Browsing by Author "Raby, Benjamin"

Now showing items 1-20 of 35

    • Analyzing networks of phenotypes in complex diseases: methodology and applications in COPD 

      Chu, Jen-hwa; Hersh, Craig P; Castaldi, Peter J; Cho, Michael H; Raby, Benjamin A; Laird, Nan; Bowler, Russell; Rennard, Stephen; Loscalzo, Joseph; Quackenbush, John; Silverman, Edwin K (BioMed Central, 2014)
      Background: The investigation of complex disease heterogeneity has been challenging. Here, we introduce a network-based approach, using partial correlations, that analyzes the relationships among multiple disease-related ...

    • The Association of a SNP Upstream of INSIG2 with Body Mass Index is Reproduced in Several but Not All Cohorts 

      Emilsson, Valur; Hinney, Anke; Heid, Iris M; Zhu, Xiaofeng; Thorleifsson, Gudmar; Gunnarsdottir, Steinunn; Walters, G. Bragi; Thorsteinsdottir, Unnur; Kong, Augustine; Gulcher, Jeffrey; Nguyen, Thuy Trang; Scherag, André; Pfeufer, Arne; Meitinger, Thomas; Brönner, Günter; Rief, Winfried; Soto-Quiros, Manuel E; Avila, Lydiana; Groop, Leif; Tuomi, Tiinamaija; Isomaa, Bo; Bengtsson, Kristina; Butler, Johannah L; Vollmert, Caren; Celedón, Juan C; Wichmann, H. Erich; Hebebrand, Johannes; Stefansson, Kari; Abecasis, Gonçalo; Lyon, Helen N; Su, Jessica Ann Lasky; Klanderman, Barbara Jordan; Raby, Benjamin Alexander; Silverman, Edwin Kepner; Weiss, Scott Tillman; Laird, Nan M.; Ding, Xiao; Cooper, Richard S; Fox, Caroline; O'Donnell, Christopher Joseph; Lange, Christoph; Hirschhorn, Joel Naom (Public Library of Science, 2007)
      A SNP upstream of the INSIG2 gene, rs7566605, was recently found to be associated with obesity as measured by body mass index (BMI) by Herbert and colleagues. The association between increased BMI and homozygosity for the ...

    • Asthma and Genes Encoding Components of the Vitamin D Pathway 

      Bossé, Yohan; Lemire, Mathieu; Poon, Audrey H; Daley, Denise; He, Jian-Qing; Sandford, Andrew; James, Alan L; Musk, Arthur William; Palmer, Lyle J; Kozyrskyj, Anita L; Becker, Allan; Hudson, Thomas J; Laprise, Catherine; White, John H.; Raby, Benjamin Alexander; Weiss, Scott Tillman (BioMed Central, 2009)
      Background: Genetic variants at the vitamin D receptor (VDR) locus are associated with asthma and atopy. We hypothesized that polymorphisms in other genes of the vitamin D pathway are associated with asthma or atopy. ...

    • Asthma-susceptibility variants identified using probands in case-control and family-based analyses 

      Murphy, Amy J; Soto-Quiros, Manuel E; Avila, Lydiana; Celedón, Juan C; O'Connor, George T; Himes, Blanca Elena; Su, Jessica Ann Lasky; Wu, Ann Chen; Wilk, Jemma B; Hunninghake, Gary Matthew; Klanderman, Barbara Jordan; Lazarus, Ross; Lange, Christoph; Raby, Benjamin Alexander; Silverman, Edwin Kepner; Weiss, Scott Tillman (BioMed Central, 2010)
      Background: Asthma is a chronic respiratory disease whose genetic basis has been explored for over two decades, most recently via genome-wide association studies. We sought to find asthma-susceptibility variants by using ...

    • Classification of childhood asthma phenotypes and long-term clinical responses to inhaled anti-inflammatory medications 

      Howrylak, Judie A.; Fuhlbrigge, Anne Louise; Strunk, Robert C.; Zeiger, Robert S.; Weiss, Scott Tillman; Raby, Benjamin Alexander (Elsevier BV, 2014)
      Background— Although recent studies have identified the presence of phenotypic clusters in asthmatic patients, the clinical significance and temporal stability of these clusters have not been explored. Objective— Our ...

    • Comprehensive Genetic Assessment of a Functional TLR9 Promoter Polymorphism: No Replicable Association with Asthma or Asthma-Related Phenotypes 

      Avila, Lydiana; Hawrylowicz, Catherine M; Lange, Nancy Elizabeth; Zhou, Xiaobo; Su, Jessica Ann Lasky; Himes, Blanca Elena; Lazarus, Ross; Raby, Benjamin Alexander; Litonjua, Augusto Ampil; Soto-Quiros, Manuel; Celedon, Juan C (BioMed Central, 2011)
      Background: Prior studies suggest a role for a variant (rs5743836) in the promoter of toll-like receptor 9 (TLR9) in asthma and other inflammatory diseases. We performed detailed genetic association studies of the functional ...

    • Ethnic-specific associations of rare and low-frequency DNA sequence variants with asthma 

      Igartua, Catherine; Myers, Rachel A.; Mathias, Rasika A.; Pino-Yanes, Maria; Eng, Celeste; Graves, Penelope E.; Levin, Albert M.; Del-Rio-Navarro, Blanca E.; Jackson, Daniel J.; Livne, Oren E.; Rafaels, Nicholas; Edlund, Christopher K.; Yang, James J.; Huntsman, Scott; Salam, Muhammad T.; Romieu, Isabelle; Mourad, Raphael; Gern, James E.; Lemanske, Robert F.; Wyss, Annah; Hoppin, Jane A.; Barnes, Kathleen C.; Burchard, Esteban G.; Gauderman, W. James; Martinez, Fernando D.; Raby, Benjamin A.; Weiss, Scott T.; Williams, L. Keoki; London, Stephanie J.; Gilliland, Frank D.; Nicolae, Dan L.; Ober, Carole (Nature Pub. Group, 2015)
      Common variants at many loci have been robustly associated with asthma but explain little of the overall genetic risk. Here we investigate the role of rare (<1%) and low-frequency (1–5%) variants using the Illumina HumanExome ...

    • Expression Quantitative Trait Loci Information Improves Predictive Modeling of Disease Relevance of Non-Coding Genetic Variation 

      Croteau-Chonka, Damien C.; Rogers, Angela J.; Raj, Towfique; McGeachie, Michael J.; Qiu, Weiliang; Ziniti, John P.; Stubbs, Benjamin J.; Liang, Liming; Martinez, Fernando D.; Strunk, Robert C.; Lemanske, Robert F.; Liu, Andrew H.; Stranger, Barbara E.; Carey, Vincent J.; Raby, Benjamin A. (Public Library of Science, 2015)
      Disease-associated loci identified through genome-wide association studies (GWAS) frequently localize to non-coding sequence. We and others have demonstrated strong enrichment of such single nucleotide polymorphisms (SNPs) ...

    • Folliculin Mutations Are Not Associated with Severe COPD 

      Cho, Michael Hyosang; Klanderman, Barbara Jordan; Litonjua, Augusto Ampil; Sparrow, David; Silverman, Edwin Kepner; Raby, Benjamin Alexander (BioMed Central, 2008)
      Background: Rare loss-of-function folliculin (FLCN) mutations are the genetic cause of Birt-Hogg-Dubé syndrome, a monogenic disorder characterized by spontaneous pneumothorax, fibrofolliculomas, and kidney tumors. ...

    • Further replication studies of the EVE Consortium meta-analysis identifies 2 asthma risk loci in European Americans 

      Myers, Rachel A.; Himes, Blanca; Gignoux, Christopher R.; Yang, James J.; Gauderman, W. James; Rebordosa, Cristina; Xie, Jianming; Torgerson, Dara G.; Levin, Albert M.; Baurley, James; Graves, Penelope E.; Mathias, Rasika A.; Romieu, Isabelle; Roth, Lindsey A.; Conti, David; Avila, Lydiana; Eng, Celeste; Vora, Hita; LeNoir, Michael A.; Soto-Quiros, Manuel; Liu, Jinghua; Celedón, Juan C.; Farber, Harold J.; Kumar, Rajesh; Avila, Pedro C.; Meade, Kelley; Serebrisky, Denise; Thyne, Shannon; Rodriguez-Cintron, William; Rodriguez-Santana, Jose R.; Borrell, Luisa N.; Lemanske, Robert F.; Bleecker, Eugene R.; Meyers, Deborah A.; London, Stephanie J.; Barnes, Kathleen C.; Raby, Benjamin Alexander; Martinez, Fernando D.; Gilliland, Frank D.; Williams, L. Keoki; Burchard, Esteban G.; Weiss, Scott Tillman; Nicolae, Dan L.; Ober, Carole (Elsevier BV, 2012)
      Background: Genome-wide association studies of asthma have implicated many genetic risk factors, with well-replicated associations at approximately 10 loci that account for only a small proportion of the genetic ...

    • Gene expression analysis uncovers novel hedgehog interacting protein (HHIP) effects in human bronchial epithelial cells 

      Zhou, Xiaobo; Qiu, Weiliang; Sathirapongsasuti, J. Fah; Cho, Michael Hyosang; Mancini, John D.; Lao, Taotao; Thibault, Derek M.; Litonjua, Augusto Ampil; Bakke, Per S.; Gulsvik, Amund; Lomas, David A.; Beaty, Terri H.; Hersh, Craig Palmer; Anderson, Christopher David; Geigenmuller, Ute; Raby, Benjamin Alexander; Rennard, Stephen I.; Perrella, Mark A.; Choi, Augustine M.K.; Quackenbush, John; Silverman, Edwin Kepner (Elsevier BV, 2013)
      Hedgehog Interacting Protein (HHIP) was implicated in chronic obstructive pulmonary disease (COPD) by genome-wide association studies (GWAS). However, it remains unclear how HHIP contributes to COPD pathogenesis. To identify ...

    • Gene expression network analyses in response to air pollution exposures in the trucking industry 

      Chu, Jen-hwa; Hart, Jaime E.; Chhabra, Divya; Garshick, Eric; Raby, Benjamin A.; Laden, Francine (BioMed Central, 2016)
      Background: Exposure to air pollution, including traffic-related pollutants, has been associated with a variety of adverse health outcomes, including increased cardiopulmonary morbidity and mortality, and increased lung ...

    • Gene-by-environment effect of house dust mite on purinergic receptor P2Y12 (P2RY12) and lung function in children with asthma 

      Bunyavanich, S.; Boyce, Joshua A.; Raby, Benjamin Alexander; Weiss, Scott Tillman (Wiley-Blackwell, 2011)
      Background— Distinct receptors likely exist for leukotriene(LT)E4, a potent mediator of airway inflammation. Purinergic receptor P2Y12 is needed for LTE4-induced airways inflammation, and P2Y12 antagonism attenuates house ...

    • Genes to Diseases (G2D) Computational Method to Identify Asthma Candidate Genes 

      Tremblay, Karine; Lemire, Mathieu; Potvin, Camille; Tremblay, Alexandre; Hudson, Thomas J.; Perez-Iratxeta, Carolina; Andrade-Navarro, Miguel A.; Laprise, Catherine; Hunninghake, Gary Matthew; Raby, Benjamin Alexander (Public Library of Science, 2008)
      Asthma is a complex trait for which different strategies have been used to identify its environmental and genetic predisposing factors. Here, we describe a novel methodological approach to select candidate genes for asthma ...

    • Genome-Wide Association Study Implicates Chromosome 9q21.31 as a Susceptibility Locus for Asthma in Mexican Children 

      Hancock, Dana B.; Romieu, Isabelle; Sienra-Monge, Juan-Jose; Chiu, Grace Y.; Li, Huiling; del Rio-Navarro, Blanca Estela; Willis-Owens, Saffron A. G.; Eng, Celeste; Chapela, Rocio; Burchard, Esteban G.; Tang, Hua; Sullivan, Patrick F.; London, Stephanie J.; Shi, Min; Wu, Hao; Weiss, Scott Tillman; Raby, Benjamin Alexander; Gao, Hong (Public Library of Science, 2009)
      Many candidate genes have been studied for asthma, but replication has varied. Novel candidate genes have been identified for various complex diseases using genome-wide association studies (GWASs). We conducted a GWAS in ...

    • Genome-wide association study of the age of onset of childhood asthma 

      Forno, Erick; Lasky-Su, Jessica A. Lasky; Himes, Blanca; Howrylak, Judie; Ramsey, Clare; Brehm, John; Klanderman, Barbara; Ziniti, John; Melén, Erik; Pershagen, Goran; Wickman, Magnus; Martinez, Fernando; Mauger, Dave; Sorkness, Christine; Tantisira, Kelan; Raby, Benjamin Alexander; Weiss, Scott Tillman; Celedón, Juan C. (Elsevier BV, 2012)
      BACKGROUND: Childhood asthma is a complex disease with known heritability and phenotypic diversity. Although an earlier onset has been associated with more severe disease, there has been no genome-wide association study ...

    • A genome-wide survey of CD4+ lymphocyte regulatory genetic variants identifies novel asthma genes 

      Sharma, Sunita; Zhou, Xiaobo; Thibault, Derek M.; Himes, Blanca E.; Liu, Andy; Szefler, Stanley J.; Strunk, Robert; Castro, Mario; Hansel, Nadia N.; Diette, Gregory B.; Vonakis, Becky M.; Adkinson, N. Franklin; Avila, Lydiana; Soto-Quiros, Manuel; Barraza-Villareal, Albino; Lemanske, Robert F.; Solway, Julian; Krishnan, Jerry; White, Steven R.; Cheadle, Chris; Berger, Alan E.; Fan, Jinshui; Boorgula, Meher Preethi; Nicolae, Dan; Gilliland, Frank; Barnes, Kathleen; London, Stephanie J.; Martinez, Fernando; Ober, Carole; Celedón, Juan C.; Carey, Vincent James; Weiss, Scott Tillman; Raby, Benjamin Alexander (Elsevier BV, 2014)
      Background: Genome-wide association studies have yet to identify the majority of genetic variants involved in asthma. We hypothesized that expression quantitative trait locus (eQTL) mapping can identify novel asthma genes ...

    • A genome-wide survey of CD4+ lymphocyte regulatory genetic variants identifies novel asthma genes 

      Sharma, Sunita; Zhou, Xiaobo; Thibault, Derek M.; Himes, Blanca; Liu, Andy; Szefler, Stanley J.; Strunk, Robert; Castro, Mario; Hansel, Nadia N.; Diette, Gregory B.; Vonakis, Becky M.; Adkinson, N. Franklin; Avila, Lydiana; Soto-Quiros, Manuel; Barraza-Villareal, Albino; Lemanske, Robert F.; Solway, Julian; Krishnan, Jerry; White, Steven James; Cheadle, Chris; Berger, Alan E.; Fan, Jinshui; Boorgula, Meher Preethi; Nicolae, Dan; Gilliland, Frank; Barnes, Kathleen; London, Stephanie J.; Martinez, Fernando; Ober, Carole; Celedón, Juan C.; Carey, Vincent James; Weiss, Scott Tillman; Raby, Benjamin Alexander (Elsevier BV, 2014)
      Background: Genome-wide association studies have yet to identify the majority of genetic variants involved in asthma. We hypothesized that expression quantitative trait locus (eQTL) mapping can identify novel asthma genes ...

    • A graphical model approach for inferring large-scale networks integrating gene expression and genetic polymorphism 

      Chu, Jen-Hwa; Weiss, Scott Tillman; Carey, Vincent James; Raby, Benjamin Alexander (BioMed Central, 2009)
      Background: Graphical models (e.g., Bayesian networks) have been used frequently to describe complex interaction patterns and dependent structures among genes and other phenotypes. Estimation of such networks has been a ...

    • Identifying Causal Rare Variants of Disease Through Family-based Analysis of Genetics Analysis Workshop 17 Data Set 

      Yip, Wai-Ki; De, Gourab; Raby, Benjamin Alexander; Laird, Nan M. (BioMed Central, 2011)
      Linkage- and association-based methods have been proposed for mapping disease-causing rare variants. Based on the family information provided in the Genetic Analysis Workshop 17 data set, we formulate a two-pronged approach ...