Resequencing and association analysis of coding regions at twenty candidate genes suggest a role for rare risk variation at AKAP9 and protective variation at NRXN1 in schizophrenia susceptibility Jos  e Javier Su  arez-Rama a, b , Manuel Arrojo a , Beatriz Sobrino a, c , Jorge Amigo a, b , Julio Brenlla a, d , Santiago Agra a, d , Eduardo Paz a, d , María Bri  on a ,  Angel Carracedo a, b, c , Mario P  aramo a, d , Javier Costas a, * a Instituto de Investigaci on Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain b Grupo de Medicina Xen omica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain c Fundaci on Pública Galega de Medicina Xen omica, Complexo Hospitalario Universitario de Santiago (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain d Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago(CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain article info Article history: Received 19 December 2014 Received in revised form 10 April 2015 Accepted 14 April 2015 Keywords: AKAP9 NRXN1 Single nucleotide variant SNV Psychosis DISC1 abstract A fraction of genetic risk to develop schizophrenia may be due to low-frequency variants. This multistep study attempted to find low-frequency variants of high effect at coding regions of eleven schizophrenia susceptibility genes supported by genome-wide association studies (GWAS) and nine genes for the DISC1 interactome, a susceptibility gene-set. During the discovery step, a total of 125 kb per sample were resequenced in 153 schizophrenia patients and 153 controls from Galicia (NW Spain), and the cumulative role of low-frequency variants at a gene or at the DISC1 gene-set were analyzed by burden and variance- based tests. Relevant results were meta-analyzed when appropriate data were available. In addition, case-only putative damaging variants were genotyped in a further 419 cases and 398 controls. The discovery step revealed a protective effect of rare missense variants at NRXN1 , a result supported by meta-analysis (OR ¼ 0.67, 95% CI: 0.47e0.94, P ¼ 0.021, based on 3848 patients and 3896 controls from six studies). The follow-up step based on case-only putative damaging variants revealed a promising risk variant at AKAP9. This variant, K873R, reached nominal significance after inclusion of 240 additional Spanish controls from databases. The variant, located in an ADCY2 binding region, is absent from large public databases. Interestingly, GWAS revealed an association between common ADCY2 variants and bipolar disorder, a disorder with considerable genetic overlap with schizophrenia. These data suggest a role of rare missense variants at NRXN1 and AKAP9 in schizophrenia susceptibility, probably related to alteration of the excitatory/inhibitory synaptic balance, deserving further investigation. © 2015 Elsevier Ltd. All rights reserved. 1. Introduction Schizophrenia is a complex disease with high heritability, esti- mated as 65e82% (Lichtenstein et al., 2009; Sullivan et al., 2003). Genome-wide association studies (GWAS) have identified several single nucleotide polymorphisms (SNPs) associated with schizo- phrenia with high confidence, although with very low effect size (Purcell et al., 2009; Ripke et al., 2013; Stefansson et al., 2009; Steinberg et al., 2011). Statistical models suggest that common variants explain at least one-third of heritability (Lee et al., 2012; Purcell et al., 2009; Ripke et al., 2013). It has been suggested that rare variants may contribute to a substantial proportion of the unexplained heritability (van Dongen and Boomsma, 2013). Some copy number variants (CNVs) are clear examples of the existence of rare variants of moderate to high effect (Rees et al., 2014). Never- theless, in general, attempts to identify rare single nucleotide * Corresponding author. Instituto de Investigaci on Sanitaria (IDIS) de Santiago de Compostela, Hospital Clínico Universitario, edificio Consultas, andar -2, Grupo de xen etica psiqui atrica, despacho 15, E-15706, Santiago de Compostela, Spain. Tel.: þ34 981955452; fax: þ34 981951473. E-mail address: javier.costas.costas@sergas.es (J. Costas). Contents lists available at ScienceDirect Journal of Psychiatric Research journal homepage: www.elsevier.com/locate/psychires http://dx.doi.org/10.1016/j.jpsychires.2015.04.013 0022-3956/© 2015 Elsevier Ltd. All rights reserved. Journal of Psychiatric Research 66-67 (2015) 38e44