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1. Cell Specific eQTL Analysis without Sorting Cells

Author

Westra, H.J. (Harm-Jan), Arends, D. (Danny), Esko, T. (Tõnu), Peters, M.J. (Marjolein), Schurmann, C. (Claudia), Schramm, K. (Katharina), Kettunen, J. (Johannes), Yaghootkar, H. (Hanieh), Fairfax, B.P. (Benjamin), Andiappan, A.K. (Anand Kumar), Li, Y. (Yang), Fu, J. (Jingyuan), Karjalainen, J. (Juha), Platteel, I. (Inge), Visschedijk, M. (Marijn), Weersma, R.K. (Rinse K.), Kasela, S. (Silva), Milani, L. (Lili), Tserel, L. (Liina), Peterson, P. (Pärt), Reinmaa, E. (Eva), Hofman, A. (Albert), Uitterlinden, A.G. (André), Rivadeneira Ramirez, F. (Fernando), Homuth, G. (Georg), Petersmann, A. (Astrid), Lorbeer, R. (Roberto), Prokisch, H. (Holger), Meitinger, T. (Thomas), Herder, C. (Christian), Roden, M. (Michael), Grallert, H. (Harald), Ripatti, S. (Samuli), Perola, M. (Markus), Wood, A.R. (Andrew), Melzer, D. (David), Ferrucci, L. (Luigi), Singleton, A. (Andrew), Hernandez, D.G. (Dena), Knight, J.C. (Julian), Melchiotti, R. (Rossella), Lee, B. (Bernett), Poidinger, M. (Michael), Zolezzi, F. (Francesca), Larbi, A. (Anis), Wang, D.Y. (De Yun), Berg, L.H. (Leonard) van den, Veldink, J.H. (Jan), Rotzschke, O. (Olaf), Makino, S. (Seiko), Salomaa, V. (Veikko), Strauch, K. (Konstantin), Völker, U. (Uwe), Meurs, J.B.J. (Joyce) van, Metspalu, A. (Andres), Wijmenga, C. (Cisca), Jansen, R.C. (Ritsert), Franke, L. (Lude), Westra, H.J. (Harm-Jan), Arends, D. (Danny), Esko, T. (Tõnu), Peters, M.J. (Marjolein), Schurmann, C. (Claudia), Schramm, K. (Katharina), Kettunen, J. (Johannes), Yaghootkar, H. (Hanieh), Fairfax, B.P. (Benjamin), Andiappan, A.K. (Anand Kumar), Li, Y. (Yang), Fu, J. (Jingyuan), Karjalainen, J. (Juha), Platteel, I. (Inge), Visschedijk, M. (Marijn), Weersma, R.K. (Rinse K.), Kasela, S. (Silva), Milani, L. (Lili), Tserel, L. (Liina), Peterson, P. (Pärt), Reinmaa, E. (Eva), Hofman, A. (Albert), Uitterlinden, A.G. (André), Rivadeneira Ramirez, F. (Fernando), Homuth, G. (Georg), Petersmann, A. (Astrid), Lorbeer, R. (Roberto), Prokisch, H. (Holger), Meitinger, T. (Thomas), Herder, C. (Christian), Roden, M. (Michael), Grallert, H. (Harald), Ripatti, S. (Samuli), Perola, M. (Markus), Wood, A.R. (Andrew), Melzer, D. (David), Ferrucci, L. (Luigi), Singleton, A. (Andrew), Hernandez, D.G. (Dena), Knight, J.C. (Julian), Melchiotti, R. (Rossella), Lee, B. (Bernett), Poidinger, M. (Michael), Zolezzi, F. (Francesca), Larbi, A. (Anis), Wang, D.Y. (De Yun), Berg, L.H. (Leonard) van den, Veldink, J.H. (Jan), Rotzschke, O. (Olaf), Makino, S. (Seiko), Salomaa, V. (Veikko), Strauch, K. (Konstantin), Völker, U. (Uwe), Meurs, J.B.J. (Joyce) van, Metspalu, A. (Andres), Wijmenga, C. (Cisca), Jansen, R.C. (Ritsert), and Franke, L. (Lude)

Abstract

The functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus (eQTL) mapping. While trait-associated variants may operate in a cell-type specific manner, eQTL datasets for such cell-types may not always be available. We performed a genome-environment interaction (GxE) meta-analysis on data from 5,683 samples to infer the cell type specificity of whole blood cis-eQTLs. We demonstrate that this method is able to predict neutrophil and lymphocyte specific cis-eQTLs and replicate these predictions in independent cell-type specific datasets. Finally, we show that SNPs associated with Crohn’s disease preferentially affect gene expression within neutrophils, including the archetypal NOD2 locus.

Published
2015
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2. Automated workflow-based exploitation of pathway databases provides new insights into genetic associations of metabolite profiles

Author

Dharuri, H. (Harish), Henneman, P. (Peter), Demirkan, A. (Ayşe), Klinken, J.B. (Jan) van, Mook-Kanamori, D.O. (Dennis), Wang-Sattler, R. (Rui), Gieger, C. (Christian), Adamski, J. (Jerzy), Hettne, K.M. (Kristina), Roos, M. (Marco), Suhre, K. (Karsten), Duijn, C.M. (Cornelia) van, Willems van Dijk, J.A.P. (Ko), Hoen, P.A.C. (Peter) 't, Ugocsai, P. (Peter), Isaacs, A.J. (Aaron), Pramstaller, P.P. (Peter Paul), Liebisch, G. (Gerhard), Wilson, J.F. (James F), Johansson, A. (Åsa), Rudan, I. (Igor), Aulchenko, Y.S. (Yurii), Kirichenko, A.V. (Anatoly), Janssens, A.C.J.W. (Cécile), Jansen, R.C. (Ritsert), Gnewuch, C. (Carsten), Domingues, I. (Inês), Pattaro, C. (Cristian), Wild, S.H. (Sarah), Jonasson, I. (Inger), Polasek, O. (Ozren), Zorkoltseva, I.V. (Irina), Hofman, A. (Albert), Karssen, L.C. (Lennart), Struchalin, M.V. (Maksim), Floyd, J. (Jamie), Igl, W. (Wilmar), Biloglav, Z. (Zrinka), Broer, L. (Linda), Pfeufer, A. (Arne), Pichler, I. (Irene), Campbell, S. (Susan), Zaboli, G. (Ghazal), Kolcic, I. (Ivana), Rivadeneira Ramirez, F. (Fernando), Huffman, J.E. (Jennifer), Hastie, N. (Nick), Uitterlinden, A.G. (André), Franke, L. (Lude), Franklin, C.S. (Christopher), Vitart, V. (Veronique), Witteman, J.C.M. (Jacqueline), Axenovich, T.I. (Tatiana), Oostra, B.A. (Ben), Meitinger, T. (Thomas), Hicks, A.A. (Andrew), Hayward, C. (Caroline), Wright, A.F. (Alan), Gyllensten, U. (Ulf), Campbell, H. (Harry), Schmitz, G. (Gerd), Dharuri, H. (Harish), Henneman, P. (Peter), Demirkan, A. (Ayşe), Klinken, J.B. (Jan) van, Mook-Kanamori, D.O. (Dennis), Wang-Sattler, R. (Rui), Gieger, C. (Christian), Adamski, J. (Jerzy), Hettne, K.M. (Kristina), Roos, M. (Marco), Suhre, K. (Karsten), Duijn, C.M. (Cornelia) van, Willems van Dijk, J.A.P. (Ko), Hoen, P.A.C. (Peter) 't, Ugocsai, P. (Peter), Isaacs, A.J. (Aaron), Pramstaller, P.P. (Peter Paul), Liebisch, G. (Gerhard), Wilson, J.F. (James F), Johansson, A. (Åsa), Rudan, I. (Igor), Aulchenko, Y.S. (Yurii), Kirichenko, A.V. (Anatoly), Janssens, A.C.J.W. (Cécile), Jansen, R.C. (Ritsert), Gnewuch, C. (Carsten), Domingues, I. (Inês), Pattaro, C. (Cristian), Wild, S.H. (Sarah), Jonasson, I. (Inger), Polasek, O. (Ozren), Zorkoltseva, I.V. (Irina), Hofman, A. (Albert), Karssen, L.C. (Lennart), Struchalin, M.V. (Maksim), Floyd, J. (Jamie), Igl, W. (Wilmar), Biloglav, Z. (Zrinka), Broer, L. (Linda), Pfeufer, A. (Arne), Pichler, I. (Irene), Campbell, S. (Susan), Zaboli, G. (Ghazal), Kolcic, I. (Ivana), Rivadeneira Ramirez, F. (Fernando), Huffman, J.E. (Jennifer), Hastie, N. (Nick), Uitterlinden, A.G. (André), Franke, L. (Lude), Franklin, C.S. (Christopher), Vitart, V. (Veronique), Witteman, J.C.M. (Jacqueline), Axenovich, T.I. (Tatiana), Oostra, B.A. (Ben), Meitinger, T. (Thomas), Hicks, A.A. (Andrew), Hayward, C. (Caroline), Wright, A.F. (Alan), Gyllensten, U. (Ulf), Campbell, H. (Harry), and Schmitz, G. (Gerd)

Abstract

Background: Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) that associate with clinical phenotypes, but these SNPs usually explain just a small part of the heritability and have relatively modest effect sizes. In contrast, SNPs that associate with metabolite levels generally explain a higher percentage of the genetic variation and demonstrate larger effect sizes. Still, the discovery of SNPs associated with metabolite levels is challenging since testing all metabolites measured in typical metabolomics studies with all SNPs comes with a severe multiple testing penalty. We have developed an automated workflow approach that utilizes prior knowledge of biochemical pathways present in databases like KEGG and BioCyc to generate a smaller SNP set relevant to the metabolite. This paper explores the opportunities and challenges in the analysis of GWAS of metabolomic phenotypes and provides novel insights into the genetic basis of metabolic variation through the re-analysis of published GWAS datasets. Results: Re-analysis of the published GWAS dataset from Illig et al. (Nature Genetics, 2010) using a pathway-based workflow (http://www.myexperiment.org/packs/319.html), confirmed previously identified hits and identified a new locus of human metabolic individuality, associating Aldehyde dehydrogenase family1 L1 (ALDH1L1) with serine/glycine ratios in blood. Replication in an independent GWAS dataset of phospholipids (Demirkan et al., PLoS Genetics, 2012) identified two novel loci supported by additional literature evidence: GPAM (Glycerol-3 phosphate acyltransferase) and CBS (Cystathionine beta-synthase). In addition, the workflow approach provided novel insight into the affected pathways and relevance of some of these gene-metabolite pairs in disease development and progression. Conclusions: We demonstrate the utility of automated exploitation of background knowledge present in pathway databases for the analysis of GWA

Published
2013
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3. Mapping of gene expression reveals CYP27A1 as a susceptibility gene for sporadic ALS

Author

Diekstra, F.P. (Frank), Saris, C.G.J. (Christiaan), Rheenen, W. (Wouter) van, Franke, L. (Lude), Jansen, R.C. (Ritsert), Es, M.A. (Michael) van, Estrada Gil, K. (Karol), Vught, P.W.J. (Paul) van, Blauw, H.M. (Hylke), Groen, E.J.N. (Ewout), Horvath, S. (Steve), Rivadeneira Ramirez, F. (Fernando), Hofman, A. (Albert), Uitterlinden, A.G. (André), Robberecht, W. (Wim), Andersen, P.M. (Peter), Melki, J. (Judith), Meininger, V. (Vincent), Hardiman, O. (Orla), Landers, J.E. (John), Brown, R.H. (Robert), Shatunov, A. (Aleksey), Shaw, C.E. (Christopher), Leigh, P.N. (Nigel), Al-Chalabi, A. (Ammar), Ophoff, R.A. (Roel), Berg, L.H. (Leonard) van den, Veldink, J.H. (Jan), Diekstra, F.P. (Frank), Saris, C.G.J. (Christiaan), Rheenen, W. (Wouter) van, Franke, L. (Lude), Jansen, R.C. (Ritsert), Es, M.A. (Michael) van, Estrada Gil, K. (Karol), Vught, P.W.J. (Paul) van, Blauw, H.M. (Hylke), Groen, E.J.N. (Ewout), Horvath, S. (Steve), Rivadeneira Ramirez, F. (Fernando), Hofman, A. (Albert), Uitterlinden, A.G. (André), Robberecht, W. (Wim), Andersen, P.M. (Peter), Melki, J. (Judith), Meininger, V. (Vincent), Hardiman, O. (Orla), Landers, J.E. (John), Brown, R.H. (Robert), Shatunov, A. (Aleksey), Shaw, C.E. (Christopher), Leigh, P.N. (Nigel), Al-Chalabi, A. (Ammar), Ophoff, R.A. (Roel), Berg, L.H. (Leonard) van den, and Veldink, J.H. (Jan)

Abstract

Amyotrophic lateral sclerosis (ALS) is a progressive, neurodegenerative disease characterized by loss of upper and lower motor neurons. ALS is considered to be a complex trait and genome-wide association studies (GWAS) have implicated a few susceptibility loci. However, many more causal loci remain to be discovered. Since it has been shown that genetic variants associated with complex traits are more likely to be eQTLs than frequency-matched variants from GWAS platforms, we conducted a two-stage genome-wide screening for eQTLs associated with ALS. In addition, we applied an eQTL analysis to finemap association loci. Expression profiles using peripheral blood of 323 sporadic ALS patients and 413 controls were mapped to genome-wide genotyping data. Subsequently, data from a two-stage GWAS (3,568 patients and 10,163 controls) were used to prioritize eQTLs identified in the first stage (162 ALS, 207 controls). These prioritized eQTLs were carried

Published
2012
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4. Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations

Author

Demirkan, A. (Ayşe), Duijn, C.M. (Cornelia) van, Ugocsai, P. (Peter), Isaacs, A.J. (Aaron), Pramstaller, P.P. (Peter Paul), Liebisch, G. (Gerhard), Wilson, J.F. (James), Johansson, A. (Åsa), Rudan, I. (Igor), Aulchenko, Y.S. (Yurii), Kirichenko, A.V. (Anatoly), Janssens, A.C.J.W. (Cécile), Jansen, R.C. (Ritsert), Gnewuch, C. (Carsten), Domingues, I. (Inês), Pattaro, C. (Cristian), Wild, S.H. (Sarah), Jonasson, I. (Inger), Polasek, O. (Ozren), Zorkoltseva, I.V. (Irina), Hofman, A. (Albert), Karssen, L.C. (Lennart), Struchalin, M.V. (Maksim), Floyd, J. (Jamie), Igl, W. (Wilmar), Biloglav, Z. (Zrinka), Broer, L. (Linda), Pfeufer, A. (Arne), Pichler, I. (Irene), Campbell, S. (Susan), Zaboli, G. (Ghazal), Kolcic, I. (Ivana), Rivadeneira Ramirez, F. (Fernando), Huffman, J.E. (Jennifer), Hastie, N. (Nick), Uitterlinden, A.G. (André), Franke, L. (Lude), Franklin, C.S. (Christopher), Vitart, V. (Veronique), Nelson, C.P. (Christopher P.), Preuss, M. (Michael), Bis, J.C. (Joshua), O'Donnell, C.J. (Christopher), Franceschini, N. (Nora), Witteman, J.C.M. (Jacqueline), Axenovich, T.I. (Tatiana), Oostra, B.A. (Ben), Meitinger, T. (Thomas), Hicks, A.A. (Andrew), Hayward, C. (Caroline), Wright, A.F. (Alan), Gyllensten, U. (Ulf), Campbell, H. (Harry), Schmitz, G. (Gerd), Demirkan, A. (Ayşe), Duijn, C.M. (Cornelia) van, Ugocsai, P. (Peter), Isaacs, A.J. (Aaron), Pramstaller, P.P. (Peter Paul), Liebisch, G. (Gerhard), Wilson, J.F. (James), Johansson, A. (Åsa), Rudan, I. (Igor), Aulchenko, Y.S. (Yurii), Kirichenko, A.V. (Anatoly), Janssens, A.C.J.W. (Cécile), Jansen, R.C. (Ritsert), Gnewuch, C. (Carsten), Domingues, I. (Inês), Pattaro, C. (Cristian), Wild, S.H. (Sarah), Jonasson, I. (Inger), Polasek, O. (Ozren), Zorkoltseva, I.V. (Irina), Hofman, A. (Albert), Karssen, L.C. (Lennart), Struchalin, M.V. (Maksim), Floyd, J. (Jamie), Igl, W. (Wilmar), Biloglav, Z. (Zrinka), Broer, L. (Linda), Pfeufer, A. (Arne), Pichler, I. (Irene), Campbell, S. (Susan), Zaboli, G. (Ghazal), Kolcic, I. (Ivana), Rivadeneira Ramirez, F. (Fernando), Huffman, J.E. (Jennifer), Hastie, N. (Nick), Uitterlinden, A.G. (André), Franke, L. (Lude), Franklin, C.S. (Christopher), Vitart, V. (Veronique), Nelson, C.P. (Christopher P.), Preuss, M. (Michael), Bis, J.C. (Joshua), O'Donnell, C.J. (Christopher), Franceschini, N. (Nora), Witteman, J.C.M. (Jacqueline), Axenovich, T.I. (Tatiana), Oostra, B.A. (Ben), Meitinger, T. (Thomas), Hicks, A.A. (Andrew), Hayward, C. (Caroline), Wright, A.F. (Alan), Gyllensten, U. (Ulf), Campbell, H. (Harry), and Schmitz, G. (Gerd)

Abstract

Phospho- and sphingolipids are crucial cellular and intracellular compounds. These lipids are required for active transport, a number of enzymatic processes, membrane formation, and cell signalling. Disruption of their metabolism leads to several diseases, with diverse neurological, psychiatric, and metabolic consequences. A large number of phospholipid and sphingolipid species can be detected and measured in human plasma. We conducted a meta-analysis of five European family-based genome-wide association studies (N = 4034) on plasma levels of 24 sphingomyelins (SPM), 9 ceramides (CER), 57 phosphatidylcholines (PC), 20 lysophosphatidylcholines (LPC), 27 phosphatidylethanolamines (PE), and 16 PE-based plasmalogens (PLPE), as well as their proportions in each major class. This effort yielded 25 genome-wide significant loci for phospholipids (smallest P-value = 9.88×10 -204) and 10 loci for sphingolipids (smallest P-value = 3.10×10 -57). After a correction for multiple comparisons (P-value&2.2×10 -9), we observed four novel loci significantly associated with phospholipids (PAQR9, AGPAT1, PKD2L1, PDXDC1) and two with sphingolipids (PLD2 and APOE) explaining up to 3.1% of the variance. Further analysis of the top findings with respect to within class molar proportions uncovered three additional loci for phospholipids (PNLIPRP2, PCDH20, and ABDH3) suggesting their involvement in either fatty acid elongation/saturation processes or fatty acid specific turnover mechanisms. Among those, 14 loci (KCNH7, AGPAT1, PNLIPRP2, SYT9, FADS1-2-3, DLG2, APOA1, ELOVL2, CDK17, LIPC, PDXDC1, PLD2, LASS4, and APOE) mapped into the glycerophospholipid and 12 loci (ILKAP, ITGA9, AGPAT1, FADS1-2-3, APOA1, PCDH20, LIPC, PDXDC1, SGPP1, APOE, LASS4, and PLD2) to the sphingolipid pathways. In large meta-analyses, associations between FADS1-2-3 and carotid intima media thickness, AGPAT1 and type 2 diabetes, and APOA1 and coronary artery disease were observed. In conclusion, our study identified nin

Published
2012
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