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1. Genome-wide association study reveals greater polygenic loading for schizophrenia in cases with a family history of illness

Author: Bigdeli, T. B, Ripke, S, Bacanu, Sa, Lee, S. H, Wray, Nr, Gejman, P. V, Rietschel, M, Cichon, S, St Clair, D, Corvin, A, Kirov, G, Mcquillin, A, Gurling, H, Rujescu, D, Andreassen, O. A, Werge, T, Blackwood, D. H. R, Pato, C. N, Pato, M. T, Malhotra, A. K, O'Donovan, M. C, Kendler, K. S, Fanous, A. H, Neale, Bm, Walters, Jt, Farh, Kh, Holmans, Pa, Lee, P, Bulik Sullivan, B, Collier, Da, Huang, H, Pers, Th, Agartz, I, Agerbo, E, Albus, M, Alexander, M, Amin, F, Begemann, M, Belliveau, Ra, Bene, J, Bergen, Se, Bevilacqua, E, Bigdeli, Tb, Black, Dw, Børglum, Ad, Bruggeman, R, Buccola, Ng, Buckner, Rl, Byerley, W, Cahn, W, Cai, G, Campion, D, Cantor, Rm, Carr, Vj, Carrera, N, Catts, Sv, Chambert, Kd, Chan, Rc, Chen, Ry, Chen, Ey, Cheng, W, Cheung, Ef, Chong, Sa, Cloninger, C, Cohen, D, Cohen, N, Cormican, P, Craddock, N, Crowley, Jj, Curtis, D, Davidson, M, Davis, Kl, Degenhardt, F, Del, Favero, J, Delisi, Le, Demontis, D, Dikeos, D, Dinan, T, Djurovic, S, Donohoe, G, Drapeau, E, Duan, J, Dudbridge, F, Durmishi, N, Eichhammer, P, Eriksson, J, Escott Price, V, Essioux, L, Fanous, Ah, Farrell, Ms, Frank, J, Franke, L, Freedman, R, Freimer, Nb, Friedl, M, Friedman, Ji, Fromer, M, Genovese, G, Georgieva, L, Gershon, Es, Giegling, I, Giusti Rodríguez, P, Godard, S, Goldstein, Ji, Golimbet, V, Gopal, S, Gratten, J, Grove, J, Haan, De, L, Hammer, C, Hamshere, Ml, Hansen, M, Hansen, T, Haroutunian, V, Hartmann, Am, Henskens, Fa, Herms, S, Hirschhorn, Jn, Hoffmann, P, Hofman, A, Hollegaard, Mv, Hougaard, Dm, Ikeda, M, Joa, I, Julìa, A, Kahn, Rs, Kalaydjieva, L, Karachanak Yankova, S, Karjalainen, J, Kavanagh, D, Keller, Mc, Kelly, Bj, Kennedy, Jl, Khrunin, A, Kim, Y, Klovins, J, Knowles, Ja, Konte, B, Kucinskas, V, Kucinskiene, Za, Kuzelova Ptackova, H, Kähler, Ak, Laurent, C, Keong, Jl, Lee, S, Legge, Se, Lerer, B, Li, M, Li, T, Liang, Ky, Lieberman, J, Limborska, S, Loughland, Cm, Lubinski, J, Lönnqvist, J, Macek, M, Magnusson, Pk, Maher, Bs, Maier, W, Mallet, J, Marsal, S, Mattheisen, M, Mattingsdal, M, Mccarley, Rw, Mcdonald, C, Mcintosh, Am, Meier, S, Meijer, Cj, Melegh, B, Melle, I, Mesholam Gately, Ri, Metspalu, A, Michie, Pt, Milani, L, Milanova, V, Mokrab, Y, Morris, Dw, Mors, O, Mortensen, Pb, Murphy, Kc, Murray, Rm, Myin Germeys, I, Müller Myhsok, B, Nelis, M, Nenadic, I, Nertney, Da, Nestadt, G, Nicodemus, Kk, Nikitina Zake, L, Nisenbaum, L, Nordin, A, O'Callaghan, E, O'Dushlaine, C, O'Neill, F, Sy, Oh, Olincy, A, Olsen, L, Jv, Os, Pantelis, C, Papadimitriou, Gn, Papiol, S, Parkhomenko, E, Pato, Mt, Paunio, T, Pejovic Milovancevic, M, Perkins, Do, Pietiläinen, O, Pimm, J, Pocklington, Aj, Powell, J, Price, A, Pulver, Ae, Purcell, Sm, Quested, D, Rasmussen, Hb, Reichenberg, A, Reimers, Ma, Richards, Al, Roffman, Jl, Roussos, P, Ruderfer, Dm, Salomaa, V, Sanders, Ar, Schall, U, Schubert, Cr, Schulze, Tg, Schwab, Sg, Scolnick, Em, Scott, Rj, Seidman, Lj, Shi, J, Sigurdsson, E, Silagadze, T, Silverman, Jm, Sim, K, Slominsky, P, Smoller, Jw, Hc, So, Spencer, Cc, Stahl, Ea, Stefansson, H, Steinberg, S, Stogmann, E, Straub, Re, Strengman, E, Strohmaier, J, Stroup, T, Subramaniam, M, Suvisaari, J, Svrakic, Dm, Szatkiewicz, Jp, Söderman, E, Thirumalai, S, Toncheva, D, Tooney, Pa, Tosato, Sarah, Veijola, J, Waddington, J, Walsh, D, Wang, D, Wang, Q, Webb, Bt, Weiser, M, Wildenauer, Db, Williams, Nm, Williams, S, Witt, Sh, Wolen, Ar, Wong, Eh, Wormley, Bk, Jq, Wu, Hs, Xi, Zai, Cc, Zheng, X, Zimprich, F, Stefansson, K, Visscher, Pm, Adolfsson, R, Andreassen, Oa, Blackwood, Dh, Bramon, E, Buxbaum, Jd, Darvasi, A, Domenici, E, Ehrenreich, H, Esko, T, Gejman, Pv, Gill, M, Hultman, Cm, Iwata, N, Jablensky, Av, Jönsson, Eg, Kendler, Ks, Knight, J, Lencz, T, Levinson, Df, Qs, Li, Liu, J, Malhotra, Ak, Mccarroll, Sa, Moran, Jl, Mowry, Bj, Nöthen, Mm, Ophoff, Ra, Owen, Mj, Palotie, A, Pato, Cn, Petryshen, Tl, Posthuma, D, Riley, Bp, Sham, Pc, Sklar, P, Clair, Ds, Weinberger, Dr, Wendland, Jr, Daly, Mj, Sullivan, Pf, O'Donovan, Mc, Complex Trait Genetics, Amsterdam Neuroscience - Complex Trait Genetics, Bigdeli, Tim B, Ripke, Stephan, Bacanu, Silviu-Alin, Lee, Sang Hong, Fanous, Ayman H, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Psychosis Endophenotype International Consortium, Wellcome Trust Case-Control Consortium 2, Other departments, Adult Psychiatry, Psychiatrie & Neuropsychologie, RS: MHeNs - R2 - Mental Health, MUMC+: MA Psychiatrie (3), MUMC+: Hersen en Zenuw Centrum (3), and Del-Favero, Jurgen
Subjects: 0301 basic medicine, Multifactorial Inheritance, Bipolar Disorder, Inheritance Patterns, Genome-wide association study, Single-nucleotide polymorphism, polygenic, heritability, Biology, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Cellular and Molecular Neuroscience, 0302 clinical medicine, medicine, Humans, SNP, GWAS, Family, Genetic Predisposition to Disease, Family history, Allele, Genetics (clinical), Genetic association, Genetics & Heredity, Psychiatry, Genetics, Depressive Disorder, Major, family history, Models, Genetic, Case-control study, medicine.disease, 3. Good health, schizophrenia, Psychiatry and Mental health, 030104 developmental biology, Schizophrenia, Case-Control Studies, Human medicine, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: Genome-wide association studies (GWAS) of schizophrenia have yielded more than 100 common susceptibility variants, and strongly support a substantial polygenic contribution of a large number of small allelic effects. It has been hypothesized that familial schizophrenia is largely a consequence of inherited rather than environmental factors. We investigated the extent to which familiality of schizophrenia is associated with enrichment for common risk variants detectable in a large GWAS. We analyzed single nucleotide polymorphism (SNP) data for cases reporting a family history of psychotic illness (N=978), cases reporting no such family history (N=4,503), and unscreened controls (N=8,285) from the Psychiatric Genomics Consortium (PGC1) study of schizophrenia. We used a multinomial logistic regression approach with model-fitting to detect allelic effects specific to either family history subgroup. We also considered a polygenic model, in which we tested whether family history positive subjects carried more schizophrenia risk alleles than family history negative subjects, on average. Several individual SNPs attained suggestive but not genome-wide significant association with either family history subgroup. Comparison of genome-wide polygenic risk scores based on GWAS summary statistics indicated a significant enrichment for SNP effects among family history positive compared to family history negative cases (Nagelkerke's R-2=0.0021; P=0.00331; P-value threshold
Published: 2016

2. Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases

Author: Gusev, A, Lee, Sh, SWE SCZ, Consortium, O'Dushlaine, Cgusev, Trynka, G, Finucane, H, Vilhjálmsson, Bj, Xu, H, Zang, C, Ripke, S, Bulik Sullivan, B, Stahl, E, Schizophrenia, Working, Neale, Bm, Corvin, A, Walters, Jt, Farh, Kh, Holmans, Pa, Lee, P, Collier, Da, Huang, H, Pers, Th, Agartz, I, Agerbo, E, Albus, M, Alexander, M, Amin, F, Bacanu, Sa, Begemann, M, Belliveau, Ra, Bene, J, Bergen, Se, Bevilacqua, E, Bigdeli, Tb, Black, Dw, Børglum, Ad, Bruggeman, R, Buccola, Ng, Buckner, Rl, Byerley, W, Cahn, W, Cai, G, Campion, D, Cantor, Rm, Carr, Vj, Carrera, N, Catts, Sv, Chambert, Kd, Chan, Rc, Chen, Ry, Chen, Ey, Cheng, W, Cheung, Ef, Chong, Sa, Cloninger, Cr, Cohen, D, Cohen, N, Cormican, P, Craddock, N, Crowley, Jj, Curtis, D, Davidson, M, Davis, Kl, Degenhardt, F, Del, Favero, Delisi, Le, Demontis, D, Dikeos, D, Dinan, T, Djurovic, S, Donohoe, G, Drapeau, E, Duan, J, Dudbridge, F, Durmishi, N, Eichhammer, P, Eriksson, J, Escott Price, V, Essioux, L, Fanous, Ah, Farrell, Ms, Frank, J, Franke, L, Freedman, R, Freimer, Nb, Friedl, M, Friedman, Ji, Fromer, M, Genovese, G, Georgieva, L, Gershon, Es, Giegling, I, Giusti Rodrguez, P, Godard, S, Goldstein, Ji, Golimbet, V, Gopal, S, Gratten, J, Grove, J, Haan, De, Hammer, C, Hamshere, Ml, Hansen, M, Hansen, T, Haroutunian, V, Hartmann, Am, Henskens, Fa, Herms, S, Hirschhorn, Jn, Hoffmann, P, Hofman, A, Hollegaard, Mv, Hougaard, Dm, Ikeda, M, Joa, I, Julià, A, Kahn, Rs, Kalaydjieva, L, Karachanak Yankova, S, Karjalainen, J, Kavanagh, D, Keller, Mc, Kelly, Bj, Kennedy, Jl, Khrunin, A, Kim, Y, Klovins, J, Knowles, Ja, Konte, B, Kucinskas, V, Kucinskiene, Za, Kuzelova Ptackova, H, Kähler, Ak, Laurent, C, Keong, Jl, Legge, Se, Lerer, B, Li, M, Li, T, Liang, Ky, Lieberman, J, Limborska, S, Loughland, Cm, Lubinski, J, Lnnqvist, J, Macek, M, Magnusson, Pk, Maher, Bs, Maier, W, Mallet, J, Marsal, S, Mattheisen, M, Mattingsdal, M, Mccarley, Rw, Mcdonald, C, Mcintosh, Am, Meier, S, Meijer, Cj, Melegh, B, Melle, I, Mesholam Gately, Ri, Metspalu, A, Michie, Pt, Milani, L, Milanova, V, Mokrab, Y, Morris, Dw, Mors, O, Mortensen, Pb, Murphy, Kc, Murray, Rm, Myin Germeys, I, Mller Myhsok, B, Nelis, M, Nenadic, I, Nertney, Da, Nestadt, G, Nicodemus, Kk, Nikitina Zake, L, Nisenbaum, L, Nordin, A, O'Callaghan, E, O'Dushlaine, C, O'Neill, Fa, Sy, Oh, Olincy, A, Olsen, L, Van, Os, Pantelis, C, Papadimitriou, Gn, Papiol, S, Parkhomenko, E, Pato, Mt, Paunio, T, Pejovic Milovancevic, M, Perkins, Do, Pietilinen, O, Pimm, J, Pocklington, Aj, Powell, J, Price, A, Pulver, Ae, Purcell, Sm, Quested, D, Rasmussen, Hb, Reichenberg, A, Reimers, Ma, Richards, Al, Roffman, Jl, Roussos, P, Ruderfer, Dm, Salomaa, V, Sanders, Ar, Schall, U, Schubert, Cr, Schulze, Tg, Schwab, Sg, Scolnick, Em, Scott, Rj, Seidman, Lj, Shi, J, Sigurdsson, E, Silagadze, T, Silverman, Jm, Sim, K, Slominsky, P, Smoller, Jw, Hc, So, Spencer, Cc, Stahl, Ea, Stefansson, H, Steinberg, S, Stogmann, E, Straub, Re, Strengman, E, Strohmaier, J, Stroup, Ts, Subramaniam, M, Suvisaari, J, Svrakic, Dm, Szatkiewicz, Jp, Sderman, E, Thirumalai, S, Toncheva, D, Tooney, Pa, Tosato, Sarah, Veijola, J, Waddington, J, Walsh, D, Wang, D, Wang, Q, Webb, Bt, Weiser, M, Wildenauer, Db, Williams, Nm, Williams, S, Witt, Sh, Wolen, Ar, Wong, Eh, Wormley, Bk, Jq, Wu, Hs, Xi, Zai, Cc, Zheng, X, Zimprich, F, Wray, Nr, Stefansson, K, Visscher, Pm, Adolfsson, R, Andreassen, Oa, Blackwood, Dh, Bramon, E, Buxbaum, Jd, Brglum, Ad, Cichon, S, Darvasi, A, Domenici, E, Ehrenreich, H, Esko, T, Gejman, Pv, Gill, M, Gurling, H, Hultman, Cm, Iwata, N, Jablensky, Av, Jönsson, Eg, Kendler, Ks, Kirov, G, Knight, J, Lencz, T, Levinson, Df, Qs, Li, Liu, J, Malhotra, Ak, Mccarroll, Sa, Mcquillin, A, Moran, Jl, Mowry, Bj, Nthen, Mm, Ophoff, Ra, Owen, Mj, Palotie, A, Pato, Cn, Petryshen, Tl, Posthuma, D, Rietschel, M, Riley, Bp, Rujescu, D, Sham, Pc, Sklar, P, Clair, St, Weinberger, Dr, Wendland, Jr, Werge, T, Daly, Mj, Sullivan, Pf, O'Donovan, Mc, Chambert, K, Akterin, S, Bergen, S, Ruderfer, D, Scolnick, E, Purcell, S, Mccarroll, S, Daly, M, Pasaniuc, B, Raychaudhuri, S, Price, Al, Gusev, Alexander, Lee, S Hong, Trynka, Gosia, Finucane, Hilary K, Price, Alkes L, Schizophrenia Working Group of the Psychiatric Genomics Consortium, SWE-SCZ Consortium, ANS - Amsterdam Neuroscience, Adult Psychiatry, Other departments, Psychiatrie & Neuropsychologie, RS: MHeNs - R2 - Mental Health, Complex Trait Genetics, Functional Genomics, and Neuroscience Campus Amsterdam - Brain Mechanisms in Health & Disease
Subjects: Linkage disequilibrium, GWAS, schizophrenia, SNP, trait heritability, disease architecture, Inheritance Patterns, Single-nucleotide polymorphism, Genome-wide association study, Biology, Article, Open Reading Frames, SDG 3 - Good Health and Well-being, Genetic, Models, Genotype, Genetics, Humans, Genetics(clinical), Computer Simulation, Regulatory Elements, Transcriptional, Exome, Genetics (clinical), genotype imputation, Genetic association, Genetics & Heredity, genome-wide association study, Models, Genetic, Genetic Diseases, Inborn, Genetic Variation, Heritability, exome chips, Regulatory Elements, Inborn, Genetic Diseases, Transcriptional, coding variants, Genome-Wide Association Study
Abstract: Regulatory and coding variants are known to be enriched with associations identified by genome-wide association studies (GWASs) of complex disease, but their contributions to trait heritability are currently unknown. We applied variance-component methods to imputed genotype data for 11 common diseases to partition the heritability explained by genotyped SNPs (h(g)(2)) across functional categories (while accounting for shared variance due to linkage disequilibrium). Extensive simulations showed that in contrast to current estimates from GWAS summary statistics, the variance-component approach partitions heritability accurately under a wide range of complex-disease architectures. Across the 11 diseases DNaseI hypersensitivity sites (DHSs) from 217 cell types spanned 16% of imputed SNPs (and 24% of genotyped SNPs) but explained an average of 79% (SE = 8%) of h(g)(2) from imputed SNPs (5.1 x enrichment; p = 3.7 x 10(-17)) and 38% (SE = 4%) of h(g)(2) from genotyped SNPs (1.6 x enrichment, p = 1.0 x 10(-4)). Further enrichment was observed at enhancer DHSs and cell-type-specific DHSs. In contrast, coding variants, which span 1% of the genome, explained
Published: 2014

3. Variability in Working Memory Performance Explained by Epistasis vs Polygenic Scores in the ZNF804A Pathway

Author: Nicodemus, Kk, Hargreaves, A, Morris, D, Anney, R, Gill, M, Corvin, A, Donohoe, G, Ripke, S, Sanders, Ar, Kendler, Ks, Levinson, Df, Sklar, P, Holmans, Pa, Lin, Dy, Duan, J, Ophoff, Ra, Andreassen, Oa, Scolnick, E, Cichon, S, Clair, St, D, Gurling, H, Werge, T, Rujescu, D, Blackwood, Dh, Pato, Cn, Malhotra, Ak, Purcell, S, Dudbridge, F, Neale, Bm, Rossin, L, Visscher, Pm, Posthuma, D, Ruderfer, Dm, Fanous, A, Stefansson, H, Steinberg, S, Mowry, Bj, Golimbet, V, Hert, De, M, Jönsson, Eg, Bitter, I, Pietiläinen, Op, Collier, Da, Tosato, Sarah, Agartz, I, Albus, M, Alexander, M, Amdur, Rl, Amin, F, Bass, N, Bergen, Se, Black, Dw, Børglum, Ad, Brown, Ma, Bruggeman, R, Buccola, Ng, Byerley, Wf, Cahn, W, Cantor, Rm, Carr, Vj, Catts, Sv, Choudhury, K, Cloninger, C, Cormican, P, Craddock, N, Danoy, Pa, Datta, S, Haan, De, L, Demontis, D, Dikeos, D, Djurovic, S, Donnelly, P, Duong, L, Dwyer, S, Fink Jensen, A, Freedman, R, Freimer, Nb, Friedl, M, Georgieva, L, Giegling, I, Glenthøj, B, Godard, S, Hamshere, M, Hansen, M, Hansen, T, Hartmann, Am, Henskens, Fa, Hougaard, Dm, Hultman, Cm, Ingason, A, Jablensky, Av, Jakobsen, Kd, Jay, M, Jürgens, G, Kahn, Rs, Keller, Mc, Kenis, G, Kenny, E, Kim, Y, Kirov, Gk, Konnerth, H, Konte, B, Krabbendam, L, Krasucki, R, Lasseter, Vk, Laurent, C, Lawrence, J, Lencz, T, Lerer, F, Liang, Ky, Lichtenstein, P, Lieberman, Ja, Linszen, Dh, Lönnqvist, J, Loughland, Cm, Maclean, Aw, Maher, Bs, Maier, W, Mallet, J, Malloy, P, Mattheisen, M, Mattingsdal, M, Mcghee, Ka, Mcgrath, Jj, Mcintosh, A, Mclean, De, Mcquillin, A, Melle, I, Michie, Pt, Milanova, V, Morris, Dw, Mors, O, Mortensen, Pb, Moskvina, V, Muglia, P, Myin Germeys, I, Nertney, Da, Nestadt, G, Nielsen, J, Nikolov, I, Nordentoft, M, Norton, N, Nöthen, Mm, O'Dushlaine, Ct, Olincy, A, Olsen, L, O'Neill, F, Ørntoft, Tf, Owen, Mj, Pantelis, C, Papadimitriou, G, Pato, Mt, Peltonen, L, Petursson, H, Pickard, B, Pimm, J, Pulver, Ae, Puri, V, Quested, D, Quinn, Em, Rasmussen, Hb, Réthelyi, Jm, Ribble, R, Rietschel, M, Riley, Bp, Ruggeri, Mirella, Schall, U, Schulze, Tg, Schwab, Sg, Scott, Rj, Shi, J, Sigurdsson, E, Silverman, Jm, Spencer, Cc, Stefansson, K, Strange, A, Strengman, E, Stroup, T, Suvisaari, J, Terenius, L, Thirumalai, S, Thygesen, Jh, Timm, S, Toncheva, D, Van, Den, Oord, E, Van, Os, Van, J, Winkel, R, Veldink, J, Walsh, D, Wang, Ag, Wiersma, D, Wildenauer, Db, Williams, Hj, Williams, Nm, Wormley, B, Zammit, S, Sullivan, Pf, O'Donovan, Mc, Daly, Mj, Gejman, P., Functional Genomics, Complex Trait Genetics, De Hert, Marc, Myin-Germeys, Inez, van Winkel, Ruud, Psychiatrie & Neuropsychologie, RS: MHeNs - R2 - Mental Health, Amsterdam Neuroscience, and Adult Psychiatry
Subjects: epistasis, Male, Multifactorial Inheritance, polygenic, Neuropsychological Tests, involvement, 0302 clinical medicine, Neural Pathways, 2.1 Biological and endogenous factors, Psychology, schizophrenia risk, psychosis variant, Aetiology, 0303 health sciences, susceptibility gene znf804a, medicine.diagnostic_test, phenotypes, Zinc Fingers, Neuropsychological test, Single Nucleotide, Middle Aged, Serious Mental Illness, Psychiatry and Mental health, Memory, Short-Term, Mental Health, Schizophrenia, Major depressive disorder, Female, Cognitive Sciences, social and economic factors, Adult, medicine.medical_specialty, Psychosis, working memory, schizophrenia, IQ, Schizoaffective disorder, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Gene interaction, Genetic, Social cognition, Memory, Clinical Research, 2.3 Psychological, Behavioral and Social Science, medicine, Genetics, Humans, Genetic Predisposition to Disease, Bipolar disorder, Polymorphism, Psychiatry, 030304 developmental biology, Other Medical and Health Sciences, Prevention, Wellcome Trust Case Control Consortium 2, Neurosciences, Genetic Variation, Epistasis, Genetic, Schizophrenia Psychiatric Genome-wide Association Study (GWAS) Consortium, medicine.disease, attention, Brain Disorders, deficits, Short-Term, Psychotic Disorders, genome-wide association, Epistasis, healthy controls, identification, Cognition Disorders, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: IMPORTANCE We investigated the variation in neuropsychological function explained by risk alleles at the psychosis susceptibility gene ZNF804A and its interacting partners using single nucleotide polymorphisms (SNPs), polygenic scores, and epistatic analyses. Of particular importance was the relative contribution of the polygenic score vs epistasis in variation explained. OBJECTIVES To (1) assess the association between SNPs in ZNF804A and the ZNF804A polygenic score with measures of cognition in cases with psychosis and (2) assess whether epistasis within the ZNF804A pathway could explain additional variation above and beyond that explained by the polygenic score. DESIGN, SETTING, AND PARTICIPANTS Patients with psychosis (n = 424)were assessed in areas of cognitive ability impaired in schizophrenia including IQ, memory, attention, and social cognition.We used the Psychiatric GWAS Consortium 1 schizophrenia genome-wide association study to calculate a polygenic score based on identified risk variants within this genetic pathway. Cognitive measures significantly associated with the polygenic score were tested for an epistatic component using a training set (n = 170), which was used to develop linear regression models containing the polygenic score and 2-SNP interactions. The best-fitting models were tested for replication in 2 independent test sets of cases: (1) 170 individuals with schizophrenia or schizoaffective disorder and (2) 84 patients with broad psychosis (including bipolar disorder, major depressive disorder, and other psychosis). MAIN OUTCOMES AND MEASURES Participants completed a neuropsychological assessment battery designed to target the cognitive deficits of schizophrenia including general cognitive function, episodic memory, working memory, attentional control, and social cognition. RESULTS Higher polygenic scores were associated with poorer performance among patients on IQ, memory, and social cognition, explaining 1%to 3%of variation on these scores (range, P = .01 to .03). Using a narrow psychosis training set and independent test sets of narrow phenotype psychosis (schizophrenia and schizoaffective disorder), broad psychosis, and control participants (n = 89), the addition of 2 interaction terms containing 2 SNPs each increased the R2 for spatial working memory strategy in the independent psychosis test sets from 1.2%using the polygenic score only to 4.8%(P = .11 and .001, respectively) but did not explain additional variation in control participants. CONCLUSIONS AND RELEVANCE These data support a role for the ZNF804A pathway in IQ, memory, and social cognition in cases. Furthermore, we showed that epistasis increases the variation explained above the contribution of the polygenic score. © 2014 American Medical Association. All rights reserved.
Published: 2014

4. Schizophrenia genetic variants are not associated with intelligence

Author: van Scheltinga, Af, Bakker, Sc, van Haren, Ne, Derks, Em, Buizer Voskamp, Je, Cahn, W, Ripke, S, Sanders, A, Kendler, K, Levinson, D, Sklar, P, Holmans, P, Lin, D., Duan, J, Ophoff, R, Andreassen, O, Scolnick, E, Cichon, S, St Clair, D, Corvin, A, Gurling, H, Werge, T, Rujescu, D, Blackwood, D, Pato, C, Malhotra, A, Purcell, S, Dudbridge, F, Neale, B, Rossin, L, Visscher, P, Posthuma, D, Ruderfer, D, Fanous, A, Stefansson, H, Steinberg, S, Mowry, B, Golimbet, V, Hert, De, M, Jonsson, E, Bitter, I, Pietilainen, O, Collier, D, Tosato, Sarah, Agartz, I, Albus, M, Alexander, M, Amdur, R, Amin, F, Bass, N, Bergen, S, Black, D, Børglum, A, Brown, M, Bruggeman, R, Buccola, N, Byerley, W, Cantor, R, Carr, V, Catts, S, Choudhury, K, Cloninger, C, Cormican, P, Craddock, N, Danoy, P, Datta, S, Haan, De, L, Demontis, D, Dikeos, D, Djurovic, S, Donnelly, P, Donohoe, G, Duong, L, Dwyer, S, Fink Jensen, A, Freedman, R, Freimer, N, Friedl, M, Georgieva, L, Giegling, I, Gill, M, Glenthøj, B, Godard, S, Hamshere, M, Hansen, M, Hansen, T, Hartmann, A, Henskens, F, Hougaard, D, Hultman, C, Ingason, A, Jablensky, A, Jakobsen, K, Jay, M, Jurgens, G, Kahn, R, Keller, M, Kenis, G, Kenny, E, Kim, Y, Kirov, G, Konnerth, H, Konte, B, Krabbendam, L, Krasucki, R, Lasseter, V, Laurent, C, Lawrence, J, Lencz, T, Lerer, F, Liang, K, Lichtenstein, P, Lieberman, J, Linszen, D, Lonnqvist, J, Loughland, C, Maclean, A, Maher, B, Maier, W, Mallet, J, Malloy, P, Mattheisen, M, Mattingsdal, M, Mcghee, K, Mcgrath, J, Mcintosh, A, Mclean, D, Mcquillin, A, Melle, I, Michie, P, Milanova, V, Morris, D, Mors, O, Mortensen, P, Moskvina, V, Muglia, P, Myin Germeys, I, Nertney, D, Nestadt, G, Nielsen, J, Nikolov, I, Nordentoft, M, Norton, N, Nothen, M, O'Dushlaine, C, Olincy, A, Olsen, L, O'Neill, F, Ørntoft, T, Owen, M, Pantelis, C, Papadimitriou, G, Pato, M, Peltonen, L, Petursson, H, Pickard, B, Pimm, J, Pulver, A, Puri, V, Quested, D, Quinn, E, Rasmussen, H, Rethelyi, Jm, Ribble, R, Rietschel, M, Riley, B, Ruggeri, Mirella, Schall, U, Schulze, T, Schwab, S, Scott, R, Shi, J, Sigurdsson, E, Silverman, J, Spencer, C, Stefansson, K, Strange, A, Strengman, E, Stroup, T, Suvisaari, J, Terenius, L, Thirumalai, S, Thygesen, J, Timm, S, Toncheva, D, van den Oord, E, van Os, J, van Winkel, R, Veldink, J, Walsh, D, Wang, A, Wiersma, D, Wildenauer, D, Williams, H, Williams, N, Wormley, B, Zammit, S, Sullivan, P, O'Donovan, M, Daly, M, Gejman, P), Ophoff, Ra, Kahn, Rs, Functional Genomics, Neuroscience Campus Amsterdam - Neurobiology of Mental Health, Neuroscience Campus Amsterdam - Brain Mechanisms in Health & Disease, Psychiatrie & Neuropsychologie, RS: MHeNs School for Mental Health and Neuroscience, ANS - Amsterdam Neuroscience, APH - Amsterdam Public Health, and Adult Psychiatry
Subjects: Oncology, Adult, Male, Psychosis, medicine.medical_specialty, Multifactorial Inheritance, DNA Copy Number Variations, Endophenotypes, Schizophrenia (object-oriented programming), Intelligence, SNP, Single-nucleotide polymorphism, Genome-wide association study, polygenic, Polymorphism, Single Nucleotide, behavioral disciplines and activities, Article, Cognition, Internal medicine, mental disorders, medicine, Humans, Genetic Predisposition to Disease, deletion, Cognitive decline, Applied Psychology, Genetic association, Genetics, Wechsler Scales, Wechsler Adult Intelligence Scale, medicine.disease, endophenotype, Psychiatry and Mental health, duplication, IQ, Endophenotype, Schizophrenia, Female, Psychology, cognition, schizophrenia, Genome-Wide Association Study
Abstract: BackgroundSchizophrenia is associated with lower pre-morbid intelligence (IQ) in addition to (pre-morbid) cognitive decline. Both schizophrenia and IQ are highly heritable traits. Therefore, we hypothesized that genetic variants associated with schizophrenia, including copy number variants (CNVs) and a polygenic schizophrenia (risk) score (PSS), may influence intelligence.MethodIQ was estimated with the Wechsler Adult Intelligence Scale (WAIS). CNVs were determined from single nucleotide polymorphism (SNP) data using the QuantiSNP and PennCNV algorithms. For the PSS, odds ratios for genome-wide SNP data were calculated in a sample collected by the Psychiatric Genome-Wide Association Study (GWAS) Consortium (8690 schizophrenia patients and 11 831 controls). These were used to calculate individual PSSs in our independent sample of 350 schizophrenia patients and 322 healthy controls.ResultsAlthough significantly more genes were disrupted by deletions in schizophrenia patients compared to controls (p = 0.009), there was no effect of CNV measures on IQ. The PSS was associated with disease status (R2 = 0.055, p = 2.1 × 10−7) and with IQ in the entire sample (R2 = 0.018, p = 0.0008) but the effect on IQ disappeared after correction for disease status.ConclusionsOur data suggest that rare and common schizophrenia-associated variants do not explain the variation in IQ in healthy subjects or in schizophrenia patients. Thus, reductions in IQ in schizophrenia patients may be secondary to other processes related to schizophrenia risk.
Published: 2013

5. Genome-wide association study identifies five new schizophrenia loci

Author: Ripke, S., Sanders, A. R., Kendler, K. S., Levinson, D. F., Sklar, P., Holmans, P. A., Lin, D., Duan, J., Ophoff, R. A., Andreassen, O. A., Scolnick, E., Cichon, S., Clair, D. S., Corvin, A., Gurling, H., Werge, T., Rujescu, D., D. H. R., Pato, C. N., Malhotra, A. K., Purcell, S., Dudbridge, F., Neale, B. M., Rossin, L., Visscher, P. M., Posthuma, D., Ruderfer, D. M., Fanous, A., Stefansson, H., Steinberg, S., Mowry, B. J., Golimbet, V., Hert, M. D., Jönsson, E. G., Bitter, I., O. P. H., Collier, D. A., Tosato, Sarah, Agartz, I., Albus, M., Alexander, M., Amdur, R. L., Amin, F., Bass, N., Bergen, S. E., Black, D. W., Børglum, A. D., Brown, M. A., Bruggeman, R., Buccola, N. G., Byerley, W. F., Cahn, W., Cantor, R. M., Carr, V. J., Catts, S. V., Choudhury, K., Cloninger, C. R., Cormican, P., Craddock, N., Danoy, P. A., Datta, S., Haan, L. d., Demontis, D., Dikeos, D., Djurovic, S., Donnelly, P., Donohoe, G., Duong, L., Dwyer, S., Fink Jensen, A., Freedman, R., Freimer, N. B., Friedl, M., Georgieva, L., Giegling, I., Gill, M., Glenthøj, B., Godard, S., Hamshere, M., Hansen, M., Hansen, T., Hartmann, A. M., Henskens, F. A., Hougaard, D. M., Hultman, C. M., Ingason, A., Jablensky, A. V., Jakobsen, K. D., Jay, M., Jürgens, G., Kahn, R. S., Keller, M. C., Kenis, G., Kenny, E., Kim, Y., Kirov, G. K., Konnerth, H., Konte, B., Krabbendam, L., Krasucki, R., Lasseter, V. K., Laurent, C., Lawrence, J., Lencz, T., Lerer, F. B., Liang, K., Lichtenstein, P., Lieberman, J. A., Linszen, D. H., Lönnqvist, J., Loughland, C. M., Maclean, A. W., Maher, B. S., Maier, W., Mallet, J., Malloy, P., Mattheisen, M., Mattingsdal, M., Mcghee, K. A., Mcgrath, J. J., Mcintosh, A., Mclean, D. E., Mcquillin, A., Melle, I., Michie, P. T., Milanova, V., Morris, D. W., Mors, O., Mortensen, P. B., Moskvina, V., Muglia, P., Myin Germeys, I., Nertney, D. A., Nestadt, G., Nielsen, J., Nikolov, I., Nordentoft, M., Norton, N., Nöthen, M. M., O'Dushlaine, C. T., Olincy, A., Olsen, L., O'Neill, F. A., Orntoft, T. F., Owen, M. J., Pantelis, C., Papadimitriou, G., Pato, M. T., Peltonen, L., Petursson, H., Pickard, B., Pimm, J., Pulver, A. E., Puri, V., Quested, D., Quinn, E. M., Rasmussen, H. B., Réthelyi, J. M., Ribble, R., Rietschel, M., Riley, B. P., Ruggeri, Mirella, Schall, U., Schulze, T. G., Schwab, S. G., Scott, R. J., Shi, J., Sigurdsson, E., Silverman, J. M., C. C. A., Stefansson, K., Strange, A., Strengman, E., Stroup, T. S., Suvisaari, J., Terenius, L., Thirumalai, S., Thygesen, J. H., Timm, S., Toncheva, D., Den, E. v., J. v., Os, Winkel, R. v., Veldink, J., Walsh, D., Wang, A. G., Wiersma, D., Wildenauer, D. B., Williams, H. J., Williams, N. M., Wormley, B., Zammit, S., Sullivan, P. F., O'Donovan, M. C., Daly, M. J., Gejman, P. V., Genome Wide, S. P., ANS - Amsterdam Neuroscience, Adult Psychiatry, Functional Genomics, Educational Neuroscience, Clinical Child and Family Studies, Neuroscience Campus Amsterdam - integrative Analysis & Modeling, Neuroscience Campus Amsterdam - Attention & Cognition, LEARN! - Brain, learning and development, Psychiatrie & Neuropsychologie, and RS: MHeNs School for Mental Health and Neuroscience
Subjects: Male, Gene Dosage, Biology, VARIANTS, SUSCEPTIBILITY, ANCESTRY, Polymorphism, Single Nucleotide, Article, Linkage Disequilibrium, White People, 03 medical and health sciences, 0302 clinical medicine, microRNA, Genetics, Humans, Genetic Predisposition to Disease, Alleles, 030304 developmental biology, 0303 health sciences, Genome, Genome, Human, HERITABILITY, MICRORNA, BIPOLAR DISORDER, 3. Good health, schizophrenia, COMMON SNPS EXPLAIN, MicroRNAs, INDIVIDUALS, Logistic Models, Gene Expression Regulation, Haplotypes, LARGE PROPORTION, Genetic Loci, Case-Control Studies, Mutation, Female, HUMAN HEIGHT, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: We examined the role of common genetic variation in schizophrenia in a genome-wide association study of substantial size: a stage 1 discovery sample of 21,856 individuals of European ancestry and a stage 2 replication sample of 29,839 independent subjects. The combined stage 1 and 2 analysis yielded genome-wide significant associations with schizophrenia for seven loci, five of which are new (1p21.3, 2q32.3, 8p23.2, 8q21.3 and 10q24.32-q24.33) and two of which have been previously implicated (6p21.32-p22.1 and 18q21.2). The strongest new finding (P = 1.6 × 10 -11) was with rs1625579 within an intron of a putative primary transcript for MIR137 (microRNA 137), a known regulator of neuronal development. Four other schizophrenia loci achieving genome-wide significance contain predicted targets of MIR137, suggesting MIR137-mediated dysregulation as a previously unknown etiologic mechanism in schizophrenia. In a joint analysis with a bipolar disorder sample (16,374 affected individuals and 14,044 controls), three loci reached genome-wide significance: CACNA1C (rs4765905, P = 7.0 × 10 -9), ANK3 (rs10994359, P = 2.5 × 10 -8) and the ITIH3-ITIH4 region (rs2239547, P = 7.8 × 10 -9). © 2011 Nature America, Inc. All rights reserved.
Published: 2011

6. Common variant at 16p11.2 conferring risk of psychosis

Author: Steinberg, S., de Jong, S., Sigurdsson, E., Murray, R., Corvin, A., Gill, M., Morris, D., O'Neill, F. A., Kendler, K., Riley, B., 2, Wellcome Trust Case Control Consortium, Craddock, N., Owen, M. J., Vassos, E., O'Donovan, M. C., Thorsteinsdottir, U., Kong, A., Ehrenreich, H., Carracedo, A., Golimbet, V., Andreassen, O. A., Børglum, A. D., Mors, O., Mortensen, P. B., Giegling, I., Werge, T., Ophoff, R. A., Nöthen, M. M., Rietschel, M., Cichon, S., Ruggeri, M., Tosato, S., Palotie, A., St Clair, D., Rujescu, D., Breuer, R., Collier, D. A., Stefansson, H., Stefansson, K., Donnelly, Peter, Barroso, Ines, Blackwell, Jenefer M, Bramon, Elvira, Brown, Matthew A, Casas, Juan P, Corvin, Aiden, Fraser, G., Deloukas, Panos, Duncanson, Audrey, Jankowski, Janusz, Markus, Hugh S, Mathew, Christopher G, Palmer, Colin N A, Plomin, Robert, Rautanen, Anna, Sawcer, Stephen J, Trembath, Richard C, Walker, N., Viswanathan, Ananth C, Wood, Nicholas W, Spencer, Chris C A, Band, Gavin, Bellenguez, Céline, Freeman, Colin, Hellenthal, Garrett, Giannoulatou, Eleni, Pirinen, Matti, Pearson, Richard, Melle, I., Strange, Amy, Su, Zhan, Vukcevic, Damjan, Langford, Cordelia, Hunt, Sarah E, Edkins, Sarah, Gwilliam, Rhian, Blackburn, Hannah, Djurovic, S., Bumpstead, Suzannah J, Dronov, Serge, Gillman, Matthew, Gray, Emma, Hammond, Naomi, Jayakumar, Alagurevathi, McCann, Owen T, Liddle, Jennifer, Potter, Simon C, Ravindrarajah, Radhi, Agartz, I., Ricketts, Michelle, Waller, Matthew, Weston, Paul, Widaa, Sara, Whittaker, Pamela, Tuulio-Henriksson, A., Mattheisen, M., Suvisaari, J., Lönnqvist, J., Paunio, T., Olsen, L., Hansen, T., Ingason, A., Pirinen, M., Strengman, E., GROUP, Hougaard, D. M., Costas, J., Orntoft, T., Didriksen, M., Hollegaard, M. V., Nordentoft, M., Abramova, L., Kaleda, V., Arrojo, M., Sanjuán, J., Arango, C., Etain, B., Demontis, D., Bellivier, F., Méary, A., Schürhoff, F., Szoke, A., Ribolsi, M., Magni, V., Siracusano, A., Sperling, S., Rossner, M., Christiansen, C., Jamain, S., Kiemeney, L. A., Franke, B., van den Berg, L. H., Veldink, J., Curran, S., Bolton, P., Poot, M., Staal, W., Rehnstrom, K., Kilpinen, H., Pietiläinen, O. P. H., Freitag, C. M., Meyer, J., Magnusson, P., Saemundsen, E., Martsenkovsky, I., Bikshaieva, I., Martsenkovska, I., Vashchenko, O., Raleva, M., Paketchieva, K., Lin, K., Stefanovski, B., Durmishi, N., Pejovic Milovancevic, M., Lecic Tosevski, D., Silagadze, T., Naneishvili, N., Mikeladze, N., Surguladze, S., Vincent, J. B., Farmer, A., Papiol, S., Mitchell, P. B., Wright, A., Schofield, P. R., Fullerton, J. M., Montgomery, G. W., Martin, N. G., Rubino, I. A., van Winkel, R., Kenis, G., De Hert, M., Huttenlocher, J., Réthelyi, J. M., Bitter, I., Terenius, L., Jönsson, E. G., Bakker, S., van Os, J., Jablensky, A., Leboyer, M., Bramon, E., Powell, J., deCODE Genet, IS-101 Reykjavik, Iceland Univ Calif Los Angeles, Ctr Neurobehav Genet, Los Angeles, CA USA Harvard Univ, Brigham & Womens Hosp, Sch Med, Channing Div Network Med, Boston, MA 02115 USA Univ Bonn, Inst Genom Math, Bonn, Germany Univ Bonn, Dept Genom, Life & Brain Ctr, Bonn, Germany CHUS, Galician Fdn Genom Med SERGAS, Santiago De Compostela, Spain Aarhus Univ, Dept Biomed, Aarhus, Denmark Aarhus Univ, iSEQ, Ctr Integrat Sequencing, Aarhus, Denmark Lundbeck Fdn Initiat Integrat Psychiat Res, iPSYCH, Aarhus, Denmark Fdn FondaMental, Creteil, France Hop Henri Mondor, INSERM, U955, F-94010 Creteil, France Univ Helsinki, Inst Mol Med Finland FIMM, Helsinki, Finland Inst Hlth & Welf, Publ Hlth Genom Unit, Helsinki, Finland Wellcome Trust Sanger Inst, Cambridge, England South London & Maudsley NHS Fdn Trust, NIHR Biomed Res Ctr Mental Hlth, Dept Neurosci, London, England Kings Coll London, London, England DFG Res Ctr Mol Physiol Brain CMPB, Gottingen, Germany Max Planck Inst Expt Med, Div Clin Neurosci, D-37075 Gottingen, Germany Univ Tubingen, Inst Human Genet, Dept Med Genet, Tubingen, Germany Natl Univ Hosp Reykjavik, Dept Psychiat, Reykjavik, Iceland Univ Iceland, Sch Med, Reykjavik, Iceland Kings Coll London, Inst Psychiat, Social Genet & Dev Psychiat Res Ctr, London, England Univ Munich, Dept Psychiat, Div Mol & Clin Neurobiol, D-80539 Munich, Germany Heidelberg Univ, Cent Inst Mental Hlth, Dept Genet Epidemiol Psychiat, Mannheim, Germany Univ Aberdeen, Dept Mental Hlth, Royal Cornhill Hosp, Aberdeen, Scotland Ravenscraig Hosp, Greenock, Scotland [Univ Oslo, Inst Clin Med, KG Jebsen Ctr Psychosis Res, Div Mental Hlth & Addict,Oslo Univ Hosp, Oslo, Norway Natl Inst Hlth & Welf, Dept Mental Hlth & Subst Abuse Serv, Helsinki, Finland Univ Helsinki, Dept Psychiat, SF-00180 Helsinki, Finland Univ Helsinki, Cent Hosp, Helsinki, Finland Natl Inst Hlth & Welf THL, Publ Hlth Genom Unit, Helsinki, Finland Univ Copenhagen, Mental Hlth Ctr Sct Hans, Inst Biol Psychiat, Roskilde, Denmark Univ Oxford, Wellcome Trust Ctr Human Genet, Oxford, England Univ Med Ctr Utrecht, Dept Med Genet, Utrecht, Netherlands Statens Serum Inst, Dept Clin Biochem Immunol & Genet, Sect Neonatal Screening & Hormones, DK-2300 Copenhagen, Denmark Aarhus Univ Hosp, Dept Mol Med, DK-8000 Aarhus, Denmark H Lundbeck & Co AS, Synapt Transmiss, Copenhagen, Denmark Copenhagen Univ Hosp, Psychiat Ctr Copenhagen, Copenhagen, Denmark Russian Acad Med Sci, Mental Hlth Res Ctr, Moscow 109801, Russia CHUS, Serv Psychiat, Santiago De Compostela, Spain Univ Valencia, Network Ctr Biomed Res Mental Hlth CIBERSAM, Unit Psychiat, Fac Med, Valencia, Spain Univ Complutense, Hosp Gen Univ Gregorio Maranon, IiSGM, CIBERSAM, E-28040 Madrid, Spain Hop H Mondor A Chenevier, AP HP, Creteil, France Univ Paris Est, Fac Med, Creteil, France Univ Roma Tor Vergata, Dept Neurosci, Sect Psychiat, Rome, Italy Max Planck Inst Expt Med, Dept Neurogenet, D-37075 Gottingen, Germany Nord Biosci, Herlev, Denmark Radboud Univ Nijmegen, Med Ctr, Dept Epidemiol & Biostat, NL-6525 ED Nijmegen, Netherlands Radboud Univ Nijmegen, Med Ctr, Dept Urol, NL-6525 ED Nijmegen, Netherlands Radboud Univ Nijmegen, Med Ctr, Dept Human Genet, NL-6525 ED Nijmegen, Netherlands Radboud Univ Nijmegen, Med Ctr, Dept Psychiat, Donders Inst Brain Cognit & Behav, NL-6525 ED Nijmegen, Netherlands Univ Med Ctr, Rudolf Magnus Inst Neurosci, Dept Neurol, Utrecht, Netherlands Kings Coll London, Inst Psychiat, Dept Child & Adolescent Psychiat, London, England Radboud Univ Nijmegen, Dept Cognit Neurosci, NL-6525 ED Nijmegen, Netherlands Goethe Univ Frankfurt, Dept Child & Adolescent Psychiat Psychosomat & Ps, D-60054 Frankfurt, Germany Univ Trier, Dept Neurobehav Genet, Trier, Germany Natl Univ Hosp Reykjavik, Dept Child & Adolescent Psychiat, Reykjavik, Iceland State Diagnost & Counseling Ctr, Kopavogur, Iceland Ukrainian Res Inst Social Forens Psychiat & Drug, Dept Child Adolescent Psychiat & Med Social Rehab, Kiev, Ukraine Univ Skopje, Dept Child & Adolescent Psychiat, Skopje, Macedonia Inst Mental Hlth, Belgrade, Serbia Univ Belgrade, Fac Med, Belgrade, Serbia Tbilisi State Med Univ TSMU, Dept Psychiat & Drug Addict, Tbilisi, Rep of Georgia Ilia State Univ, Social & Affect Neurosci Lab, Tbilisi, Rep of Georgia Ctr Addict & Mental Hlth CAMH, Mol Neuropsychiat & Dev Lab, Toronto, ON, Canada Prince Wales Hosp, Black Dog Inst, Randwick, NSW 2031, Australia Univ New S Wales, Sch Psychiat, Sydney, NSW, Australia Neurosci Res Australia, Sydney, NSW, Australia Univ New S Wales, Sch Med Sci, Sydney, NSW, Australia Queensland Inst Med Res, Brisbane, Qld 4006, Australia Catholic Univ Louvain, Univ Psychiat Ctr, Kortenberg, Belgium Maastricht Univ, European Grad Sch Neurosci EURON,Med Ctr, Sch Mental Hlth & Neurosci,Dept Psychiat & Psycho, South Limburg Mental Hlth Res & Teaching Network, Maastricht, Netherlands Semmelweis Univ, Dept Psychiat & Psychotherapy, H-1085 Budapest, Hungary Karolinska Hosp & Inst, HUBIN Project, Dept Clin Neurosci, Stockholm, Sweden Univ Med Ctr, Rudolf Magnus Inst Neurosci, Dept Psychiat, Utrecht, Netherlands Maastricht Univ, Dept Psychiat, Med Ctr, Maastricht, Netherlands Univ Western Australia, Graylands Hosp, CCRN, Perth, WA 6009, Australia UCL, Mental Hlth Sci Unit, London, England UCL, Inst Cognit Neurosci, London, England South London & Maudsley NHS Fdn Trust, NIHR Biomed Res Ctr Mental Hlth, Dept Psychosis Studies, London, England Trinity Coll Dublin, Sch Med, Neuropsychiat Genet Res Grp, Dublin, Ireland Queens Univ Belfast, Dept Psychiat, Belfast, Antrim, North Ireland Virginia Commonwealth Univ, Dept Human Genet, Richmond, VA USA Virginia Commonwealth Univ, Virginia Inst Psychiat & Behav Genet, Richmond, VA USA Virginia Commonwealth Univ, Dept Psychiat, Richmond, VA USA Cardiff Univ, Sch Med, Inst Psychol Med & Clin Neurosci, MRC Ctr Neuropsychiat Genet & Genom, Cardiff CF10 3AX, S Glam, Wales Univ Santiago de Compostela, Biomed Network Res Ctr Rare Dis CIBERER, Galician Fdn Genom Med, Genom Med Grp, Santiago De Compostela, Spain Aarhus Univ Hosp, Ctr Psychiat Res, Risskov, Denmark Aarhus Univ, Natl Ctr Register Based Res, Aarhus, Denmark German Ctr Neurodegenerat Disorders DZNE, Bonn, Germany Univ Bonn, Inst Human Genet, Bonn, Germany Inst Neurosci & Med INM 1, Julich, Germany Univ Verona, Sect Psychiat, I-37100 Verona, Italy Broad Inst MIT & Harvard, Program Med & Populat Genet & Genet Anal Platform, Cambridge, MA USA Univ Helsinki, Dept Med Genet, Helsinki, Finland Univ Cent Hosp, Helsinki, Finland Univ Halle Wittenberg, Dept Psychiat, D-06108 Halle, Germany Eli Lilly & Co Ltd, Erl Wood Manor, Windlesham, Surrey, England, Psychiatrie & Neuropsychologie, MUMC+: MA Psychiatrie (3), MUMC+: Hersen en Zenuw Centrum (3), and RS: MHeNs - R2 - Mental Health
Subjects: Oncology, Male, association, Bipolar disorder, cross-disorder, schizophrenia, 1p11.2, Bipolar Disorder, International Cooperation, Genome-wide association study, Disease, 0302 clinical medicine, Risk Factors, Epidemiology, Odds Ratio, Medicine, genetics [Schizophrenia], Oligonucleotide Array Sequence Analysis, Genetics, Aged, 80 and over, bipolar disorder, 0303 health sciences, Middle Aged, 16p11.2, 3. Good health, Europe, Psychiatry and Mental health, genetics [Chromosomes, Human, Pair 16], epidemiology [Bipolar Disorder], Urological cancers Radboud Institute for Health Sciences [Radboudumc 15], genetics [Polymorphism, Single Nucleotide], Female, Adult, medicine.medical_specialty, Psychosis, Genotype, complications [Bipolar Disorder], epidemiology [Schizophrenia], Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Cellular and Molecular Neuroscience, Young Adult, complications [Schizophrenia], Internal medicine, mental disorders, Humans, Genetic Predisposition to Disease, ddc:610, Molecular Biology, Settore MED/25 - Psichiatria, 030304 developmental biology, Aged, Chromosome Aberrations, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], business.industry, Gene Expression Profiling, Odds ratio, medicine.disease, Schizophrenia, Autism, business, Body mass index, genetics [Bipolar Disorder], 030217 neurology & neurosurgery, Chromosomes, Human, Pair 16, Genome-Wide Association Study
Abstract: To access publisher's full text version of this article. Please click on the hyperlink in Additional Links field. Epidemiological and genetic data support the notion that schizophrenia and bipolar disorder share genetic risk factors. In our previous genome-wide association study, meta-analysis and follow-up (totaling as many as 18 206 cases and 42 536 controls), we identified four loci showing genome-wide significant association with schizophrenia. Here we consider a mixed schizophrenia and bipolar disorder (psychosis) phenotype (addition of 7469 bipolar disorder cases, 1535 schizophrenia cases, 333 other psychosis cases, 808 unaffected family members and 46 160 controls). Combined analysis reveals a novel variant at 16p11.2 showing genome-wide significant association (rs4583255[T]; odds ratio=1.08; P=6.6 × 10(-11)). The new variant is located within a 593-kb region that substantially increases risk of psychosis when duplicated. In line with the association of the duplication with reduced body mass index (BMI), rs4583255[T] is also associated with lower BMI (P=0.0039 in the public GIANT consortium data set; P=0.00047 in 22 651 additional Icelanders). National Institute of Mental Health N01 MH900001 MH074027 1U24MH081810 R01 MH078075 Eli Lilly and Company Pritzker Neuropsychiatric Disorders Research Fund L.L.C. Massachusetts General Hospital in Boston, MA (NIMH) 2N01MH080001-001 Wellcome Trust 076113 085475 075491/Z/04 085475/B/08/Z 085475/Z/08/Z Medical Research Council G0601030 Anthony P Monaco, PI, University of Oxford National Genome Research Network of the German Federal Ministry of Education and Research (BMBF) 01GS08144 01GS08147 Centre of Excellence for Complex Disease Genetics of the Academy of Finland 213506 129680 Biocentrum Helsinki Foundation Research Program for Molecular Medicine, Faculty of Medicine, University of Helsinki Stanley Medical Research Institute Danish Council for Strategic Research 2101-07-0059 H Lundbeck A/S; the Research Council of Norway 163070/V50 Danish Medical Research Council South-East Norway Health Authority 2004-123 Medical Research Council Ministerio de Sanidad y Consumo, Spain PI081522 Xunta de Galicia 08CSA005208PR Swedish Research Council Wellcome Trust Case Control Consortium 2 Max Planck Society; Saarland University T6 03 10 00-45 Netherlands Foundation for Brain Research (Hersenstichting) 2008(1).34 2006-037761 PIAP-GA-2008-218251 HEALTH-F2-2009-223423 HEALTH-F4-2009-242257 info:eu-repo/grantAgreement/EC/FP7/218251
Published: 2014

7. Convergent lines of evidence support CAMKK2 as a schizophrenia susceptibility gene

Author: Luo, XJ, Li, M, Huang, L, Steinberg, S, Mattheisen, M, Liang, G, Donohoe, G, Shi, Y, Chen, C, Yue, W, Alkelai, A, Lerer, B, Li, Z, Yi, Q, Rietschel, M, Cichon, S, Collier, DA, Tosato, S, Suvisaari, J, Rujescu, D, Golimbet, V, Silagadze, T, Durmishi, N, Milovancevic, MP, Stefansson, H, Schulze, TG, Nöthen, MM, Lyne, R, Morris, DW, Gill, M, Corvin, A, Zhang, D, Dong, Q, Moyzis, RK, Stefansson, K, Sigurdsson, E, Hu, F, SCZ Consortium36, Su, B, Gan, L, and College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China [2] Department of Ophthalmology and Flaum Eye Institute, University of Rochester, Rochester, NY, USA. 2Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA. 31] Nanchang University, Nanchang, China [2] Gannan Medical University, Ganzhou, China [3] Jiangxi Provincial People's Hospital, Nanchang, China. 4deCODE Genetics, Reykjavik, Iceland. 5Department of Biomedicine, Aarhus University, Aarhus C, Denmark. 6College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China. 7Neuropsychiatric Genetics Group and Department of Psychiatry, Institute of Molecular Medicine and Trinity College Institute of Neuroscience, Trinity College Dublin, St James Hospital, Dublin, Ireland. 8Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China. 9Department of Psychology and Social Behavior, University of California, Irvine, CA, USA. 101] Institute of Mental Health, Peking University, Beijing, China [2] Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China. 11Department of Psychiatry, Biological Psychiatry Laboratory, Hadassah-Hebrew University Medical Center, Jerusalem, Israel. 12Department of Psychiatry, the First Teaching Hospital of Xinjiang Medical University, Urumqi, China. 13Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, University of Mannheim, Mannheim, Germany. 14Department of Genomics, Life and Brain Center, and Institute of Human Genetics, University of Bonn, Bonn, Germany. 151] Social, Genetic and Developmental Psychiatry Research Centre, Institute of Psychiatry, King's College, London, UK [2] Eli Lilly and Co. Ltd, Erl Wood Manor, Surrey, UK. 16Section of Psychiatry, University of Verona, Verona, Italy. 17Mental Health and Substance Abuse Services, National Institute for Health and Welfare THL, Helsinki, Finland. 181] Division of Molecular and Clinical Neurobiology, Department of Psychiatry, Ludwig-Maximilians University, Munich, Germany [2] Department of Psychiatry, University of Halle-Wittenberg, Halle, Germany. 19Mental Health Research Center, Russian Academy of Medical Sciences, Moscow, Russia. 20Department of Psychiatry and Drug Addiction, Tbilisi State Medical University (TSMU), Tbilisi, Georgia. 21Department of Child and Adolescent Psychiatry, University of Skopje, Skopje, Macedonia. 22Medical Faculty, University of Belgrade, Belgrade, Serbia. 23Department of Psychiatry and Psychotherapy, University Medical Center Georg-August-Universität, Goettingen, Germany. 24State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China. 25Department of Biological Chemistry, University of California, Irvine, CA, USA. 261] deCODE Genetics, Reykjavik, Iceland [2] School of Medicine, University of Iceland, Reykjavik, Iceland. 271] School of Medicine, University of Iceland, Reykjavik, Iceland [2] Department of Psychiatry, National University Hospital, Reykjavik, Iceland. 28Affiliated Eye Hospital of Nanchang University, Nanchang, China. 29State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Subjects: Pathogenesis, protein-protein interaction, 0302 clinical medicine, Cognition, Gene expression, Genamengi, Databases, Genetic, Protein Interaction Maps, European Continental Ancestry Group/genetics, Psychotic Disorders/genetics, CAMKK2, Schizophrenic Psychology, Genetics, 0303 health sciences, Brain, Chromosome Mapping, Polymorphism, Single Nucleotide/genetics, Psychiatry and Mental health, Geðsjúkdómar, Personality, Genotype, Schizophrenia (object-oriented programming), Down-Regulation, Calcium-Calmodulin-Dependent Protein Kinase Kinase, Single-nucleotide polymorphism, Calcium-Calmodulin-Dependent Protein Kinase, Biology, eQTL, Polymorphism, Single Nucleotide, White People, 03 medical and health sciences, Cellular and Molecular Neuroscience, Asian People, Geðklofi, Personality/genetics, Kinase/metabolism, expression, SNP, Brain/metabolism, Humans, Genetic Predisposition to Disease, Asian Continental Ancestry Group/genetics, Allele, Molecular Biology, Gene, association, schizophrenia, Alleles, 030304 developmental biology, Arfgengi, Kinase/genetics, Schizophrenia/genetics, Case-Control Studies, Protein Interaction Maps/genetics, 030217 neurology & neurosurgery, Chromosomes, Human, Pair 17, Genome-Wide Association Study
Abstract: To access publisher's full text version of this article click on the hyperlink at the bottom of the page Genes that are differentially expressed between schizophrenia patients and healthy controls may have key roles in the pathogenesis of schizophrenia. We analyzed two large-scale genome-wide expression studies, which examined changes in gene expression in schizophrenia patients and their matched controls. We found calcium/calmodulin (CAM)-dependent protein kinase kinase 2 (CAMKK2) is significantly downregulated in individuals with schizophrenia in both studies. To seek the potential genetic variants that may regulate the expression of CAMKK2, we investigated the association between single-nucleotide polymorphisms (SNPs) within CAMKK2 and the expression level of CAMKK2. We found one SNP, rs1063843, which is located in intron 17 of CAMKK2, is strongly associated with the expression level of CAMKK2 in human brains (P=1.1 × 10(-6)) and lymphoblastoid cell lines (the lowest P=8.4 × 10(-6)). We further investigated the association between rs1063843 and schizophrenia in multiple independent populations (a total of 130 623 subjects) and found rs1063843 is significantly associated with schizophrenia (P=5.17 × 10(-5)). Interestingly, we found the T allele of rs1063843, which is associated with lower expression level of CAMKK2, has a higher frequency in individuals with schizophrenia in all of the tested samples, suggesting rs1063843 may be a causal variant. We also found that rs1063843 is associated with cognitive function and personality in humans. In addition, protein-protein interaction (PPI) analysis revealed that CAMKK2 participates in a highly interconnected PPI network formed by top schizophrenia genes, which further supports the potential role of CAMKK2 in the pathogenesis of schizophrenia. Taken together, these converging lines of evidence strongly suggest that CAMKK2 may have pivotal roles in schizophrenia susceptibility. National Natural Science Foundation of China/81271006/ 81060081 Hangzhou City Health Science Foundation/20120633B01 Jiangxi Provincial Natural Science Foundation/2010GZY0089/20114BAB215006 Natural Science Foundation of China/U1202225/81130022/ 81272302/31000553 863 Program 2012AA02A515 EU/HEALTH-2011-286213 HEALTH-F2-2009-223423 111 Project of the Ministry of Education of China/B07008 Israel Science Foundation info:eu-repo/grantAgreement/EC/FP7/286213
Published: 2014

8. All SNPs are not created equal: genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs

Author: Aj, Schork, Wk, Thompson, Pham P, Torkamani A, Jc, Roddey, Pf, Sullivan, Jr, Kelsoe, Donovan Mc, O., Furberg H, Tobacco and Genetics Consortium, Bipolar Disorder Psychiatric Genomics Consortium, Schizophrenia Psychiatric Genomics Consortium, Nj, Schork, Oa, Andreassen, Am, Dale, Absher D, Agudo A, Almgren P, Ardissino D, Tl, Assimes, Bandinelli S, Barzan L, Bencko V, Benhamou S, Ej, Benjamin, Bernardinelli L, Bis J, Boehnke M, Boerwinkle E, Di, Boomsma, Brennan P, Canova C, Castellsagué X, Chanock S, Chasman D, Di, Conway, Dackor J, Ej, Geus, Duan J, Elosua R, Everett B, Fabianova E, Ferrucci L, Foretova L, Sp, Fortmann, Franceschini N, Frayling T, Furberg C, Pv, Gejman, Groop L, Gu F, Guralnik J, Se, Hankinson, Haritunians T, Healy C, Hofman A, Holcátová I, Dj, Hunter, Sj, Hwang, Jp, Ioannidis, Iribarren C, Au, Jackson, Janout V, Kaprio J, Kim Y, Kjaerheim K, Jw, Knowles, Kraft P, Ladenvall C, Lagiou P, Lanthrop M, Lerman C, Df, Levinson, Levy D, Md, Li, Dy, Lin, Eh, Lips, Lissowska J, Lowry R, Lucas G, Tv, Macfarlane, Maes H, Pm, Mannucci, Mates D, Mauri F, Ja, Mcgovern, Jd, Mckay, McKnight B, Melander O, Pa, Merlini, Milaneschi Y, Kl, Mohlke, Donnell Cj, O., Pare G, Bw, Penninx, Perry J, Posthuma D, Sr, Preis, Psaty B, Quertermous T, Vs, Ramachandran, Richiardi L, Ridker P, Rose J, Rudnai P, Salomaa V, Ar, Sanders, Sm, Schwartz, Shi J, Jh, Smit, Hm, Stringham, Szeszenia-Dabrowska N, Tanaka T, Taylor K, Thacker E, Thornton L, Tiemeier H, Tuomilehto J, Ag, Uitterlinden, Cm, Duijn, Jm, Vink, Vogelzangs N, Bf, Voight, Walter S, Willemsen G, Zaridze D, Znaor A, Akil H, Anjorin A, Backlund L, Ja, Badner, Jd, Barchas, Tb, Barrett, Bass N, Bauer M, Bellivier F, Se, Bergen, Berrettini W, Blackwood D, Cs, Bloss, Breen G, Breuer R, We, Bunner, Burmeister M, Byerley W, Caesar S, Chambert K, Cichon S, St Clair D, Da, Collier, Corvin A, Wh, Coryell, Craddock N, Dw, Craig, Daly M, Day R, Degenhardt F, Djurovic S, Dudbridge F, Hj, Edenberg, Elkin A, Etain B, Ae, Farmer, Ma, Ferreira, Ferrier I, Flickinger M, Foroud T, Frank J, Fraser C, Frisén L, Es, Gershon, Gill M, Gordon-Smith K, Ek, Green, Ta, Greenwood, Grozeva D, Guan W, Gurling H, Ó, Gustafsson, Ml, Hamshere, Hautzinger M, Herms S, Hipolito M, Pa, Holmans, Cm, Hultman, Jamain S, Eg, Jones, Jones I, Jones L, Kandaswamy R, Jl, Kennedy, Gk, Kirov, Dl, Koller, Kwan P, Landén M, Langstrom N, Lathrop M, Lawrence J, Wb, Lawson, Leboyer M, Ph, Lee, Li J, Lichtenstein P, Lin D, Liu C, Fw, Lohoff, Lucae S, Pb, Mahon, Maier W, Ng, Martin, Mattheisen M, Matthews K, Mattingsdal M, Ka, Mcghee, McGuffin P, Mg, Mcinnis, McIntosh A, McKinney R, Aw, Mclean, Fj, Mcmahon, McQuillin A, Meier S, Melle I, Meng F, Pb, Mitchell, Gw, Montgomery, Moran J, Morken G, Dw, Morris, Moskvina V, Muglia P, Tw, Mühleisen, Wj, Muir, Müller-Myhsok B, Rm, Myers, Cm, Nievergelt, Nikolov I, Nimgaonkar V, Mm, Nöthen, Ji, Nurnberger, Ea, Nwulia, O'Dushlaine C, Osby U, Óskarsson H, Mj, Owen, Petursson H, Bs, Pickard, Porgeirsson P, Jb, Potash, Propping P, Sm, Purcell, Quinn E, Raychaudhuri S, Rice J, Rietschel M, Ruderfer D, Schalling M, Af, Schatzberg, Wa, Scheftner, Pr, Schofield, Tg, Schulze, Schumacher J, Mm, Schwarz, Scolnick E, Lj, Scott, Pd, Shilling, Sigurdsson E, Sklar P, En, Smith, Stefansson H, Stefansson K, Steffens M, Steinberg S, Strauss J, Strohmaier J, Szelinger S, Rc, Thompson, Tozzi F, Treutlein J, Jb, Vincent, Sj, Watson, Tf, Wienker, Williamson R, Sh, Witt, Wright A, Xu W, Ah, Young, Pp, Zandi, Zhang P, Zöllner S, Agartz I, Albus M, Alexander M, Rl, Amdur, Amin F, Bitter I, Dw, Black, Ad, Børglum, Ma, Brown, Bruggeman R, Ng, Buccola, Wf, Byerley, Cahn W, Rm, Cantor, Vj, Carr, Sv, Catts, Choudhury K, Cloninger C, Cormican P, Pa, Danoy, Datta S, DeHert M, Demontis D, Dikeos D, Donnelly P, Donohoe G, Duong L, Dwyer S, Fanous A, Fink-Jensen A, Freedman R, Nb, Freimer, Friedl M, Georgieva L, Giegling I, Glenthøj B, Godard S, Golimbet V, de Haan L, Hansen M, Hansen T, Am, Hartmann, Fa, Henskens, Dm, Hougaard, Ingason A, Av, Jablensky, Kd, Jakobsen, Jay M, Eg, Jönsson, Jürgens G, Rs, Kahn, Mc, Keller, Ks, Kendler, Kenis G, Kenny E, Konnerth H, Konte B, Krabbendam L, Krasucki R, Vk, Lasseter, Laurent C, Lencz T, Lerer F, Ky, Liang, Ja, Lieberman, Dh, Linszen, Lönnqvist J, Cm, Loughland, Aw, Maclean, Bs, Maher, Ak, Malhotra, Mallet J, Malloy P, Jj, Mcgrath, McLean DE, Pt, Michie, Milanova V, Mors O, Pb, Mortensen, Bj, Mowry, Myin-Germeys I, Neale B, Da, Nertney, Nestadt G, Nielsen J, Nordentoft M, Norton N, O'Neill F, Olincy A, Olsen L, Ra, Ophoff, Tf, Ørntoft, van Os J, Pantelis C, Papadimitriou G, Cn, Pato, Mt, Pato, Peltonen L, Pickard B, Op, Pietiläinen, Pimm J, Ae, Pulver, Puri V, Digby Quested, Hb, Rasmussen, Jm, Réthelyi, Ribble R, Bp, Riley, Rossin L, Ruggeri M, Rujescu D, Schall U, Sg, Schwab, Rj, Scott, Jm, Silverman, Cc, Spencer, Strange A, Strengman E, Stroup T, Suvisaari J, Terenius L, Thirumalai S, Timm S, Toncheva D, Tosato S, Ej, Den Oord, Veldink J, Pm, Visscher, Walsh D, Ag, Wang, Werge T, Wiersma D, Db, Wildenauer, Hj, Williams, Nm, Williams, van Winkel R, Wormley B., Biological Psychology, Functional Genomics, Educational Neuroscience, Neuroscience Campus Amsterdam - Brain Mechanisms in Health & Disease, LEARN! - Social cognition and learning, Biophotonics and Medical Imaging, LEARN! - Brain, learning and development, Neuroscience Campus Amsterdam - Neurobiology of Mental Health, EMGO+ - Mental Health, Neuroscience Campus Amsterdam - Brain Imaging Technology, LaserLaB - Biophotonics and Microscopy, ANS - Amsterdam Neuroscience, Adult Psychiatry, Psychiatry, Human genetics, Epidemiology and Data Science, NCA - Brain mechanisms in health and disease, NCA - Neurobiology of mental health, EMGO - Mental health, NCA - Brain imaging technology, Psychiatrie & Neuropsychologie, RS: MHeNs School for Mental Health and Neuroscience, Gibson, Greg, Germeys, Inez, van Winkel, Ruud, and De Hert, Marc
Subjects: False discovery rate, Netherlands Twin Register (NTR), Cancer Research, Linkage disequilibrium, Genome-wide association study, Linkage Disequilibrium, 0302 clinical medicine, 2.1 Biological and endogenous factors, Aetiology, Genetics (clinical), Genetics, 0303 health sciences, Statistics, Genomics, Single Nucleotide, Genome Scans, Tobacco and Genetics Consortium, Functional Genomics, Phenotype, complex trait, Research Article, Bipolar Disorder Psychiatric Genomics Consortium, lcsh:QH426-470, SNP, Single-nucleotide polymorphism, Computational biology, Biostatistics, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, "genome-wide association study", Genome Analysis Tools, Clinical Research, Schizophrenia Psychiatric Genomics Consortium, Genome-Wide Association Studies, Humans, Genetic Predisposition to Disease, Statistical Methods, Polymorphism, Molecular Biology, Genetic Association Studies, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Genetic association, Linkage (software), Human Genome, Computational Biology, Human Genetics, Heritability, R1, schizophrenia, lcsh:Genetics, Schizophrenia, Mathematics, 030217 neurology & neurosurgery, Genome-Wide Association Study, Developmental Biology
Abstract: Recent results indicate that genome-wide association studies (GWAS) have the potential to explain much of the heritability of common complex phenotypes, but methods are lacking to reliably identify the remaining associated single nucleotide polymorphisms (SNPs). We applied stratified False Discovery Rate (sFDR) methods to leverage genic enrichment in GWAS summary statistics data to uncover new loci likely to replicate in independent samples. Specifically, we use linkage disequilibrium-weighted annotations for each SNP in combination with nominal p-values to estimate the True Discovery Rate (TDR = 1−FDR) for strata determined by different genic categories. We show a consistent pattern of enrichment of polygenic effects in specific annotation categories across diverse phenotypes, with the greatest enrichment for SNPs tagging regulatory and coding genic elements, little enrichment in introns, and negative enrichment for intergenic SNPs. Stratified enrichment directly leads to increased TDR for a given p-value, mirrored by increased replication rates in independent samples. We show this in independent Crohn's disease GWAS, where we find a hundredfold variation in replication rate across genic categories. Applying a well-established sFDR methodology we demonstrate the utility of stratification for improving power of GWAS in complex phenotypes, with increased rejection rates from 20% in height to 300% in schizophrenia with traditional FDR and sFDR both fixed at 0.05. Our analyses demonstrate an inherent stratification among GWAS SNPs with important conceptual implications that can be leveraged by statistical methods to improve the discovery of loci., Author Summary Modern genome-wide association studies (GWAS) have failed to identify large portions of the genetic basis of common, complex traits. Recent work suggested this could be because many genetic variants, each with individually small effects, compose their genetic architecture, limiting the power of GWAS. Moreover, these variants appear more abundantly in and near genes. Using genome annotations, summary statistics from several of the largest GWAS, and established statistical methods for quantifying distributions of test statistics, we show a consistency across studies. Namely, we show that, across all assessed traits, the test statistics resulting from SNPs that are related to the 5′ UTR of genes show the largest abundance of associations, while SNPs related to exons and the 3′UTR are also enriched. SNPs related to introns are only moderately enriched, and intergenic SNPs show a depletion of associations relative to the average SNP. This enrichment corresponds directly to increased replication across independent samples and can be incorporated a priori into statistical methods to improve discovery and prediction. Our results contribute to on-going debates about the functional nature of the genetic architecture of complex traits and point to avenues for leveraging existing GWAS data for discovery in future GWA and sequencing studies.
Published: 2013

9. Genome-wide association analysis identifies 13 new risk loci for schizophrenia

Author: Ripke, S, O'Dushlaine, C, Chambert, K, Moran, Jl, Kähler, Ak, Akterin, S, Bergen, Se, Collins, Al, Crowley, Jj, Fromer, M, Kim, Y, Lee, Sh, Magnusson, Pk, Sanchez, N, Stahl, Ea, Williams, S, Wray, Nr, Xia, K, Bettella, F, Borglum, Ad, Bulik Sullivan, Bk, Cormican, P, Craddock, N, Leeuw, De, C, Durmishi, N, Gill, M, Golimbet, V, Hamshere, Ml, Holmans, P, Hougaard, Dm, Kendler, Ks, Lin, K, Morris, Dw, Mors, O, Mortensen, Pb, Neale, Bm, O'Neill, Fa, Owen, Mj, Milovancevic, Mp, Posthuma, D, Powell, J, Richards, Al, Riley, Bp, Ruderfer, D, Rujescu, D, Sigurdsson, E, Silagadze, T, Smit, Ab, Stefansson, H, Steinberg, S, Suvisaari, J, Tosato, Sarah, Verhage, M, Walters, Jt, Multicenter Genetic Studies of Schizophrenia Consortium, Levinson, Df, Gejman, Pv, Laurent, C, Mowry, Bj, O'Donovan, Mc, Pulver, Ae, Schwab, Sg, Wildenauer, Db, Dudbridge, F, Shi, J, Albus, M, Alexander, M, Campion, D, Cohen, D, Dikeos, D, Duan, J, Eichhammer, P, Godard, S, Hansen, M, Lerer, Fb, Liang, Ky, Maier, W, Mallet, J, Nertney, Da, Nestadt, G, Norton, N, Papadimitriou, Gn, Ribble, R, Sanders, Ar, Silverman, Jm, Walsh, D, Williams, Nm, Wormley, B, Psychosis Endophenotypes International Consortium, Arranz, Mj, Bakker, S, Bender, S, Bramon, E, Collier, D, Crespo Facorro, B, Hall, J, Iyegbe, C, Jablensky, A, Kahn, Rs, Kalaydjieva, L, Lawrie, S, Lewis, Cm, Linszen, Dh, Mata, I, Mcintosh, A, Murray, Rm, Ophoff, Ra, Van, Os, J, Walshe, M, Weisbrod, M, Wiersma, D, Wellcome Trust Case Control Consortium 2, Donnelly, P, Barroso, I, Blackwell, Jm, Brown, Ma, Casas, Jp, Corvin, Ap, Deloukas, P, Duncanson, A, Jankowski, J, Markus, Hs, Mathew, Cg, Palmer, Cn, Plomin, R, Rautanen, A, Sawcer, Sj, Trembath, Rc, Viswanathan, Ac, Wood, Nw, Spencer, Cc, Band, G, Bellenguez, C, Freeman, C, Hellenthal, G, Giannoulatou, E, Pirinen, M, Pearson, Rd, Strange, A, Su, Z, Vukcevic, D, Langford, C, Hunt, Se, Edkins, S, Gwilliam, R, Blackburn, H, Bumpstead, Sj, Dronov, S, Gillman, M, Gray, E, Hammond, N, Jayakumar, A, Mccann, Ot, Liddle, J, Potter, Sc, Ravindrarajah, R, Ricketts, M, Tashakkori Ghanbaria, A, Waller, Mj, Weston, P, Widaa, S, Whittaker, P, Mccarthy, Mi, Stefansson, K, Scolnick, E, Purcell, S, Mccarroll, Sa, Sklar, P, Hultman, Cm, Sullivan, P. F., Functional Genomics, Molecular and Cellular Neurobiology, AIMMS, Neuroscience Campus Amsterdam - Neurobiology of Mental Health, Neuroscience Campus Amsterdam - Brain Mechanisms in Health & Disease, Adult Psychiatry, Ripke, Stephan, O'Dushlaine, Colm, Chambert, Kimberly, Moran, Jennifer L, Lee, Sang Hong, Sullivan, Patrick F, Multicenter Genetic Studies of Schizophrenia Consortium, Psychosis Endophenotypes International Consortium, Wellcome Trust Case Control Consortium 2, Massachusetts Gen Hosp, Analyt & Translat Genet Unit, Boston, MA 02114 USA Broad Inst MIT & Harvard, Stanley Ctr Psychiat Res, Cambridge, MA USA Univ N Carolina, Dept Genet, Chapel Hill, NC 27515 USA Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden Oslo Univ Hosp, Div Mental Hlth & Addict, Oslo, Norway Icahn Sch Med Mt Sinai, Dept Psychiat, Div Psychiat Genom, New York, NY USA Univ Queensland, Queensland Brain Inst, Brisbane, Qld, Australia Univ N Carolina, Dept Psychiat, Chapel Hill, NC USA deCODE Genet, Reykjavik, Iceland Aarhus Univ Hosp, Risskov, Denmark Aarhus Univ, Ctr Integrat Sequencing iSEQ, Aarhus, Denmark Lundbeck Fdn Initiat Integrat Psychiat Res iPSYCH, Aarhus, Denmark Lundbeck Fdn Initiat Integrat Psychiat Res iPSYCH, Copenhagen, Denmark Univ Dublin Trinity Coll, Dept Psychiat, Dublin 2, Ireland Cardiff Univ, Sch Med, Ctr Psychiat Genet & Genom, MRC, Cardiff CF10 3AX, S Glam, Wales Vrije Univ Amsterdam, Ctr Neurogen & Cognit Res, Dept Funct Genom, Amsterdam, Netherlands Vrije Univ Amsterdam Med Ctr, Amsterdam, Netherlands Radboud Univ Nijmegen, Inst Comp & Informat Sci, NL-6525 ED Nijmegen, Netherlands Univ Clin Psychiat, Dept Child & Adolescent Psychiat, Skopje, Macedonia Univ Dublin Trinity Coll, Neuropsychiat Genet Res Grp, Dublin 2, Ireland Russian Acad Med Sci, Mental Hlth Res Ctr, Moscow 109801, Russia Statens Serum Inst, DK-2300 Copenhagen, Denmark Virginia Commonwealth Univ, Dept Psychiat, Richmond, VA USA Virginia Commonwealth Univ, Virginia Inst Psychiat & Behav Genet, Richmond, VA USA Kings Coll London, Inst Psychiat, London, England Aarhus Univ Hosp, Ctr Psychiat Res, Risskov, Denmark Aarhus Univ, Natl Ctr Register Based Res, Aarhus, DenmarkQueens Univ Belfast, Ctr Publ Hlth, Belfast, Antrim, North Ireland Univ Belgrade, Fac Med, Belgrade, Serbia Erasmus Univ, Med Ctr, Dept Child & Adolescent Psychiat, Rotterdam, Netherlands Kings Coll London, Dept Neurosci, London, England Virginia Commonwealth Univ, Dept Human & Mol Genet, Richmond, VA USA Univ Halle, Dept Psychiat, Halle, Germany Univ Munich, Dept Psychiat, D-80539 Munich, Germany Univ Iceland, Dept Psychiat, Reykjavik, Iceland Landspitali University Hospital Reykjavik, Iceland Tbilisi State Univ, Dept Psychiat, GE-380086 Tbilisi, Rep of Georgia Vrije Univ Amsterdam, Ctr Neurogen & Cognit Res, Amsterdam, Netherlands Vrije Univ Amsterdam, Dept Mol & Cellular Neurosci, Amsterdam, Netherlands Natl Inst Hlth & Welf, Mental Hlth & Subst Abuse Serv, Helsinki, Finland Univ Verona, Sect Psychiat, I-37100 Verona, Italy UCL, Inst Cognit Neurosci, London, England UCL, Mental Hlth Sci Unit, London, England Massachusetts Gen Hosp, Psychiat & Neurodev Genet Unit, Boston, MA 02114 USA Harvard Univ, Sch Med, Dept Genet, Boston, MA USA, Child and Adolescent Psychiatry / Psychology, Psychiatrie & Neuropsychologie, RS: MHeNs School for Mental Health and Neuroscience, Human genetics, NCA - Brain mechanisms in health and disease, and NCA - Neurobiology of mental health
Subjects: Male, Candidate gene, SNP, Single-nucleotide polymorphism, Genome-wide association study, Disease, Biology, heritability, neuronal calcium signaling, Polymorphism, Single Nucleotide, 03 medical and health sciences, 0302 clinical medicine, SDG 3 - Good Health and Well-being, Genetics, medicine, Humans, GWAS, Genetic Predisposition to Disease, Bipolar disorder, 030304 developmental biology, Genetic association, Sweden, Genetics & Heredity, 0303 health sciences, medicine.disease, 3. Good health, genome sequencing, schizophrenia, Schizophrenia, Meta-analysis, Case-Control Studies, genetic variation, Female, genome-wide scan, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: To access publisher's full text version of this article. Please click on the hyperlink in Additional Links field. Schizophrenia is an idiopathic mental disorder with a heritable component and a substantial public health impact. We conducted a multi-stage genome-wide association study (GWAS) for schizophrenia beginning with a Swedish national sample (5,001 cases and 6,243 controls) followed by meta-analysis with previous schizophrenia GWAS (8,832 cases and 12,067 controls) and finally by replication of SNPs in 168 genomic regions in independent samples (7,413 cases, 19,762 controls and 581 parent-offspring trios). We identified 22 loci associated at genome-wide significance; 13 of these are new, and 1 was previously implicated in bipolar disorder. Examination of candidate genes at these loci suggests the involvement of neuronal calcium signaling. We estimate that 8,300 independent, mostly common SNPs (95% credible interval of 6,300-10,200 SNPs) contribute to risk for schizophrenia and that these collectively account for at least 32% of the variance in liability. Common genetic variation has an important role in the etiology of schizophrenia, and larger studies will allow more detailed understanding of this disorder. NIMH R01 MH077139 R01 MH095034 Stanley Center for Psychiatric Research Sylvan Herman Foundation Friedman Brain Institute at the Mount Sinai School of Medicine Karolinska Institutet, Karolinska University Hospital Swedish Research Council Swedish County Council Soderstrom Konigska Foundation Netherlands Scientific Organization NWO 645-000-003 info:eu-repo/grantAgreement/EC/FP7/223423 Danish Strategic Research Council H. Lundbeck A/S Faculty of Health Sciences at Aarhus University Lundbeck Foundation Stanley Research Foundation Wellcome Trust 085475/B/08/Z 085475/Z/08/Z
Published: 2013

10. Genetic schizophrenia risk variants jointly modulate total brain and white matter volume

Author: Terwisscha van Scheltinga, Af, Bakker, Sc, van Haren, Ne, Derks, Em, Buizer Voskamp, Je, Boos, Hb, Cahn, W, Hulshoff, Pol, Ripke, S, Ophoff, Ra, Kahn, Rs, Sanders, Ar, Kendler, Ks, Levinson, Df, Sklar, P, Holmans, Pa, Lin, Dy, Duan, J, Andreassen, Oa, Scolnick, E, Cichon, S, Clair, St, D, Corvin, A, Gurling, H, Werge, T, Rujescu, D, Blackwood, Dh, Pato, Cn, Malhotra, Ak, Purcell, S, Dudbridge, F, Neale, Bm, Rossin, L, Visscher, Pm, Posthuma, D, Ruderfer, Dm, Fanous, A, Stefansson, H, Steinberg, S, Mowry, Bj, Golimbet, V, Hert, De, M, Jonsson, Eg, Bitter, I, Pietiläinen, Op, Collier, Da, Tosato, Sarah, Agartz, I, Albus, M, Alexander, M, Amdur, Rl, Amin, F, Bass, N, Bergen, Se, Black, Dw, Børglum, Ad, Brown, Ma, Bruggeman, R, Buccola, Ng, Byerley, Wf, Cantor, Rm, Carr, Vj, Catts, Sv, Choudhury, K, Cloninger, C, Cormican, P, Craddock, N, Danoy, Pa, Datta, S, Haan, De, L, Demontis, D, Dikeos, D, Djurovic, S, Donnelly, P, Donohoe, G, Duong, L, Dwyer, S, Fink Jensen, A, Freedman, R, Freimer, Nb, Friedl, M, Georgieva, L, Giegline, I, Gill, M, Glenthøj, B, Godard, S, Hamshere, M, Hansen, M, Hansen, T, Hartmann, Am, Henskens, Fa, Hougaard, Dm, Hultman, Cm, Ingason, A, Jablensky, Av, Jakobsen, Kd, Jay, M, Jürgens, G, Keller, Mc, Kenis, G, Kenny, E, Kim, Y, Kirov, Gk, Konnerth, H, Konte, B, Krabbendam, L, Krasucki, R, Lasseter, Vk, Laurent, C, Lawrence, J, Lencz, T, Lerer, F, Liang, Ky, Lichtenstein, P, Lieberman, Ja, Linszen, Dh, Lönnqvist, J, Loughland, Cm, Maclean, Aw, Maher, Bs, Maier, W, Mallet, J, Malloy, P, Mattheisen, M, Mattingsdal, M, Mcghee, Ka, Mcgrath, Jj, Mcintosh, A, Mclean, De, Mcquillin, A, Melle, I, Michie, Pt, Milanova, V, Morris, Dw, Mors, O, Mortensen, Pb, Moskvina, V, Muglia, P, Myin Germeys, I, Nertney, Da, Nestadt, G, Nielsen, J, Nikolov, I, Nordentoft, M, Norton, N, Nöthen, Mm, O'Dushlaine, C, Olincy, A, Olsen, L, O'Neill, F, Ørntoft, Tf, Owen, Mj, Pantelis, C, Papadimitriou, G, Pato, Mt, Peltonen, L, Petursson, H, Pickard, B, Pimm, J, Pulver, Ae, Puri, V, Quested, D, Quinn, Em, Rasmussen, Hb, Réthelyi, Jm, Ribble, R, Rietschel, M, Riley, Bp, Ruggeri, Mirella, Schall, U, Schulze, Tg, Schwab, Sg, Scott, Rj, Shi, J, Sigurdsson, E, Silverman, Jm, Spencer, Cc, Stefansson, K, Strange, A, Strengman, E, Stroup, Ts, Suvisaari, J, Terenius, L, Thirumalai, S, Thygesen, Jh, Timm, S, Toncheva, D, van den Oord, E, van Os, J, Van, Winkel, R, Veldink, J, Walsh, D, Wang, Ag, Wiersma, D, Wildenauer, Db, Williams, Hj, Williams, Nm, Wormley, B, Zammit, S, Sullivan, Pf, O'Donovan, Mc, Daly, Mj, Gejman, Pv, ANS - Amsterdam Neuroscience, APH - Amsterdam Public Health, Adult Psychiatry, Functional Genomics, Neuroscience Campus Amsterdam - Neurobiology of Mental Health, Neuroscience Campus Amsterdam - Brain Mechanisms in Health & Disease, Psychiatrie & Neuropsychologie, RS: MHeNs School for Mental Health and Neuroscience, Myin-Germeys, Inez, De Hert, Marc, and van Winkel, Ruud
Subjects: Adult, Male, Psychosis, Genotype, Single-nucleotide polymorphism, Genome-wide association study, Biology, Nerve Fibers, Myelinated, Polymorphism, Single Nucleotide, Article, White matter, genome-wide, 03 medical and health sciences, 0302 clinical medicine, SDG 3 - Good Health and Well-being, mental disorders, medicine, Genetic predisposition, Humans, Genetic Predisposition to Disease, Biological Psychiatry, structural MRI, Genetics, neuroimaging, Case-control study, Brain, imaging, medicine.disease, 030227 psychiatry, 3. Good health, schizophrenia, Endophenotype, Phenotype, medicine.anatomical_structure, psychiatric, Schizophrenia, Case-Control Studies, Female, endophenotype, Genome-Wide Association Study, SNPs, Atrophy, 030217 neurology & neurosurgery
Abstract: BACKGROUND: Thousands of common single nucleotide polymorphisms (SNPs) are weakly associated with schizophrenia. It is likely that subsets of disease-associated SNPs are associated with distinct heritable disease-associated phenotypes. Therefore, we examined the shared genetic susceptibility modulating schizophrenia and brain volume. METHODS: Odds ratios for genome-wide SNP data were calculated in the sample collected by the Psychiatric Genome-wide Association Study Consortium (8690 schizophrenia patients and 11,831 control subjects, excluding subjects from the present study). These were used to calculate individual polygenic schizophrenia (risk) scores in an independent sample of 152 schizophrenia patients and 142 healthy control subjects with available structural magnetic resonance imaging scans. RESULTS: In the entire group, the polygenic schizophrenia score was significantly associated with total brain volume (R2 = .048, p = 1.6 × 10(-4)) and white matter volume (R2 = .051, p = 8.6 × 10(-5)) equally in patients and control subjects. The number of (independent) SNPs that substantially influenced both disease risk and white matter (n = 2020) was much smaller than the entire set of SNPs that modulated disease status (n = 14,751). From the set of 2020 SNPs, a group of 186 SNPs showed most evidence for association with white matter volume and an explorative functional analysis showed that these SNPs were located in genes with neuronal functions. CONCLUSIONS: These results indicate that a relatively small subset of schizophrenia genetic risk variants is related to the (normal) development of white matter. This, in turn, suggests that disruptions in white matter growth increase the susceptibility to develop schizophrenia.
Published: 2013

11. Genome-wide association study identifies five new schizophrenia loci

Author: Ripke, S. Sanders, A.R. Kendler, K.S. Levinson, D.F. Sklar, P. Holmans, P.A. Lin, D.-Y. Duan, J. Ophoff, R.A. Andreassen, O.A. Scolnick, E. Cichon, S. St. Clair, D. Corvin, A. Gurling, H. Werge, T. Rujescu, D. Blackwood, D.H.R. Pato, C.N. Malhotra, A.K. Purcell, S. Dudbridge, F. Neale, B.M. Rossin, L. Visscher, P.M. Posthuma, D. Ruderfer, D.M. Fanous, A. Stefansson, H. Steinberg, S. Mowry, B.J. Golimbet, V. De Hert, M. Jönsson, E.G. Bitter, I. Pietiläinen, O.P.H. Collier, D.A. Tosato, S. Agartz, I. Albus, M. Alexander, M. Amdur, R.L. Amin, F. Bass, N. Bergen, S.E. Black, D.W. Børglum, A.D. Brown, M.A. Bruggeman, R. Buccola, N.G. Byerley, W.F. Cahn, W. Cantor, R.M. Carr, V.J. Catts, S.V. Choudhury, K. Cloninger, C.R. Cormican, P. Craddock, N. Danoy, P.A. Datta, S. De Haan, L. Demontis, D. Dikeos, D. Djurovic, S. Donnelly, P. Donohoe, G. Duong, L. Dwyer, S. Fink-Jensen, A. Freedman, R. Freimer, N.B. Friedl, M. Georgieva, L. Giegling, I. Gill, M. Glenthøj, B. Godard, S. Hamshere, M. Hansen, M. Hansen, T. Hartmann, A.M. Henskens, F.A. Hougaard, D.M. Hultman, C.M. Ingason, A. Jablensky, A.V. Jakobsen, K.D. Jay, M. Jürgens, G. Kahn, R.S. Keller, M.C. Kenis, G. Kenny, E. Kim, Y. Kirov, G.K. Konnerth, H. Konte, B. Krabbendam, L. Krasucki, R. Lasseter, V.K. Laurent, C. Lawrence, J. Lencz, T. Lerer, F.B. Liang, K.-Y. Lichtenstein, P. Lieberman, J.A. Linszen, D.H. Lönnqvist, J. Loughland, C.M. MacLean, A.W. Maher, B.S. Maier, W. Mallet, J. Malloy, P. Mattheisen, M. Mattingsdal, M. McGhee, K.A. McGrath, J.J. McIntosh, A. McLean, D.E. McQuillin, A. Melle, I. Michie, P.T. Milanova, V. Morris, D.W. Mors, O. Mortensen, P.B. Moskvina, V. Muglia, P. Myin-Germeys, I. Nertney, D.A. Nestadt, G. Nielsen, J. Nikolov, I. Nordentoft, M. Norton, N. Nöthen, M.M. O'Dushlaine, C.T. Olincy, A. Olsen, L. O'Neill, F.A. Ørntoft, T.F. Owen, M.J. Pantelis, C. Papadimitriou, G. Pato, M.T. Peltonen, L. Petursson, H. Pickard, B. Pimm, J. Pulver, A.E. Puri, V. Quested, D. Quinn, E.M. Rasmussen, H.B. Réthelyi, J.M. Ribble, R. Rietschel, M. Riley, B.P. Ruggeri, M. Schall, U. Schulze, T.G. Schwab, S.G. Scott, R.J. Shi, J. Sigurdsson, E. Silverman, J.M. Spencer, C.C.A. Stefansson, K. Strange, A. Strengman, E. Stroup, T.S. Suvisaari, J. Terenius, L. Thirumalai, S. Thygesen, J.H. Timm, S. Toncheva, D. Van Den Oord, E. Van Os, J. Van Winkel, R. Veldink, J. Walsh, D. Wang, A.G. Wiersma, D. Wildenauer, D.B. Williams, H.J. Williams, N.M. Wormley, B. Zammit, S. Sullivan, P.F. O'Donovan, M.C. Daly, M.J. Gejman, P.V.
Abstract: We examined the role of common genetic variation in schizophrenia in a genome-wide association study of substantial size: a stage 1 discovery sample of 21,856 individuals of European ancestry and a stage 2 replication sample of 29,839 independent subjects. The combined stage 1 and 2 analysis yielded genome-wide significant associations with schizophrenia for seven loci, five of which are new (1p21.3, 2q32.3, 8p23.2, 8q21.3 and 10q24.32-q24.33) and two of which have been previously implicated (6p21.32-p22.1 and 18q21.2). The strongest new finding (P = 1.6 × 10 -11) was with rs1625579 within an intron of a putative primary transcript for MIR137 (microRNA 137), a known regulator of neuronal development. Four other schizophrenia loci achieving genome-wide significance contain predicted targets of MIR137, suggesting MIR137-mediated dysregulation as a previously unknown etiologic mechanism in schizophrenia. In a joint analysis with a bipolar disorder sample (16,374 affected individuals and 14,044 controls), three loci reached genome-wide significance: CACNA1C (rs4765905, P = 7.0 × 10 -9), ANK3 (rs10994359, P = 2.5 × 10 -8) and the ITIH3-ITIH4 region (rs2239547, P = 7.8 × 10 -9). © 2011 Nature America, Inc. All rights reserved.
Published: 2011

12. Common variants at VRK2 and TCF4 conferring risk of schizophrenia

Author: Steinberg, S., Jong, S. d., Genomics, I. S., Andreassen, O. A., Werge, T., Børglum, A. D., Mors, O., Mortensen, P. B., Gustafsson, O., Costas, J., O. P. H., Demontis, D., Papiol, S., Huttenlocher, J., Mattheisen, M., Breuer, R., Vassos, E., Giegling, I., Fraser, G., Walker, N., Tuulio Henriksson, A., Suvisaari, J., Lönnqvist, J., Paunio, T., Agartz, I., Melle, I., Djurovic, S., Strengman, E., G. R. O., Jürgens, G., Glenthøj, B., Terenius, L., Hougaard, D. M., Orntoft, T., Wiuf, C., Didriksen, M., Hollegaard, M. V., Nordentoft, M., Winkel, R. v., Kenis, G., Abramova, L., Kaleda, V., Arrojo, M., Sanjuán, J., Arango, C., Sperling, S., Rossner, M., Ribolsi, M., Magni, V., Siracusano, A., Christiansen, C., Kiemeney, L. A., Veldink, J., Den, L. v., Ingason, A., Muglia, P., Murray, R., Nöthen, M. M., Sigurdsson, E., Petursson, H., Thorsteinsdottir, U., Kong, A., Rubino, I. A., Hert, M. D., Réthelyi, J. M., Bitter, I., Jönsson, E. G., Golimbet, V., Carracedo, A., Ehrenreich, H., Craddock, N., Owen, M. J., O'Donovan, M. C., Case, W. T., Ruggeri, Mirella, Tosato, Sarah, Peltonen, L., Ophoff, R. A., Collier, D. A., Clair, D. S., Rietschel, M., Cichon, S., Stefansson, H., Rujescu, D., Stefansson, K., Psychiatrie & Neuropsychologie, RS: MHeNs School for Mental Health and Neuroscience, Amsterdam Neuroscience, Adult Psychiatry, and deCODE Genetics, IS-101 Reykjavik, Iceland.
Subjects: schizophrenia, sequence variants, TCF4, Genome-wide association study, Transcription Factor 4, 0302 clinical medicine, VRK2 protein, human, Polymorphism (computer science), Genotype, genetics [Schizophrenia], Neurogranin, Genetics (clinical), Schizophrenia, Risk, Alleles, Polymorphism, Single Nucleotide, Transcription Factors, Humans, Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, Genetic Predisposition to Disease, Protein-Serine-Threonine Kinases, Genome-Wide Association Study, Genetics, 0303 health sciences, Association Studies Articles, Single Nucleotide, General Medicine, genetics [Transcription Factors], 3. Good health, Protein Serine-Threonine Kinases, Biology, genetics [Protein-Serine-Threonine Kinases], Molecular epidemiology [NCEBP 1], 03 medical and health sciences, ddc:570, Polymorphism, Allele, genetics [Basic Helix-Loop-Helix Leucine Zipper Transcription Factors], Settore MED/25 - Psichiatria, Molecular Biology, Molecular epidemiology Aetiology, screening and detection [NCEBP 1], 030304 developmental biology, Intron, Odds ratio, Molecular biology, TCF4 protein, human, 030217 neurology & neurosurgery
Abstract: To access publisher full text version of this article. Please click on the hyperlink in Additional Links field. Common sequence variants have recently joined rare structural polymorphisms as genetic factors with strong evidence for association with schizophrenia. Here we extend our previous genome-wide association study and meta-analysis (totalling 7 946 cases and 19 036 controls) by examining an expanded set of variants using an enlarged follow-up sample (up to 10 260 cases and 23 500 controls). In addition to previously reported alleles in the major histocompatibility complex region, near neurogranin (NRGN) and in an intron of transcription factor 4 (TCF4), we find two novel variants showing genome-wide significant association: rs2312147[C], upstream of vaccinia-related kinase 2 (VRK2) [odds ratio (OR) = 1.09, P = 1.9 × 10(-9)] and rs4309482[A], between coiled-coiled domain containing 68 (CCDC68) and TCF4, about 400 kb from the previously described risk allele, but not accounted for by its association (OR = 1.09, P = 7.8 × 10(-9)). European Union LSHM-CT-2006-037761 PIAP-GA-2008-218251 HEALTH-F2-2009-223423 National Genome Research Network of the German Federal Ministry of Education and Research (BMBF) 01GS08144 01GS08147 National Institute of Mental Health R01 MH078075 N01 MH900001 MH074027 Centre of Excellence for Complex Disease Genetics of the Academy of Finland 213506 129680 Biocentrum Helsinki Foundation Faculty of Medicine, University of Helsinki Stanley Medical Research Institute Danish Council for Strategic Research 2101-07-0059 H. Lundbeck A/S Research Council of Norway 163070/V50 South-East Norway Health Authority 2004-123 Medical Research Council Ministerio de Sanidad y Consumo, Spain PI081522 Xunta de Galicia 08CSA005208PR Swedish Research Council Wellcome Trust 083948/Z/07/Z Max Planck Society Eli Lilly and Company info:eu-repo/grantAgreement/EC/FP7/218251
Published: 2011

13. Common variants conferring risk of schizophrenia

Author: Stefansson, H., Ophoff, R. A., Steinberg, S., Andreassen, O. A., Chichon, S., Rujescu, D., Werge, T., Pietilainen, O. P., Mors, O., Mortensen, P. B., Sigurdsson, E., Gustafsson, O., Nyegaard, M., Tuulio Henriksson, A., Ingason, A., Hansen, T., Suvisaari, J., Lonnqvist, J., Paunio, T., Borglum, A. D., Hartmann, A., Fink Jensen, A., Nordentoft, M., Hougaard, D., Norgaard Petersen, B., Bottcher, J., Olesen, J., Breuer, R., Moller, H. J., Giegling, I., Rasmussen, H. B., Timm, S., Mattheisen, M., Bitter, I., Rethelyi, J. M., Magnusdottir, B. B., Sigmundsson, T., Olason, P. I., Masson, G., Gulcher, J. R., Haraldsson, M., Fossdal, R., Thorgeirsson, T. E., Thorsteinsdottir, U., Ruggeri, Mirella, Tosato, Sarah, Franke, B., Strengman, E., Kiemeney, L. A., Group, Melle, I., Djurovic, S., Abramova, I., Kaleda, V., Sanjuan, J., de Frutos, R., Bramon, E., Vassos, E., Fraser, G., Ettinger, U., Picchioni, M., Walker, N., Toulopoulou, T., Need, A. C., Ge, D., Lim Yoon, J., Shianna, K. V., Freimer, N. B., Cator, R. M., Murray, R., Kong, A., Golimbet, V., Carracedo, A., Arango, C., Costas, J., Jonsson, E. G., Terenius, L., Agartz, I., Petursson, H., Nothen, M. M., Rietschel, M., Matthews, P. M., Muglia, P., Peltonen, L., St Clair, D., Goldstein, D. B., Collier, D., Genetic, Risk, Outcome in Psychosis, Kahn, R. S., Linszen, D. H., Van Os, J., Wiersma, D., Bruggeman, R., Cahn, H., de Haan, L., Krabbendam, L., Myin Germeys, I., ANS - Amsterdam Neuroscience, Adult Psychiatry, deCODE genetics, Sturlugata 8, IS-101 Reykjavik, Iceland., Clinical Child and Family Studies, LEARN! - Brain, learning and development, and Germeys, Inez
Subjects: Pair 6/genetics, Genetics and epigenetic pathways of disease [NCMLS 6], Genome-wide association study, Aetiology, screening and detection [ONCOL 5], 1Q21.1, Major Histocompatibility Complex/genetics, Major Histocompatibility Complex, Transcription Factor 4, 0302 clinical medicine, Chemicals And Cas Registry Numbers, Perception and Action [DCN 1], Copy-number variation, POPULATION, Genetics, Pair 18/genetics, 0303 health sciences, education.field_of_study, Genome, Human/genetics, Multidisciplinary, Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, Schizophrenia/*genetics/immunology, Genetic Predisposition to Disease/*genetics, 3. Good health, DNA-Binding Proteins, Neurogranin/genetics, DISEASES, Chromosomes, Human, Pair 6, Single Nucleotide/*genetics, Functional Neurogenomics [DCN 2], Zinc finger protein 804A, Human, Genetic Markers, Psychosis, Genotype, Population, Transcription Factors/genetics, Single-nucleotide polymorphism, Biology, Polymorphism, Single Nucleotide, Chromosomes, Pair 11/genetics, Article, DNA-Binding Proteins/genetics, Genetic Markers/genetics, Genome-Wide Association Study, Humans, Polymorphism, Genomic disorders and inherited multi-system disorders [IGMD 3], Molecular epidemiology [NCEBP 1], 03 medical and health sciences, Translational research [ONCOL 3], medicine, SNP, Genetic Predisposition to Disease, GENOME-WIDE ASSOCIATION, education, 030304 developmental biology, Genetic association, Hereditary cancer and cancer-related syndromes [ONCOL 1], Genome, Human, Chromosomes, Human, Pair 11, MEMORY, medicine.disease, GENE, NEUROGRANIN, DELETIONS, Schizophrenia, biology.protein, Neurogranin, Chromosomes, Human, Pair 18, MENTAL-RETARDATION, SCAN, 030217 neurology & neurosurgery, Transcription Factors
Abstract: Schizophrenia is a complex disorder, caused by both genetic and environmental factors and their interactions. Research on pathogenesis has traditionally focused on neurotransmitter systems in the brain, particularly those involving dopamine. Schizophrenia has been considered a separate disease for over a century, but in the absence of clear biological markers, diagnosis has historically been based on signs and symptoms. A fundamental message emerging from genome-wide association studies of copy number variations (CNVs) associated with the disease is that its genetic basis does not necessarily conform to classical nosological disease boundaries. Certain CNVs confer not only high relative risk of schizophrenia but also of other psychiatric disorders. The structural variations associated with schizophrenia can involve several genes and the phenotypic syndromes, or the ĝ€ genomic disordersĝ€™, have not yet been characterized. Single nucleotide polymorphism (SNP)-based genome-wide association studies with the potential to implicate individual genes in complex diseases may reveal underlying biological pathways. Here we combined SNP data from several large genome-wide scans and followed up the most significant association signals. We found significant association with several markers spanning the major histocompatibility complex (MHC) region on chromosome 6p21.3-22.1, a marker located upstream of the neurogranin gene (NRGN) on 11q24.2 and a marker in intron four of transcription factor 4 (TCF4) on 18q21.2. Our findings implicating the MHC region are consistent with an immune component to schizophrenia risk, whereas the association with NRGN and TCF4 points to perturbation of pathways involved in brain development, memory and cognition. © 2009 Macmillan Publishers Limited., link_to_OA_fulltext
Published: 2009

14. Collection of DNA samples from patients with endogenic psychoses: Perspectives of its application for molecular genetic studies in psychiatry

Author: Golimbet, V. E., Trubnikov, V. I., Orlova, V. A., Panteleyeva Galina, and Tsutsulkovskaya Ya, M.

15. Serotonin Transporter Polymorphism and Depressive-Related Symptoms in Schizophrenia

Author: Golimbet, V. E., Margarita Alfimova, Shchebatykh, T. V., Abramova, L. I., Kaleda, V. G., and Rogaev, E. I.

16. Dopamine system genes interaction and neurocognitive traits in patients with schizophrenia, their relatives and healthy controls from general population

Author: Alfimova, M. V., Golimbet, V. E., Gritsenko, I. K., Lezheiko, T. V., Abramova, L. I., Streltsova, M. A., Khlopina, I. V., and Richard Ebstein

17. Functional siate of serotoninergic system and the 5-HTTLPR polymorphism of the serotonin transporter gene in patients with schizophrenia

Author: Golimbet, V. E., Korovaǐtseva, G. I., Magnolia Faktor, Ganisheva, T. K., and Dmitriev, D. A.

18. Genetic counseling in the mental health research center of the Russian academy of medical sciences

Author: Golimbet, V. E., Demikova, N. S., Margarita Alfimova, Uvarova, L. G., Lezheǐko, T. V., and Asanov, A. Iu

19. The effect of the serotonin transporter 5-HTTLPR polymorphism on the recognition of facial emotions in schizophrenia

Author: Alfimova, M. V., Golimbet, V. E., Galina Korovaitseva, Lezheiko, T. V., Abramova, L. I., Aksenova, E. V., and Bolgov, M. I.

20. Serotonin transporter gene polymorphism in families with schizophrenia

Author: Golimbet, V. E., Shcherbatykh, T. V., Abramova Liliya, Kaleda, V. G., Oleichik, I. V., Orlova, V. A., and Rogaev, E. I.

21. Serotonin transporter gene polymorphism modulates psychic maladaptation in relatives of patients with endogenic psychoses

Author: Alfimova, M. V., Golimbet, V. E., Galina Korovaitseva, Lezheiko, T. V., Abramova, L. I., Kaleda, V. G., and Barkhatova, A. N.

22. TaqlB allele polymorphism of the dopamine receptor D2 gene in patients with endogenous psychoses

Author: Aksenova, M. G., Ab, O. V., Golimbet, V. E., Abramova Liliya, Orlova, V. A., Kaleda, V. G., Oleichik, I. V., and Nosikov, V. V.

23. Insertion/Deletion Polymorphism of the Serotonin Transporter Gene and Neuroticism as a Temperament Trait in Affective Patients and Healthy Individuals

Author: Golimbet, V. E., Alfimova, M. V., Shcherbatykh, T. V., Abramova, L. I., Kaleda Vasily, and Rogaev, E. I.

24. Serotonin transporter and serotonin receptor 2A genes and personality in relatives of patients with major psychoses

Author: Margarita Alfimova, Golimbet, V., Mitushina, N., Yurov, Y., Shcherbatuch, T., Rogaev, E., and Genisheva, T.

25. Schizoaffective psychosis and schizophrenia with-or without affective syndrome: A comparative clinical, neuropsychological and molecular-genetic study

Author: Golimbet, V. E., Alfimova, M. V., Kaleda, V. G., Abramova Liliya, Korovaitseva, G. I., Lavrushina, O. M., and Lezheiko, T. V.

26. Association of allelic DRD2 dopamine receptor gene polymorphism with mental diseases of schizophrenic spectrum and affective disorders

Author: Golimbet, V. E., Aksenova, M. G., Abramova, L. I., Kaleda Vasily, Orlova, V. A., Braga, E. A., Nosikov, V. V., and Trubnikov, V. I.

27. Serotonin receptor gene allele polymorphism (5HTR2A) and clinical pathogenetic characteristics in patients with schizophrenia and schizophrenia spectrum disorders | Allel'nyi poliforfizm gena serotoninovogo retseptora (5HTR2A) i kliniko-patogeneticheskie osobennosti bol'nykh shizofreniei i rasstroistvami shizofrenicheskogo spektra

Author: Golimbet, V. E., Manandian, K. K., Abramova, L. I., Orlova, V. A., Kaleda, V. G., Igor Oleichik, Iurov, I. B., and Trubnikov, V. I.

28. Polymorphism C366G of gene GRIN2B and verbal episodic memory: No association with schizophrenia

Author: Alfimova, M. V., Golimbet, V. E., Galina Korovaitseva, Lezheiko, T. V., Abramova, L. I., and Kaleda, V. G.

29. The Cys allele of the DRD2 (Ser311Cys polymorphism) is associated with schizophrenia and worse sustained attention in patients

Author: Golimbet, V. E., Lebedeva, I. S., Monakhov Mikhail, Korovaitseva, G. I., Lezheiko, T. V., Abramova, L. I., Kaleda, V. G., and Karpov, V. L.

30. A study of IL-1β and IDO gene polymorphisms in patients with schizophrenia

Author: Golimbet, V. E., Galina Korovaitseva, Gabaeva, M. V., Velikaya, N. V., Snegireva, A. A., Kasparov, S. V., Kolesina, N. Y., Ganisheva, T. K., and Savel Eva, T. M.

31. Investigation of association of the brain-derived neurotrophic factor (BDNF) and a serotonin receptor 2A (5-HTR2A) genes with voluntary and involuntary attention in schizophrenia

Author: Alfimova, M. V., Lezheiko, T. V., Golimbet, V. E., Korovaitseva, G. I., Lavrushina, O. M., Kolesina, N. Yu, Frolova, L. P., Muratova, A. A., Abramova Liliya, and Kaleda, V. G.

32. A study of some genes related to serotoninergic and dopaminergic systems and auditory evoked-potentials (P300) in patients with schizophrenia and spectrum disorders and their first-degree relatives

Author: Golimbet, V. E., Lebedeva, I. S., Gritsenko, I. K., Korovaitseva, G. I., Margarita Alfimova, Lezheiko, T. V., Abramova, L. I., Kaleda, V. G., Ebstein, R. P., and Rogaev, E. I.

33. Molecular genetic polymorphism of the genes of neurotransmitter systems in schizophrenics with early manifestation of the disease

Author: Golimbet, V. E., Mityushina, N. G., Scherbatykh, T. V., Aksenova, M. G., Abramova Liliya, Kaleda, V. G., Nosikov, V. V., Yurov, Yu B., and Rogaev, E. I.

34. Serotonin type 2a (5-HTR2A) receptor gene polymorphism and personality traits in patients with major psychoses

Author: Golimbet, V. E., Alfimova, M. V., Manandyanj, K. K., Mitushina, N. G., Abramova, L. I., Kaleda, V. G., Oleichik, I. V., Yuri Yurov, and Trubnikov, V. I.

35. Association of kynurenine-3-monooxygenase gene with schizophrenia

Author: Golimbet, V. E., Lezheiko Tatiana, Alfimova, M. V., Abramova, L. I., and Kondrat Ev, N. V.

36. Facial affect recognition deficit as a marker of genetic vulnerability to schizophrenia

Author: Margarita Alfimova, Abramova, L. I., Barhatova, A. I., Yumatova, P. E., Lyachenko, G. L., and Golimbet, V. E.

37. SNAP-25 and DTNBP1 as candidate genes for cognitive reserve in schizophrenia

Author: Alfimova, M. V., Golimbet, V. E., Monakhov, M. V., Abramova Liliya, Aksenova, E. V., Kaleda, V. G., and Velikaya, N. V.

38. TaqIB allele polymorphism of the dopamine receptor D2 gene in patients with endogenous psychoses

Author: Aksenova, M. G., Ab, O. V., Golimbet, V. E., Abramova Liliya, Orlova, V. A., Kaleda, V. G., Oleichik, I. V., and Nosikov, V. V.

39. Interaction effects of anxiety and the BDNF Val66Met polymorphism on attention in patients with schizophrenia spectrum disorders

Author: Golimbet, V. E., Irina Lebedeva, Alfimova, M. V., Korovaitseva, G. I., and Lezheiko, T. V.

40. The role of genotype-environment interactions in the development of symptoms of anxiety and depression related to the disease burden for family

Author: Alfimova, M. V., Golimbet, V. E., Aleksandra Barkhatova, Golubev, S. A., and Korovaitseva, G. I.

41. Molecular-genetic study of early-onset schizophrenia

Author: Pakhomova, S. A., Galina Korovaitseva, Monchakovskaya, M. Yu, Vil Ianov, V. B., Frolova, L. P., Kasparov, S. V., Kolesnichenko, E. V., and Golimbet, V. E.

42. The association study of the DRD2 gene C939T polymorphism and schizophrenia

Author: Monakhov Mikhail, Golimbet, V. E., Chubabria, K. V., Zykov, V. V., Kovtun, A. L., and Karpov, V. L.

43. The association between the NRG1 gene polymorphism and cognitive functions in patients with schizophrenia and healthy controls

Author: Margarita Alfimova, Abramova, L. I., Aksenova, E. V., Golubev, S. A., Frolova, L. F., Ganisheva, T. K., Shemiakina, T. K., Orlov, V. A., and Golimbet, V. E.

44. D3 dopamine receptor gene Ser9Gly polymorphism in Russian patients with schizophrenia | Izuchenie polimorfizma Ser9Gly gena dofaminovogo retseptora D3 u bol'nykh shizofreniei iz russkoi populiatsii

Author: Aksenova, M. G., Shestakova, I. N., Abramova Liliya, Frolova, L. P., Shemiakina, T. K., Lezheiko, T. V., Lavrushina, O. M., Barkhatova, A. N., Nosikov, V. V., and Golimbet, V. E.

45. Association between the Val66Met polymorphism of brain-derived neurotrophic factor gene and schizophrenia in Russians

Author: Golimbet, V. E., Korovaǐtseva, G. I., Abramova Liliya, Kasparov, S. V., and Uvarova, L. G.

46. Dopamine receptor DRD4 gene polymorphism and its association with schizophrenia spectrum disorders and personality traits of patients

Author: Golimbet, V. E., Gritsenko, I. K., Alfimova, M. V., Lezheiko, T. V., Abramova Liliya, Barkhatova, A. N., Kasparov, S. V., and Ebstein, R. P.

47. Association between serotonin receptor 2C gene Cys23Ser polymorphism and social behavior in schizophrenia patients and healthy individuals

Author: Alfimova, M. V., Golimbet, V. E., Galina Korovaitseva, Abramova, L. I., and Kaleda, V. G.

48. Association between the apolipoprotein E (APOE) gene and various forms of Alzheimer's disease

Author: Korovaitseva, G. I., Sherbatich, T. V., Selezneva, N. V., Svetlana Gavrilova, Golimbet, V. E., Voskresenskaya, N. I., and Rogaev, E. I.

49. Linkage sib-pair analysis of dopamine receptor D2 gene Taq1A and Taq1B polymorphism and schizophrenia | Analiz stsepleniia lokusov Taq1A i Taq1B gena dofaminovogo retseptora D 2 s shizofreniei u bol'nykh i ikh siblingov

Author: Golimbet, V. E., Aksenova, M. G., Nosikov, V. V., Orlova, V. A., and Kaleda Vasily

50. The molecular-genetic aspects of differentiation of schizoaffective psychosis and attack-like progressive schizophrenia

Author: Golimbet, V. Ye, Abramova, L. I., Kaleda, V. G., Margarita Alfimova, Korovaytseva, G. I., Lavrushina, O. M., and Barkhatova, A. N.

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