Identification of putative second genetic hits in schizophrenia carriers of high-risk copy number variants and resequencing in additional samples
- 251 Downloads
Copy number variants (CNVs) conferring risk of schizophrenia present incomplete penetrance, suggesting the existence of second genetic hits. Identification of second hits may help to find genes with rare variants of susceptibility to schizophrenia. The aim of this work was to search for second hits of moderate/high risk in schizophrenia carriers of risk CNVs and resequencing of the relevant genes in additional samples. To this end, ten patients with risk CNVs at cytobands 15q11.2, 15q11.2-13.1, 16p11.2, or 16p13.11, were subjected to whole-exome sequencing. Rare single nucleotide variants, defined as those absent from main public databases, were classified according to bioinformatic prediction of pathogenicity by CADD scores. The average number of rare predicted pathogenic variants per sample was 13.6 (SD 2.01). Two genes, BFAR and SYNJ1, presented rare predicted pathogenic variants in more than one sample. Follow-up resequencing of these genes in 432 additional cases and 432 controls identified a significant excess of rare predicted pathogenic variants in case samples at SYNJ1. Taking into account its function in clathrin-mediated synaptic vesicle endocytosis at presynaptic terminals, our results suggest an impairment of this process in schizophrenia.
KeywordsHigh-throughput nucleotide sequencing Exome DNA copy number variations Psychosis Rare variant
This work was supported by Grant CP11/00163 from Instituto de Salud Carlos III, cofounded by FEDER; to JC, by agreement between SERGAS and Fundación Pública Galega de Medicina Xenómica, and by the Innopharma project (USC). The founders had no role in study design; in the collection, analysis and interpretation of data; in the writing of the report; and in the decision to submit the article for publication. The genotyping service was carried out at CEGEN-PRB2-ISCIII; it is supported by Grant PT13/0001, ISCIII-SGEFI/FEDER. The authors would like to thank Centro de Supercomputación de Galicia (CESGA) for the use of their computing facilities and the NHLBI GO Exome Sequencing Project and its ongoing studies which produced and provided exome variant calls for comparison: the Lung GO Sequencing Project (HL-102923), the WHI Sequencing Project (HL-102924), the Broad GO Sequencing Project (HL-102925), the Seattle GO Sequencing Project (HL-102926), and the Heart GO Sequencing Project (HL-103010).
Compliance with ethical standards
Conflict of interest
On behalf of all authors, the corresponding author states that there is no conflict of interest.
- 2.Rees E, Walters JT, Georgieva L, Isles AR, Chambert KD, Richards AL, Mahoney-Davies G, Legge SE, Moran JL, McCarroll SA, O’Donovan MC, Owen MJ, Kirov G (2014) Analysis of copy number variations at 15 schizophrenia-associated loci. Br J Psychiatry 204:108–114. doi: 10.1192/bjp.bp.113.131052 CrossRefPubMedPubMedCentralGoogle Scholar
- 10.Need AC, McEvoy JP, Gennarelli M, Heinzen EL, Ge D, Maia JM et al (2012) Exome sequencing followed by large-scale genotyping suggests a limited role for moderately rare risk factors of strong effect in schizophrenia. Am J Hum Genet 91:303–312. doi: 10.1016/j.ajhg.2012.06.018 CrossRefPubMedPubMedCentralGoogle Scholar
- 14.McCarthy SE, Gillis J, Kramer M, Lihm J, Yoon S, Berstein Y et al (2014) De novo mutations in schizophrenia implicate chromatin remodeling and support a genetic overlap with autism and intellectual disability. Mol Psychiatry 19:652–658. doi: 10.1038/mp.2014.29 CrossRefPubMedPubMedCentralGoogle Scholar
- 16.Egawa J, Hoya S, Watanabe Y, Nunokawa A, Shibuya M, Ikeda M et al (2016) Rare UNC13B variations and risk of schizophrenia: whole-exome sequencing in a multiplex family and follow-up resequencing and a case-control study. Am J Med Genet B Neuropsychiatr Genet 171:797–805. doi: 10.1002/ajmg.b.32444 CrossRefPubMedGoogle Scholar
- 17.Timms AE, Dorschner MO, Wechsler J, Choi KY, Kirkwood R, Girirajan S et al (2013) Support for the N-methyl-d-aspartate receptor hypofunction hypothesis of schizophrenia from exome sequencing in multiplex families. JAMA Psychiatry 70:582–590. doi: 10.1001/jamapsychiatry.2013.1195 CrossRefPubMedGoogle Scholar
- 25.Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A et al (2013) From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics 43:11.10.1-33. doi: 10.1002/0471250953.bi1110s43 PubMedCrossRefGoogle Scholar
- 29.Plagnol V, Curtis J, Epstein M, Mok KY, Stebbings E, Grigoriadou S et al (2012) A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics 28:2747–2754. doi: 10.1093/bioinformatics/bts526 CrossRefPubMedPubMedCentralGoogle Scholar
- 30.Kearney HM, Thorland EC, Brown KK, Quintero-Rivera F, South ST, Working Group of the American College of Medical Genetics Laboratory Quality Assurance Committee (2011) American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genet Med 13:680–685. doi: 10.1097/GIM.0b013e3182217a3a CrossRefPubMedGoogle Scholar
- 35.Schubert KO, Föcking M, Prehn JH, Cotter DR (2012) Hypothesis review: are clathrin-mediated endocytosis and clathrin-dependent membrane and protein trafficking core pathophysiological processes in schizophrenia and bipolar disorder? Mol Psychiatr 17:669–681. doi: 10.1038/mp.2011.123 CrossRefGoogle Scholar