Cross-national comparisons of the prevalences and correlates of mental disorders. WHO international consortium in psychiatric epidemiology. Bull World Health Organ. 2000;78(4):413–26.
Google Scholar
Schizophrenia Psychiatric Genome-Wide Association Study (GWAS) Consortium. Genome-wide association study identifies five new schizophrenia loci. Nat Genet. 2011;43(10):969–76.
Psychiatric GWAS Consortium Bipolar Disorder Working Group. Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. Nat Genet. 2011;43(10):977–83.
Article
Google Scholar
Neale BM, Medland SE, Ripke S, Asherson P, Franke B, Lesch KP, Faraone SV, Nguyen TT, Schafer H, Holmans P, et al. Meta-analysis of genome-wide association studies of attention-deficit/hyperactivity disorder. J Am Acad Child Adolesc Psychiatry. 2010;49(9):884–97.
Article
PubMed
PubMed Central
Google Scholar
Marshall CR, Noor A, Vincent JB, Lionel AC, Feuk L, Skaug J, Shago M, Moessner R, Pinto D, Ren Y, et al. Structural variation of chromosomes in autism spectrum disorder. Am J Hum Genet. 2008;82(2):477–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Devanna P, Chen XS, Ho J, Gajewski D, Smith SD, Gialluisi A, Francks C, Fisher SE, Newbury DF, Vernes SC. Next-gen sequencing identifies non-coding variation disrupting miRNA-binding sites in neurological disorders. Mol Psychiatry. 2017;23(5):1375–84.
Pauls DL. The genetics of obsessive-compulsive disorder: a review. Dialogues Clin Neurosci. 2010;12(2):149–63.
PubMed
PubMed Central
Google Scholar
Pauls DL. The genetics of obsessive compulsive disorder: a review of the evidence. Am J Med Genet C: Semin Med Genet. 2008;148C(2):133–9.
Article
Google Scholar
Sullivan PF, Daly MJ, O'Donovan M. Genetic architectures of psychiatric disorders: the emerging picture and its implications. Nat Rev Genet. 2012;13(8):537–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Visscher PM, Brown MA, McCarthy MI, Yang J. Five years of GWAS discovery. Am J Hum Genet. 2012;90(1):7–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sekar A, Bialas AR, de Rivera H, Davis A, Hammond TR, Kamitaki N, Tooley K, Presumey J, Baum M, Van Doren V, et al. Schizophrenia risk from complex variation of complement component 4. Nature. 2016;530(7589):177–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Simon-Sanchez J, Singleton A. Genome-wide association studies in neurological disorders. Lancet Neurol. 2008;7(11):1067–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
O'Dushlaine C, Rossin L, Lee PH, Duncan L, Parikshak NN, Newhouse S, Ripke S, Neale BM, Purcell SM, Posthuma D, et al. Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways. Nat Neurosci. 2015;18(2):199–209.
Article
CAS
Google Scholar
Glessner JT, Reilly MP, Kim CE, Takahashi N, Albano A, Hou CP, Bradfield JP, Zhang HT, Sleiman PMA, Flory JH, et al. Strong synaptic transmission impact by copy number variations in schizophrenia. Proc Natl Acad Sci U S A. 2010;107(23):10584–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, et al. Functional impact of global rare copy number variation in autism spectrum disorders. Nature. 2010;466(7304):368–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zarrei M, MacDonald JR, Merico D, Scherer SW. A copy number variation map of the human genome. Nat Rev Genet. 2015;16(3):172–83.
Article
CAS
PubMed
Google Scholar
Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, Walsh T, Yamrom B, Yoon S, Krasnitz A, Kendall J, et al. Strong association of de novo copy number mutations with autism. Science. 2007;316(5823):445–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fromer M, Pocklington AJ, Kavanagh DH, Williams HJ, Dwyer S, Gormley P, Georgieva L, Rees E, Palta P, Ruderfer DM, et al. De novo mutations in schizophrenia implicate synaptic networks. Nature. 2014;506(7487):179–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu B, Ionita-Laza J, Roos JL, Boone B, Woodrick S, Sun Y, Levy S, Gogos JA, Karayiorgou M. De novo gene mutations highlight patterns of genetic and neural complexity in schizophrenia. Nat Genet. 2012;44(12):1365–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
de Kluiver H, Buizer-Voskamp JE, Dolan CV, Boomsma DI. Paternal age and psychiatric disorders: a review. Am J Med Genet B. 2017;174(3):202–13.
Article
Google Scholar
Yu C, Arcos-Burgos M, Baune BT, Arolt V, Dannlowski U, Wong ML, Licinio J. Low-frequency and rare variants may contribute to elucidate the genetics of major depressive disorder. Transl Psychiatry. 2018;8(1):70.
Ament SA, Szelinger S, Glusman G, Ashworth J, Hou LP, Akula N, Shekhtman T, Badner JA, Brunkow ME, Mauldin DE, et al. Rare variants in neuronal excitability genes influence risk for bipolar disorder. Proc Natl Acad Sci U S A. 2015;112(11):3576–81.
Hyman SE. The daunting polygenicity of mental illness: making a new map. Philos Trans R Soc Lond B Biol Sci. 2018;373(1742):20170031.
Huddleston J, Chaisson MJP, Steinberg KM, Warren W, Hoekzema K, Gordon D, Graves-Lindsay TA, Munson KM, Kronenberg ZN, Vives L, et al. Discovery and genotyping of structural variation from long-read haploid genome sequence data. Genome Res. 2017;27(5):677–85.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, et al. Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A. 2014;111(17):6131–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014;46(3):310–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Quang D, Chen Y, Xie X. DANN: a deep learning approach for annotating the pathogenicity of genetic variants. Bioinformatics. 2015;31(5):761–3.
Article
CAS
PubMed
Google Scholar
Ritchie GR, Dunham I, Zeggini E, Flicek P. Functional annotation of noncoding sequence variants. Nat Methods. 2014;11(3):294–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shihab HA, Rogers MF, Gough J, Mort M, Cooper DN, Day IN, Gaunt TR, Campbell C. An integrative approach to predicting the functional effects of non-coding and coding sequence variation. Bioinformatics. 2015;31(10):1536–43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer MA. A method to predict the impact of regulatory variants from DNA sequence. Nat Genet. 2015;47(8):955–61.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou J, Troyanskaya OG. Predicting effects of noncoding variants with deep learning-based sequence model. Nat Methods. 2015;12(10):931–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Consortium GT. The genotype-tissue expression (GTEx) project. Nat Genet. 2013;45(6):580–5.
Article
Google Scholar
Petrovski S, Wang Q, Heinzen EL, Allen AS, Goldstein DB. Genic intolerance to functional variation and the interpretation of personal genomes. PLoS Genet. 2013;9(8):e1003709.
Article
CAS
PubMed
PubMed Central
Google Scholar
Khan A, Wang K. A deep learning based scoring system for prioritizing susceptibility variants for mental disorders. In: 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Kansas City, MO, USA; 2017: pp. 1698–705.
Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38(16):e164.
Article
PubMed
PubMed Central
Google Scholar
Ionita-Laza I, McCallum K, Xu B, Buxbaum JD. A spectral approach integrating functional genomic annotations for coding and noncoding variants. Nat Genet. 2016;48(2):214–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
PsychENCODE Consortium, Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, et al. The PsychENCODE project. Nat Neurosci. 2015;18(12):1707–12.
Tebbenkamp AT, Willsey AJ, State MW, Sestan N. The developmental transcriptome of the human brain: implications for neurodevelopmental disorders. Curr Opin Neurol. 2014;27(2):149–56.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hwang Y, Kim J, Shin JY, Kim JI, Seo JS, Webster MJ, Lee D, Kim S. Gene expression profiling by mRNA sequencing reveals increased expression of immune/inflammation-related genes in the hippocampus of individuals with schizophrenia. Transl Psychiatry. 2013;3:e321.
Article
CAS
PubMed
PubMed Central
Google Scholar
Luo R, Sanders SJ, Tian Y, Voineagu I, Huang N, Chu SH, Klei L, Cai C, Ou J, Lowe JK, et al. Genome-wide transcriptome profiling reveals the functional impact of rare de novo and recurrent CNVs in autism spectrum disorders. Am J Hum Genet. 2012;91(1):38–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Henrichsen CN, Chaignat E, Reymond A. Copy number variants, diseases and gene expression. Hum Mol Genet. 2009;18(R1):R1–8.
Article
CAS
PubMed
Google Scholar
Myers AJ, Gibbs JR, Webster JA, Rohrer K, Zhao A, Marlowe L, Kaleem M, Leung D, Bryden L, Nath P, et al. A survey of genetic human cortical gene expression. Nat Genet. 2007;39(12):1494–9.
Article
CAS
PubMed
Google Scholar
Webster JA, Gibbs JR, Clarke J, Ray M, Zhang W, Holmans P, Rohrer K, Zhao A, Marlowe L, Kaleem M, et al. Genetic control of human brain transcript expression in Alzheimer disease. Am J Hum Genet. 2009;84(4):445–58.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim Y, Xia K, Tao R, Giusti-Rodriguez P, Vladimirov V, van den Oord E, Sullivan PF. A meta-analysis of gene expression quantitative trait loci in brain. Transl Psychiatry. 2014;4:e459.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fromer M, Roussos P, Sieberts SK, Johnson JS, Kavanagh DH, Perumal TM, Ruderfer DM, Oh EC, Topol A, Shah HR, et al. Gene expression elucidates functional impact of polygenic risk for schizophrenia. Nat Neurosci. 2016;19(11):1442–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB, et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016;536(7616):285–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chauhan G, Arnold CR, Chu AY, Fornage M, Reyahi A, Bis JC, Havulinna AS, Sargurupremraj M, Smith AV, Adams HHH, et al. Identification of additional risk loci for stroke and small vessel disease: a meta-analysis of genome-wide association studies. Lancet Neurol. 2016;15(7):695–707.
Article
Google Scholar
Kim YJ, Go MJ, Hu C, Hong CB, Kim YK, Lee JY, Hwang JY, Oh JH, Kim DJ, Kim NH, et al. Large-scale genome-wide association studies in east Asians identify new genetic loci influencing metabolic traits. Nat Genet. 2011;43(10):990–5.
Stranger BE, Stahl EA, Raj T. Progress and promise of genome-wide association studies for human complex trait genetics. Genetics. 2011;187(2):367–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Folkersen L, van't Hooft F, Chernogubova E, Agardh HE, Hansson GK, Hedin U, Liska J, Syvanen AC, Paulsson-Berne G, Franco-Cereceda A, et al. Association of genetic risk variants with expression of proximal genes identifies novel susceptibility genes for cardiovascular disease. Circ Cardiovasc Genet. 2010;3(4):365–73.
Article
CAS
PubMed
Google Scholar
Altshuler D, Daly MJ, Lander ES. Genetic mapping in human disease. Science. 2008;322(5903):881–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang N, Lee I, Marcotte EM, Hurles ME. Characterising and predicting haploinsufficiency in the human genome. PLoS Genet. 2010;6(10):e1001154.
Article
PubMed
PubMed Central
Google Scholar
Yang H, Robinson PN, Wang K. Phenolyzer: phenotype-based prioritization of candidate genes for human diseases. Nat Methods. 2015;12(9):841–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang F, Gu W, Hurles ME, Lupski JR. Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet. 2009;10:451–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marshall CR, Howrigan DP, Merico D, Thiruvahindrapuram B, Wu W, Greer DS, Antaki D, Shetty A, Holmans PA, Pinto D, et al. Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects. Nat Genet. 2017;49(1):27–35.
Article
CAS
PubMed
Google Scholar
Kong A, Frigge ML, Masson G, Besenbacher S, Sulem P, Magnusson G, Gudjonsson SA, Sigurdsson A, Jonasdottir A, Jonasdottir A, et al. Rate of de novo mutations and the importance of father's age to disease risk. Nature. 2012;488(7412):471–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Veltman JA, Brunner HG. De novo mutations in human genetic disease. Nat Rev Genet. 2012;13(8):565–75.
Article
CAS
PubMed
Google Scholar
Acuna-Hidalgo R, Veltman JA, Hoischen A. New insights into the generation and role of de novo mutations in health and disease. Genome Biol. 2016;17:241.
Article
PubMed
PubMed Central
Google Scholar
Ronemus M, Iossifov I, Levy D, Wigler M. The role of de novo mutations in the genetics of autism spectrum disorders. Nat Rev Genet. 2014;15(2):133–41.
Article
CAS
PubMed
Google Scholar
Uddin M, Tammimies K, Pellecchia G, Alipanahi B, Hui PZ, Wang ZZ, Pinto D, Lau L, Nalpathamkalam T, Marshall CR, et al. Brain-expressed exons under purifying selection are enriched for de novo mutations in autism spectrum disorder. Nat Genet. 2014;46(7):742–7.
Article
CAS
PubMed
Google Scholar
Malaspina D. Paternal factors and schizophrenia risk: De novo mutations and imprinting. Schizophrenia Bull. 2001;27(3):379–93.
Article
CAS
Google Scholar
Turner TN, Yi Q, Krumm N, Huddleston J, Hoekzema K, FS HA, Doebley AL, Bernier RA, Nickerson DA, Eichler EE. denovo-db: a compendium of human de novo variants. Nucleic Acids Res. 2017;45(D1):D804–11.
Article
CAS
PubMed
Google Scholar
Oba S, Sato M, Takemasa I, Monden M, Matsubara K, Ishii S. A Bayesian missing value estimation method for gene expression profile data. Bioinformatics. 2003;19(16):2088–96.
Article
CAS
PubMed
Google Scholar
Lunardon N, Menardi G, Torelli N. ROSE: a package for binary imbalanced learning. R J. 2014;6(1):79–89.
Google Scholar
Buchanan CC, Torstenson ES, Bush WS, Ritchie MD. A comparison of cataloged variation between international HapMap consortium and 1000 genomes project data. J Am Med Inform Assoc. 2012;19(2):289–94.
Li MJ, Pan ZC, Liu ZP, Wu JX, Wang PW, Zhu Y, Xu F, Xia ZY, Sham PC, Kocher JPA, et al. Predicting regulatory variants with composite statistic. Bioinformatics. 2016;32(18):2729–36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brown CD, Mangravite LM, Engelhardt BE. Integrative modeling of eQTLs and cis-regulatory elements suggests mechanisms underlying cell type specificity of eQTLs. PLoS Genet. 2013;9(8):e1003649.
Article
CAS
PubMed
PubMed Central
Google Scholar
Leslie R, O’Donnell CJ, Johnson AD. GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database. Bioinformatics. 2014;30(12):i185–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Genomes Project C, Abecasis GR, Auton A, Brooks LD, MA DP, Durbin RM, Handsaker RE, Kang HM, Marth GT, GA MV. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491(7422):56–65.
Article
Google Scholar
Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature. 2014;511(7510):421–7.
Anney RJL, Ripke S, Anttila V, Grove J, Holmans P, Huang H, Klei L, Lee PH, Medland SE, Neale B, et al. Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia. Mol Autism. 2017;8:21.
Article
Google Scholar
Gelfman S, Wang Q, McSweeney KM, Ren Z, La Carpia F, Halvorsen M, Schoch K, Ratzon F, Heinzen EL, Boland MJ, et al. Annotating pathogenic non-coding variants in genic regions. Nat Commun. 2017;8(1):236.
Article
PubMed
PubMed Central
Google Scholar
Dong C, Wei P, Jian X, Gibbs R, Boerwinkle E, Wang K, Liu X. Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Hum Mol Genet. 2015;24(8):2125–37.
Article
CAS
PubMed
Google Scholar
Huang YF, Gulko B, Siepel A. Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data. Nat Genet. 2017;49(4):618–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shi L, Zhang X, Golhar R, Otieno FG, He M, Hou C, Kim C, Keating B, Lyon GJ, Wang K, et al. Whole-genome sequencing in an autism multiplex family. Mol Autism. 2013;4(1):8.