Ganesh Chauhan, Christopher P L H Chen, Vincent Chouraki, Anton J M de Craen, Fabrice Crivello, Ian J Deary, Joris Deelen, Philip L De Jager, Carole Dufouil, Mitchell S V Elkind, Denis A Evans, Paul Freudenberger, Rebecca F Gottesman, Vilmundur Guðnason, Mohamad Habes, Susan R Heckbert, Gerardo Heiss, Saima Hilal, Edith Hofer, Albert Hofman, Carla A Ibrahim-Verbaas, David S Knopman, Cora E Lewis, Jiemin Liao, David C M Liewald, Michelle Luciano, Aad van der Lugt, Oliver O Martinez, Richard Mayeux, Bernard Mazoyer, Mike Nalls, Matthias Nauck, Wiro J Niessen, Ben A Oostra, Bruce M Psaty, Kenneth M Rice, Jerome I Rotter, Bettina von Sarnowski, Helena Schmidt, Pamela J Schreiner, Maaike Schuur, Stephen S Sidney, Sigurdur Sigurdsson, P Eline Slagboom, David J M Stott, John C van Swieten, Alexander Teumer, Anna Maria Töglhofer, Matthew Traylor, Stella Trompet, Stephen T Turner, Christophe Tzourio, Hae-Won Uh, André G Uitterlinden, Meike W Vernooij, Jing J Wang, Tien Y Wong, Joanna M Wardlaw, B Gwen Windham, Katharina Wittfeld, Christiane Wolf, Clinton B Wright, Qiong Yang, Wei Zhao, Alex Zijdenbos, J Wouter Jukema, Ralph L Sacco, Sharon L R Kardia, Philippe Amouyel, Thomas H Mosley, W T Longstreth, Charles C DeCarli, Cornelia M van Duijn, Reinhold Schmidt, Lenore J Launer, Hans J Grabe, Sudha S Seshadri, M Arfan Ikram, Myriam Fornage
The burden of cerebral white matter hyperintensities (WMH) is associated with an increased risk of stroke, dementia, and death. WMH are highly heritable, but their genetic underpinnings are incompletely characterized. To identify novel genetic variants influencing WMH burden, we conducted a meta-analysis of multiethnic genome-wide association studies.

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Feb
2015

PARK2, a gene associated with Parkinson disease, is a tumor suppressor in human malignancies. Here, we show that c.823C>T (p.

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Apr
2015

L-Selectin is constitutively expressed on leukocytes and mediates their interaction with endothelial cells during inflammation. Previous studies on the association of soluble L-selectin (sL-selectin) with cardiovascular disease (CVD) are inconsistent. Genetic variants associated with sL-selectin levels may be a better surrogate of levels over a lifetime.

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Dec
1969

The electronic MEdical Records and GEnomics (eMERGE) network brings together DNA biobanks linked to electronic health records (EHRs) from multiple institutions. Approximately 51,000 DNA samples from distinct individuals have been genotyped using genome-wide SNP arrays across the nine sites of the network. The eMERGE Coordinating Center and the Genomics Workgroup developed a pipeline to impute and merge genomic data across the different SNP arrays to maximize sample size and power to detect associations with a variety of clinical endpoints.

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May
2015

Genome-wide association study of kidney function decline in individuals of European descent.

Kidney Int 2015 May 10;87(5):1017-29. Epub 2014 Dec 10.
Mathias Gorski, Adrienne Tin, Maija Garnaas, Gearoid M McMahon, Audrey Y Chu, Bamidele O Tayo, Cristian Pattaro, Alexander Teumer, Daniel I Chasman, John Chalmers, Pavel Hamet, Johanne Tremblay, Marc Woodward, Thor Aspelund, Gudny Eiriksdottir, Vilmundur Gudnason, Tamara B Harris, Lenore J Launer, Albert V Smith, Braxton D Mitchell, Jeffrey R O'Connell, Alan R Shuldiner, Josef Coresh, Man Li, Paul Freudenberger, Edith Hofer, Helena Schmidt, Reinhold Schmidt, Elizabeth G Holliday, Paul Mitchell, Jie Jin Wang, Ian H de Boer, Guo Li, David S Siscovick, Zoltan Kutalik, Tanguy Corre, Peter Vollenweider, Gérard Waeber, Jayanta Gupta, Peter A Kanetsky, Shih-Jen Hwang, Matthias Olden, Qiong Yang, Mariza de Andrade, Elizabeth J Atkinson, Sharon L R Kardia, Stephen T Turner, Jeanette M Stafford, Jingzhong Ding, Yongmei Liu, Cristina Barlassina, Daniele Cusi, Erika Salvi, Jan A Staessen, Paul M Ridker, Harald Grallert, Christa Meisinger, Martina Müller-Nurasyid, Bernhard K Krämer, Holly Kramer, Sylvia E Rosas, Ilja M Nolte, Brenda W Penninx, Harold Snieder, M Fabiola Del Greco, Andre Franke, Ute Nöthlings, Wolfgang Lieb, Stephan J L Bakker, Ron T Gansevoort, Pim van der Harst, Abbas Dehghan, Oscar H Franco, Albert Hofman, Fernando Rivadeneira, Sanaz Sedaghat, André G Uitterlinden, Stefan Coassin, Margot Haun, Barbara Kollerits, Florian Kronenberg, Bernhard Paulweber, Nicole Aumann, Karlhans Endlich, Mike Pietzner, Uwe Völker, Rainer Rettig, Vincent Chouraki, Catherine Helmer, Jean-Charles Lambert, Marie Metzger, Benedicte Stengel, Terho Lehtimäki, Leo-Pekka Lyytikäinen, Olli Raitakari, Andrew Johnson, Afshin Parsa, Murielle Bochud, Iris M Heid, Wolfram Goessling, Anna Köttgen, W H Linda Kao, Caroline S Fox, Carsten A Böger
Genome-wide association studies (GWASs) have identified multiple loci associated with cross-sectional eGFR, but a systematic genetic analysis of kidney function decline over time is missing. Here we conducted a GWAS meta-analysis among 63,558 participants of European descent, initially from 16 cohorts with serial kidney function measurements within the CKDGen Consortium, followed by independent replication among additional participants from 13 cohorts. In stage 1 GWAS meta-analysis, single-nucleotide polymorphisms (SNPs) at MEOX2, GALNT11, IL1RAP, NPPA, HPCAL1, and CDH23 showed the strongest associations for at least one trait, in addition to the known UMOD locus, which showed genome-wide significance with an annual change in eGFR.

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Dec
1969

Thyroid stimulating hormone (TSH) hormone levels are normally tightly regulated within an individual; thus, relatively small variations may indicate thyroid disease. Genome-wide association studies (GWAS) have identified variants in PDE8B and FOXE1 that are associated with TSH levels. However, prior studies lacked racial/ethnic diversity, limiting the generalization of these findings to individuals of non-European ethnicities.

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Dec
1969

Combining samples across multiple cohorts in large-scale scientific research programs is often required to achieve the necessary power for genome-wide association studies. Controlling for genomic ancestry through principal component analysis (PCA) to address the effect of population stratification is a common practice. In addition to local genomic variation, such as copy number variation and inversions, other factors directly related to combining multiple studies, such as platform and site recruitment bias, can drive the correlation patterns in PCA.

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Dec
2014

Epidemiological studies show strong associations between kidney dysfunction and risk of ischemic stroke (IS), the mechanisms of which are incompletely understood. We investigated whether these associations may reflect shared heritability because of a common polygenic basis and whether this differed for IS subtypes.
Polygenic models were derived using genome-wide association studies meta-analysis results for 3 kidney traits: estimated glomerular filtration rate using serum creatinine (eGFRcrea: n=73 998), eGFR using cystatin C (eGFRcys: n=22 937), and urinary albumin to creatinine ratio (n=31 580).

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