%0 Journal Article %J Sci Rep %D 2017 %T 1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function. %A Gorski, Mathias %A van der Most, Peter J %A Teumer, Alexander %A Chu, Audrey Y %A Li, Man %A Mijatovic, Vladan %A Nolte, Ilja M %A Cocca, Massimiliano %A Taliun, Daniel %A Gomez, Felicia %A Li, Yong %A Tayo, Bamidele %A Tin, Adrienne %A Feitosa, Mary F %A Aspelund, Thor %A Attia, John %A Biffar, Reiner %A Bochud, Murielle %A Boerwinkle, Eric %A Borecki, Ingrid %A Bottinger, Erwin P %A Chen, Ming-Huei %A Chouraki, Vincent %A Ciullo, Marina %A Coresh, Josef %A Cornelis, Marilyn C %A Curhan, Gary C %A d'Adamo, Adamo Pio %A Dehghan, Abbas %A Dengler, Laura %A Ding, Jingzhong %A Eiriksdottir, Gudny %A Endlich, Karlhans %A Enroth, Stefan %A Esko, Tõnu %A Franco, Oscar H %A Gasparini, Paolo %A Gieger, Christian %A Girotto, Giorgia %A Gottesman, Omri %A Gudnason, Vilmundur %A Gyllensten, Ulf %A Hancock, Stephen J %A Harris, Tamara B %A Helmer, Catherine %A Höllerer, Simon %A Hofer, Edith %A Hofman, Albert %A Holliday, Elizabeth G %A Homuth, Georg %A Hu, Frank B %A Huth, Cornelia %A Hutri-Kähönen, Nina %A Hwang, Shih-Jen %A Imboden, Medea %A Johansson, Åsa %A Kähönen, Mika %A König, Wolfgang %A Kramer, Holly %A Krämer, Bernhard K %A Kumar, Ashish %A Kutalik, Zoltán %A Lambert, Jean-Charles %A Launer, Lenore J %A Lehtimäki, Terho %A de Borst, Martin %A Navis, Gerjan %A Swertz, Morris %A Liu, Yongmei %A Lohman, Kurt %A Loos, Ruth J F %A Lu, Yingchang %A Lyytikäinen, Leo-Pekka %A McEvoy, Mark A %A Meisinger, Christa %A Meitinger, Thomas %A Metspalu, Andres %A Metzger, Marie %A Mihailov, Evelin %A Mitchell, Paul %A Nauck, Matthias %A Oldehinkel, Albertine J %A Olden, Matthias %A Wjh Penninx, Brenda %A Pistis, Giorgio %A Pramstaller, Peter P %A Probst-Hensch, Nicole %A Raitakari, Olli T %A Rettig, Rainer %A Ridker, Paul M %A Rivadeneira, Fernando %A Robino, Antonietta %A Rosas, Sylvia E %A Ruderfer, Douglas %A Ruggiero, Daniela %A Saba, Yasaman %A Sala, Cinzia %A Schmidt, Helena %A Schmidt, Reinhold %A Scott, Rodney J %A Sedaghat, Sanaz %A Smith, Albert V %A Sorice, Rossella %A Stengel, Bénédicte %A Stracke, Sylvia %A Strauch, Konstantin %A Toniolo, Daniela %A Uitterlinden, André G %A Ulivi, Sheila %A Viikari, Jorma S %A Völker, Uwe %A Vollenweider, Peter %A Völzke, Henry %A Vuckovic, Dragana %A Waldenberger, Melanie %A Jin Wang, Jie %A Yang, Qiong %A Chasman, Daniel I %A Tromp, Gerard %A Snieder, Harold %A Heid, Iris M %A Fox, Caroline S %A Köttgen, Anna %A Pattaro, Cristian %A Böger, Carsten A %A Fuchsberger, Christian %K Computational Biology %K Gene Frequency %K Genetic Loci %K Genome, Human %K Genome-Wide Association Study %K Genotyping Techniques %K Humans %K Kidney %K Polymorphism, Single Nucleotide %X

HapMap imputed genome-wide association studies (GWAS) have revealed >50 loci at which common variants with minor allele frequency >5% are associated with kidney function. GWAS using more complete reference sets for imputation, such as those from The 1000 Genomes project, promise to identify novel loci that have been missed by previous efforts. To investigate the value of such a more complete variant catalog, we conducted a GWAS meta-analysis of kidney function based on the estimated glomerular filtration rate (eGFR) in 110,517 European ancestry participants using 1000 Genomes imputed data. We identified 10 novel loci with p-value < 5 × 10 previously missed by HapMap-based GWAS. Six of these loci (HOXD8, ARL15, PIK3R1, EYA4, ASTN2, and EPB41L3) are tagged by common SNPs unique to the 1000 Genomes reference panel. Using pathway analysis, we identified 39 significant (FDR < 0.05) genes and 127 significantly (FDR < 0.05) enriched gene sets, which were missed by our previous analyses. Among those, the 10 identified novel genes are part of pathways of kidney development, carbohydrate metabolism, cardiac septum development and glucose metabolism. These results highlight the utility of re-imputing from denser reference panels, until whole-genome sequencing becomes feasible in large samples.

%B Sci Rep %V 7 %P 45040 %8 2017 04 28 %G eng %1 http://www.ncbi.nlm.nih.gov/pubmed/28452372?dopt=Abstract %R 10.1038/srep45040 %0 Journal Article %J Nat Commun %D 2016 %T Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function. %A Pattaro, Cristian %A Teumer, Alexander %A Gorski, Mathias %A Chu, Audrey Y %A Li, Man %A Mijatovic, Vladan %A Garnaas, Maija %A Tin, Adrienne %A Sorice, Rossella %A Li, Yong %A Taliun, Daniel %A Olden, Matthias %A Foster, Meredith %A Yang, Qiong %A Chen, Ming-Huei %A Pers, Tune H %A Johnson, Andrew D %A Ko, Yi-An %A Fuchsberger, Christian %A Tayo, Bamidele %A Nalls, Michael %A Feitosa, Mary F %A Isaacs, Aaron %A Dehghan, Abbas %A d'Adamo, Pio %A Adeyemo, Adebowale %A Dieffenbach, Aida Karina %A Zonderman, Alan B %A Nolte, Ilja M %A van der Most, Peter J %A Wright, Alan F %A Shuldiner, Alan R %A Morrison, Alanna C %A Hofman, Albert %A Smith, Albert V %A Dreisbach, Albert W %A Franke, Andre %A Uitterlinden, André G %A Metspalu, Andres %A Tönjes, Anke %A Lupo, Antonio %A Robino, Antonietta %A Johansson, Åsa %A Demirkan, Ayse %A Kollerits, Barbara %A Freedman, Barry I %A Ponte, Belen %A Oostra, Ben A %A Paulweber, Bernhard %A Krämer, Bernhard K %A Mitchell, Braxton D %A Buckley, Brendan M %A Peralta, Carmen A %A Hayward, Caroline %A Helmer, Catherine %A Rotimi, Charles N %A Shaffer, Christian M %A Müller, Christian %A Sala, Cinzia %A van Duijn, Cornelia M %A Saint-Pierre, Aude %A Ackermann, Daniel %A Shriner, Daniel %A Ruggiero, Daniela %A Toniolo, Daniela %A Lu, Yingchang %A Cusi, Daniele %A Czamara, Darina %A Ellinghaus, David %A Siscovick, David S %A Ruderfer, Douglas %A Gieger, Christian %A Grallert, Harald %A Rochtchina, Elena %A Atkinson, Elizabeth J %A Holliday, Elizabeth G %A Boerwinkle, Eric %A Salvi, Erika %A Bottinger, Erwin P %A Murgia, Federico %A Rivadeneira, Fernando %A Ernst, Florian %A Kronenberg, Florian %A Hu, Frank B %A Navis, Gerjan J %A Curhan, Gary C %A Ehret, George B %A Homuth, Georg %A Coassin, Stefan %A Thun, Gian-Andri %A Pistis, Giorgio %A Gambaro, Giovanni %A Malerba, Giovanni %A Montgomery, Grant W %A Eiriksdottir, Gudny %A Jacobs, Gunnar %A Li, Guo %A Wichmann, H-Erich %A Campbell, Harry %A Schmidt, Helena %A Wallaschofski, Henri %A Völzke, Henry %A Brenner, Hermann %A Kroemer, Heyo K %A Kramer, Holly %A Lin, Honghuang %A Leach, I Mateo %A Ford, Ian %A Guessous, Idris %A Rudan, Igor %A Prokopenko, Inga %A Borecki, Ingrid %A Heid, Iris M %A Kolcic, Ivana %A Persico, Ivana %A Jukema, J Wouter %A Wilson, James F %A Felix, Janine F %A Divers, Jasmin %A Lambert, Jean-Charles %A Stafford, Jeanette M %A Gaspoz, Jean-Michel %A Smith, Jennifer A %A Faul, Jessica D %A Wang, Jie Jin %A Ding, Jingzhong %A Hirschhorn, Joel N %A Attia, John %A Whitfield, John B %A Chalmers, John %A Viikari, Jorma %A Coresh, Josef %A Denny, Joshua C %A Karjalainen, Juha %A Fernandes, Jyotika K %A Endlich, Karlhans %A Butterbach, Katja %A Keene, Keith L %A Lohman, Kurt %A Portas, Laura %A Launer, Lenore J %A Lyytikäinen, Leo-Pekka %A Yengo, Loic %A Franke, Lude %A Ferrucci, Luigi %A Rose, Lynda M %A Kedenko, Lyudmyla %A Rao, Madhumathi %A Struchalin, Maksim %A Kleber, Marcus E %A Cavalieri, Margherita %A Haun, Margot %A Cornelis, Marilyn C %A Ciullo, Marina %A Pirastu, Mario %A de Andrade, Mariza %A McEvoy, Mark A %A Woodward, Mark %A Adam, Martin %A Cocca, Massimiliano %A Nauck, Matthias %A Imboden, Medea %A Waldenberger, Melanie %A Pruijm, Menno %A Metzger, Marie %A Stumvoll, Michael %A Evans, Michele K %A Sale, Michele M %A Kähönen, Mika %A Boban, Mladen %A Bochud, Murielle %A Rheinberger, Myriam %A Verweij, Niek %A Bouatia-Naji, Nabila %A Martin, Nicholas G %A Hastie, Nick %A Probst-Hensch, Nicole %A Soranzo, Nicole %A Devuyst, Olivier %A Raitakari, Olli %A Gottesman, Omri %A Franco, Oscar H %A Polasek, Ozren %A Gasparini, Paolo %A Munroe, Patricia B %A Ridker, Paul M %A Mitchell, Paul %A Muntner, Paul %A Meisinger, Christa %A Smit, Johannes H %A Kovacs, Peter %A Wild, Philipp S %A Froguel, Philippe %A Rettig, Rainer %A Mägi, Reedik %A Biffar, Reiner %A Schmidt, Reinhold %A Middelberg, Rita P S %A Carroll, Robert J %A Penninx, Brenda W %A Scott, Rodney J %A Katz, Ronit %A Sedaghat, Sanaz %A Wild, Sarah H %A Kardia, Sharon L R %A Ulivi, Sheila %A Hwang, Shih-Jen %A Enroth, Stefan %A Kloiber, Stefan %A Trompet, Stella %A Stengel, Bénédicte %A Hancock, Stephen J %A Turner, Stephen T %A Rosas, Sylvia E %A Stracke, Sylvia %A Harris, Tamara B %A Zeller, Tanja %A Zemunik, Tatijana %A Lehtimäki, Terho %A Illig, Thomas %A Aspelund, Thor %A Nikopensius, Tiit %A Esko, Tõnu %A Tanaka, Toshiko %A Gyllensten, Ulf %A Völker, Uwe %A Emilsson, Valur %A Vitart, Veronique %A Aalto, Ville %A Gudnason, Vilmundur %A Chouraki, Vincent %A Chen, Wei-Min %A Igl, Wilmar %A März, Winfried %A Koenig, Wolfgang %A Lieb, Wolfgang %A Loos, Ruth J F %A Liu, Yongmei %A Snieder, Harold %A Pramstaller, Peter P %A Parsa, Afshin %A O'Connell, Jeffrey R %A Susztak, Katalin %A Hamet, Pavel %A Tremblay, Johanne %A de Boer, Ian H %A Böger, Carsten A %A Goessling, Wolfram %A Chasman, Daniel I %A Köttgen, Anna %A Kao, W H Linda %A Fox, Caroline S %K Gene Expression Regulation %K Genetic Predisposition to Disease %K Genome-Wide Association Study %K Genotype %K Humans %K Renal Insufficiency, Chronic %X

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. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways.

%B Nat Commun %V 7 %P 10023 %8 2016 %G eng %1 http://www.ncbi.nlm.nih.gov/pubmed/26831199?dopt=Abstract %R 10.1038/ncomms10023 %0 Journal Article %J Hum Mol Genet %D 2014 %T Trans-ethnic meta-analysis of white blood cell phenotypes. %A Keller, Margaux F %A Reiner, Alexander P %A Okada, Yukinori %A van Rooij, Frank J A %A Johnson, Andrew D %A Chen, Ming-Huei %A Smith, Albert V %A Morris, Andrew P %A Tanaka, Toshiko %A Ferrucci, Luigi %A Zonderman, Alan B %A Lettre, Guillaume %A Harris, Tamara %A Garcia, Melissa %A Bandinelli, Stefania %A Qayyum, Rehan %A Yanek, Lisa R %A Becker, Diane M %A Becker, Lewis C %A Kooperberg, Charles %A Keating, Brendan %A Reis, Jared %A Tang, Hua %A Boerwinkle, Eric %A Kamatani, Yoichiro %A Matsuda, Koichi %A Kamatani, Naoyuki %A Nakamura, Yusuke %A Kubo, Michiaki %A Liu, Simin %A Dehghan, Abbas %A Felix, Janine F %A Hofman, Albert %A Uitterlinden, André G %A van Duijn, Cornelia M %A Franco, Oscar H %A Longo, Dan L %A Singleton, Andrew B %A Psaty, Bruce M %A Evans, Michelle K %A Cupples, L Adrienne %A Rotter, Jerome I %A O'Donnell, Christopher J %A Takahashi, Atsushi %A Wilson, James G %A Ganesh, Santhi K %A Nalls, Mike A %K African Americans %K Asian Continental Ancestry Group %K Bayes Theorem %K European Continental Ancestry Group %K Genome, Human %K Genome-Wide Association Study %K Genotype %K Humans %K Leukocyte Count %K Leukocytes %K Linkage Disequilibrium %K Phenotype %K Polymorphism, Single Nucleotide %K Quantitative Trait Loci %X

White blood cell (WBC) count is a common clinical measure used as a predictor of certain aspects of human health, including immunity and infection status. WBC count is also a complex trait that varies among individuals and ancestry groups. Differences in linkage disequilibrium structure and heterogeneity in allelic effects are expected to play a role in the associations observed between populations. Prior genome-wide association study (GWAS) meta-analyses have identified genomic loci associated with WBC and its subtypes, but much of the heritability of these phenotypes remains unexplained. Using GWAS summary statistics for over 50 000 individuals from three diverse populations (Japanese, African-American and European ancestry), a Bayesian model methodology was employed to account for heterogeneity between ancestry groups. This approach was used to perform a trans-ethnic meta-analysis of total WBC, neutrophil and monocyte counts. Ten previously known associations were replicated and six new loci were identified, including several regions harboring genes related to inflammation and immune cell function. Ninety-five percent credible interval regions were calculated to narrow the association signals and fine-map the putatively causal variants within loci. Finally, a conditional analysis was performed on the most significant SNPs identified by the trans-ethnic meta-analysis (MA), and nine secondary signals within loci previously associated with WBC or its subtypes were identified. This work illustrates the potential of trans-ethnic analysis and ascribes a critical role to multi-ethnic cohorts and consortia in exploring complex phenotypes with respect to variants that lie outside the European-biased GWAS pool.

%B Hum Mol Genet %V 23 %P 6944-60 %8 2014 Dec 20 %G eng %N 25 %1 http://www.ncbi.nlm.nih.gov/pubmed/25096241?dopt=Abstract %R 10.1093/hmg/ddu401 %0 Journal Article %J PLoS Genet %D 2012 %T Genome-wide association and functional follow-up reveals new loci for kidney function. %A Pattaro, Cristian %A Köttgen, Anna %A Teumer, Alexander %A Garnaas, Maija %A Böger, Carsten A %A Fuchsberger, Christian %A Olden, Matthias %A Chen, Ming-Huei %A Tin, Adrienne %A Taliun, Daniel %A Li, Man %A Gao, Xiaoyi %A Gorski, Mathias %A Yang, Qiong %A Hundertmark, Claudia %A Foster, Meredith C %A O'Seaghdha, Conall M %A Glazer, Nicole %A Isaacs, Aaron %A Liu, Ching-Ti %A Smith, Albert V %A O'Connell, Jeffrey R %A Struchalin, Maksim %A Tanaka, Toshiko %A Li, Guo %A Johnson, Andrew D %A Gierman, Hinco J %A Feitosa, Mary %A Hwang, Shih-Jen %A Atkinson, Elizabeth J %A Lohman, Kurt %A Cornelis, Marilyn C %A Johansson, Åsa %A Tönjes, Anke %A Dehghan, Abbas %A Chouraki, Vincent %A Holliday, Elizabeth G %A Sorice, Rossella %A Kutalik, Zoltán %A Lehtimäki, Terho %A Esko, Tõnu %A Deshmukh, Harshal %A Ulivi, Sheila %A Chu, Audrey Y %A Murgia, Federico %A Trompet, Stella %A Imboden, Medea %A Kollerits, Barbara %A Pistis, Giorgio %A Harris, Tamara B %A Launer, Lenore J %A Aspelund, Thor %A Eiriksdottir, Gudny %A Mitchell, Braxton D %A Boerwinkle, Eric %A Schmidt, Helena %A Cavalieri, Margherita %A Rao, Madhumathi %A Hu, Frank B %A Demirkan, Ayse %A Oostra, Ben A %A de Andrade, Mariza %A Turner, Stephen T %A Ding, Jingzhong %A Andrews, Jeanette S %A Freedman, Barry I %A Koenig, Wolfgang %A Illig, Thomas %A Döring, Angela %A Wichmann, H-Erich %A Kolcic, Ivana %A Zemunik, Tatijana %A Boban, Mladen %A Minelli, Cosetta %A Wheeler, Heather E %A Igl, Wilmar %A Zaboli, Ghazal %A Wild, Sarah H %A Wright, Alan F %A Campbell, Harry %A Ellinghaus, David %A Nöthlings, Ute %A Jacobs, Gunnar %A Biffar, Reiner %A Endlich, Karlhans %A Ernst, Florian %A Homuth, Georg %A Kroemer, Heyo K %A Nauck, Matthias %A Stracke, Sylvia %A Völker, Uwe %A Völzke, Henry %A Kovacs, Peter %A Stumvoll, Michael %A Mägi, Reedik %A Hofman, Albert %A Uitterlinden, André G %A Rivadeneira, Fernando %A Aulchenko, Yurii S %A Polasek, Ozren %A Hastie, Nick %A Vitart, Veronique %A Helmer, Catherine %A Wang, Jie Jin %A Ruggiero, Daniela %A Bergmann, Sven %A Kähönen, Mika %A Viikari, Jorma %A Nikopensius, Tiit %A Province, Michael %A Ketkar, Shamika %A Colhoun, Helen %A Doney, Alex %A Robino, Antonietta %A Giulianini, Franco %A Krämer, Bernhard K %A Portas, Laura %A Ford, Ian %A Buckley, Brendan M %A Adam, Martin %A Thun, Gian-Andri %A Paulweber, Bernhard %A Haun, Margot %A Sala, Cinzia %A Metzger, Marie %A Mitchell, Paul %A Ciullo, Marina %A Kim, Stuart K %A Vollenweider, Peter %A Raitakari, Olli %A Metspalu, Andres %A Palmer, Colin %A Gasparini, Paolo %A Pirastu, Mario %A Jukema, J Wouter %A Probst-Hensch, Nicole M %A Kronenberg, Florian %A Toniolo, Daniela %A Gudnason, Vilmundur %A Shuldiner, Alan R %A Coresh, Josef %A Schmidt, Reinhold %A Ferrucci, Luigi %A Siscovick, David S %A van Duijn, Cornelia M %A Borecki, Ingrid %A Kardia, Sharon L R %A Liu, Yongmei %A Curhan, Gary C %A Rudan, Igor %A Gyllensten, Ulf %A Wilson, James F %A Franke, Andre %A Pramstaller, Peter P %A Rettig, Rainer %A Prokopenko, Inga %A Witteman, Jacqueline C M %A Hayward, Caroline %A Ridker, Paul %A Parsa, Afshin %A Bochud, Murielle %A Heid, Iris M %A Goessling, Wolfram %A Chasman, Daniel I %A Kao, W H Linda %A Fox, Caroline S %K African Americans %K Aged %K Animals %K Caspase 9 %K Cyclin-Dependent Kinases %K DEAD-box RNA Helicases %K DNA Helicases %K European Continental Ancestry Group %K Female %K Follow-Up Studies %K Gene Knockdown Techniques %K Genome-Wide Association Study %K Glomerular Filtration Rate %K Humans %K Kidney %K Kidney Failure, Chronic %K Male %K Middle Aged %K Phosphoric Diester Hydrolases %K Zebrafish %X

Chronic kidney disease (CKD) is an important public health problem with a genetic component. We performed genome-wide association studies in up to 130,600 European ancestry participants overall, and stratified for key CKD risk factors. We uncovered 6 new loci in association with estimated glomerular filtration rate (eGFR), the primary clinical measure of CKD, in or near MPPED2, DDX1, SLC47A1, CDK12, CASP9, and INO80. Morpholino knockdown of mpped2 and casp9 in zebrafish embryos revealed podocyte and tubular abnormalities with altered dextran clearance, suggesting a role for these genes in renal function. By providing new insights into genes that regulate renal function, these results could further our understanding of the pathogenesis of CKD.

%B PLoS Genet %V 8 %P e1002584 %8 2012 %G eng %N 3 %1 http://www.ncbi.nlm.nih.gov/pubmed/22479191?dopt=Abstract %R 10.1371/journal.pgen.1002584 %0 Journal Article %J Hum Mol Genet %D 2012 %T Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function. %A Chasman, Daniel I %A Fuchsberger, Christian %A Pattaro, Cristian %A Teumer, Alexander %A Böger, Carsten A %A Endlich, Karlhans %A Olden, Matthias %A Chen, Ming-Huei %A Tin, Adrienne %A Taliun, Daniel %A Li, Man %A Gao, Xiaoyi %A Gorski, Mathias %A Yang, Qiong %A Hundertmark, Claudia %A Foster, Meredith C %A O'Seaghdha, Conall M %A Glazer, Nicole %A Isaacs, Aaron %A Liu, Ching-Ti %A Smith, Albert V %A O'Connell, Jeffrey R %A Struchalin, Maksim %A Tanaka, Toshiko %A Li, Guo %A Johnson, Andrew D %A Gierman, Hinco J %A Feitosa, Mary F %A Hwang, Shih-Jen %A Atkinson, Elizabeth J %A Lohman, Kurt %A Cornelis, Marilyn C %A Johansson, Åsa %A Tönjes, Anke %A Dehghan, Abbas %A Lambert, Jean-Charles %A Holliday, Elizabeth G %A Sorice, Rossella %A Kutalik, Zoltán %A Lehtimäki, Terho %A Esko, Tõnu %A Deshmukh, Harshal %A Ulivi, Sheila %A Chu, Audrey Y %A Murgia, Federico %A Trompet, Stella %A Imboden, Medea %A Coassin, Stefan %A Pistis, Giorgio %A Harris, Tamara B %A Launer, Lenore J %A Aspelund, Thor %A Eiriksdottir, Gudny %A Mitchell, Braxton D %A Boerwinkle, Eric %A Schmidt, Helena %A Cavalieri, Margherita %A Rao, Madhumathi %A Hu, Frank %A Demirkan, Ayse %A Oostra, Ben A %A de Andrade, Mariza %A Turner, Stephen T %A Ding, Jingzhong %A Andrews, Jeanette S %A Freedman, Barry I %A Giulianini, Franco %A Koenig, Wolfgang %A Illig, Thomas %A Meisinger, Christa %A Gieger, Christian %A Zgaga, Lina %A Zemunik, Tatijana %A Boban, Mladen %A Minelli, Cosetta %A Wheeler, Heather E %A Igl, Wilmar %A Zaboli, Ghazal %A Wild, Sarah H %A Wright, Alan F %A Campbell, Harry %A Ellinghaus, David %A Nöthlings, Ute %A Jacobs, Gunnar %A Biffar, Reiner %A Ernst, Florian %A Homuth, Georg %A Kroemer, Heyo K %A Nauck, Matthias %A Stracke, Sylvia %A Völker, Uwe %A Völzke, Henry %A Kovacs, Peter %A Stumvoll, Michael %A Mägi, Reedik %A Hofman, Albert %A Uitterlinden, André G %A Rivadeneira, Fernando %A Aulchenko, Yurii S %A Polasek, Ozren %A Hastie, Nick %A Vitart, Veronique %A Helmer, Catherine %A Wang, Jie Jin %A Stengel, Bénédicte %A Ruggiero, Daniela %A Bergmann, Sven %A Kähönen, Mika %A Viikari, Jorma %A Nikopensius, Tiit %A Province, Michael %A Ketkar, Shamika %A Colhoun, Helen %A Doney, Alex %A Robino, Antonietta %A Krämer, Bernhard K %A Portas, Laura %A Ford, Ian %A Buckley, Brendan M %A Adam, Martin %A Thun, Gian-Andri %A Paulweber, Bernhard %A Haun, Margot %A Sala, Cinzia %A Mitchell, Paul %A Ciullo, Marina %A Kim, Stuart K %A Vollenweider, Peter %A Raitakari, Olli %A Metspalu, Andres %A Palmer, Colin %A Gasparini, Paolo %A Pirastu, Mario %A Jukema, J Wouter %A Probst-Hensch, Nicole M %A Kronenberg, Florian %A Toniolo, Daniela %A Gudnason, Vilmundur %A Shuldiner, Alan R %A Coresh, Josef %A Schmidt, Reinhold %A Ferrucci, Luigi %A Siscovick, David S %A van Duijn, Cornelia M %A Borecki, Ingrid B %A Kardia, Sharon L R %A Liu, Yongmei %A Curhan, Gary C %A Rudan, Igor %A Gyllensten, Ulf %A Wilson, James F %A Franke, Andre %A Pramstaller, Peter P %A Rettig, Rainer %A Prokopenko, Inga %A Witteman, Jacqueline %A Hayward, Caroline %A Ridker, Paul M %A Parsa, Afshin %A Bochud, Murielle %A Heid, Iris M %A Kao, W H Linda %A Fox, Caroline S %A Köttgen, Anna %K Amino Acid Transport Systems, Basic %K Antigens, CD98 Heavy Chain %K Genetic Predisposition to Disease %K Genome-Wide Association Study %K Glomerular Filtration Rate %K Humans %K Inhibin-beta Subunits %K Intracellular Signaling Peptides and Proteins %K Low Density Lipoprotein Receptor-Related Protein-2 %K Membrane Proteins %K Polymorphism, Single Nucleotide %X

In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P = 5.6 × 10(-9)) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 × 10(-4)-2.2 × 10(-7). Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general.

%B Hum Mol Genet %V 21 %P 5329-43 %8 2012 Dec 15 %G eng %N 24 %1 http://www.ncbi.nlm.nih.gov/pubmed/22962313?dopt=Abstract %R 10.1093/hmg/dds369 %0 Journal Article %J PLoS Genet %D 2011 %T Multiple loci are associated with white blood cell phenotypes. %A Nalls, Michael A %A Couper, David J %A Tanaka, Toshiko %A van Rooij, Frank J A %A Chen, Ming-Huei %A Smith, Albert V %A Toniolo, Daniela %A Zakai, Neil A %A Yang, Qiong %A Greinacher, Andreas %A Wood, Andrew R %A Garcia, Melissa %A Gasparini, Paolo %A Liu, Yongmei %A Lumley, Thomas %A Folsom, Aaron R %A Reiner, Alex P %A Gieger, Christian %A Lagou, Vasiliki %A Felix, Janine F %A Völzke, Henry %A Gouskova, Natalia A %A Biffi, Alessandro %A Döring, Angela %A Völker, Uwe %A Chong, Sean %A Wiggins, Kerri L %A Rendon, Augusto %A Dehghan, Abbas %A Moore, Matt %A Taylor, Kent %A Wilson, James G %A Lettre, Guillaume %A Hofman, Albert %A Bis, Joshua C %A Pirastu, Nicola %A Fox, Caroline S %A Meisinger, Christa %A Sambrook, Jennifer %A Arepalli, Sampath %A Nauck, Matthias %A Prokisch, Holger %A Stephens, Jonathan %A Glazer, Nicole L %A Cupples, L Adrienne %A Okada, Yukinori %A Takahashi, Atsushi %A Kamatani, Yoichiro %A Matsuda, Koichi %A Tsunoda, Tatsuhiko %A Tanaka, Toshihiro %A Kubo, Michiaki %A Nakamura, Yusuke %A Yamamoto, Kazuhiko %A Kamatani, Naoyuki %A Stumvoll, Michael %A Tönjes, Anke %A Prokopenko, Inga %A Illig, Thomas %A Patel, Kushang V %A Garner, Stephen F %A Kuhnel, Brigitte %A Mangino, Massimo %A Oostra, Ben A %A Thein, Swee Lay %A Coresh, Josef %A Wichmann, H-Erich %A Menzel, Stephan %A Lin, JingPing %A Pistis, Giorgio %A Uitterlinden, André G %A Spector, Tim D %A Teumer, Alexander %A Eiriksdottir, Gudny %A Gudnason, Vilmundur %A Bandinelli, Stefania %A Frayling, Timothy M %A Chakravarti, Aravinda %A van Duijn, Cornelia M %A Melzer, David %A Ouwehand, Willem H %A Levy, Daniel %A Boerwinkle, Eric %A Singleton, Andrew B %A Hernandez, Dena G %A Longo, Dan L %A Soranzo, Nicole %A Witteman, Jacqueline C M %A Psaty, Bruce M %A Ferrucci, Luigi %A Harris, Tamara B %A O'Donnell, Christopher J %A Ganesh, Santhi K %K Genetic Loci %K Genome-Wide Association Study %K Humans %K Leukocyte Count %K Leukocytes %K Molecular Epidemiology %K Multigene Family %K Phenotype %K Polymorphism, Single Nucleotide %K Ubiquitin-Protein Ligases %X

White blood cell (WBC) count is a common clinical measure from complete blood count assays, and it varies widely among healthy individuals. Total WBC count and its constituent subtypes have been shown to be moderately heritable, with the heritability estimates varying across cell types. We studied 19,509 subjects from seven cohorts in a discovery analysis, and 11,823 subjects from ten cohorts for replication analyses, to determine genetic factors influencing variability within the normal hematological range for total WBC count and five WBC subtype measures. Cohort specific data was supplied by the CHARGE, HeamGen, and INGI consortia, as well as independent collaborative studies. We identified and replicated ten associations with total WBC count and five WBC subtypes at seven different genomic loci (total WBC count-6p21 in the HLA region, 17q21 near ORMDL3, and CSF3; neutrophil count-17q21; basophil count- 3p21 near RPN1 and C3orf27; lymphocyte count-6p21, 19p13 at EPS15L1; monocyte count-2q31 at ITGA4, 3q21, 8q24 an intergenic region, 9q31 near EDG2), including three previously reported associations and seven novel associations. To investigate functional relationships among variants contributing to variability in the six WBC traits, we utilized gene expression- and pathways-based analyses. We implemented gene-clustering algorithms to evaluate functional connectivity among implicated loci and showed functional relationships across cell types. Gene expression data from whole blood was utilized to show that significant biological consequences can be extracted from our genome-wide analyses, with effect estimates for significant loci from the meta-analyses being highly corellated with the proximal gene expression. In addition, collaborative efforts between the groups contributing to this study and related studies conducted by the COGENT and RIKEN groups allowed for the examination of effect homogeneity for genome-wide significant associations across populations of diverse ancestral backgrounds.

%B PLoS Genet %V 7 %P e1002113 %8 2011 Jun %G eng %N 6 %1 http://www.ncbi.nlm.nih.gov/pubmed/21738480?dopt=Abstract %R 10.1371/journal.pgen.1002113