Clyde Francks

Publications

Displaying 1 - 26 of 26
  • Carrion Castillo, A., Van der Haegen, L., Tzourio-Mazoyer, N., Kavaklioglu, T., Badillo, S., Chavent, M., Saracco, J., Brysbaert, M., Fisher, S. E., Mazoyer, B., & Francks, C. (2019). Genome sequencing for rightward hemispheric language dominance. Genes, Brain and Behavior, 18(5): e12572. doi:10.1111/gbb.12572.

    Abstract

    Most people have left‐hemisphere dominance for various aspects of language processing, but only roughly 1% of the adult population has atypically reversed, rightward hemispheric language dominance (RHLD). The genetic‐developmental program that underlies leftward language laterality is unknown, as are the causes of atypical variation. We performed an exploratory whole‐genome‐sequencing study, with the hypothesis that strongly penetrant, rare genetic mutations might sometimes be involved in RHLD. This was by analogy with situs inversus of the visceral organs (left‐right mirror reversal of the heart, lungs and so on), which is sometimes due to monogenic mutations. The genomes of 33 subjects with RHLD were sequenced and analyzed with reference to large population‐genetic data sets, as well as 34 subjects (14 left‐handed) with typical language laterality. The sample was powered to detect rare, highly penetrant, monogenic effects if they would be present in at least 10 of the 33 RHLD cases and no controls, but no individual genes had mutations in more than five RHLD cases while being un‐mutated in controls. A hypothesis derived from invertebrate mechanisms of left‐right axis formation led to the detection of an increased mutation load, in RHLD subjects, within genes involved with the actin cytoskeleton. The latter finding offers a first, tentative insight into molecular genetic influences on hemispheric language dominance.

    Additional information

    gbb12572-sup-0001-AppendixS1.docx
  • Eising, E., Carrion Castillo, A., Vino, A., Strand, E. A., Jakielski, K. J., Scerri, T. S., Hildebrand, M. S., Webster, R., Ma, A., Mazoyer, B., Francks, C., Bahlo, M., Scheffer, I. E., Morgan, A. T., Shriberg, L. D., & Fisher, S. E. (2019). A set of regulatory genes co-expressed in embryonic human brain is implicated in disrupted speech development. Molecular Psychiatry, 24, 1065-1078. doi:10.1038/s41380-018-0020-x.

    Abstract

    Genetic investigations of people with impaired development of spoken language provide windows into key aspects of human biology. Over 15 years after FOXP2 was identified, most speech and language impairments remain unexplained at the molecular level. We sequenced whole genomes of nineteen unrelated individuals diagnosed with childhood apraxia of speech, a rare disorder enriched for causative mutations of large effect. Where DNA was available from unaffected parents, we discovered de novo mutations, implicating genes, including CHD3, SETD1A and WDR5. In other probands, we identified novel loss-of-function variants affecting KAT6A, SETBP1, ZFHX4, TNRC6B and MKL2, regulatory genes with links to neurodevelopment. Several of the new candidates interact with each other or with known speech-related genes. Moreover, they show significant clustering within a single co-expression module of genes highly expressed during early human brain development. This study highlights gene regulatory pathways in the developing brain that may contribute to acquisition of proficient speech.

    Additional information

    Eising_etal_2018sup.pdf
  • Francks, C. (2019). In search of the biological roots of typical and atypical human brain asymmetry. Physics of Life Reviews, 30, 22-24. doi:10.1016/j.plrev.2019.07.004.
  • Francks, C. (2019). The genetic bases of brain lateralization. In P. Hagoort (Ed.), Human language: From genes and brain to behavior (pp. 595-608). Cambridge, MA: MIT Press.
  • Gialluisi, A., Andlauer, T. F. M., Mirza-Schreiber, N., Moll, K., Becker, J., Hoffmann, P., Ludwig, K. U., Czamara, D., St Pourcain, B., Brandler, W., Honbolygó, F., Tóth, D., Csépe, V., Huguet, G., Morris, A. P., Hulslander, J., Willcutt, E. G., DeFries, J. C., Olson, R. K., Smith, S. D. and 25 moreGialluisi, A., Andlauer, T. F. M., Mirza-Schreiber, N., Moll, K., Becker, J., Hoffmann, P., Ludwig, K. U., Czamara, D., St Pourcain, B., Brandler, W., Honbolygó, F., Tóth, D., Csépe, V., Huguet, G., Morris, A. P., Hulslander, J., Willcutt, E. G., DeFries, J. C., Olson, R. K., Smith, S. D., Pennington, B. F., Vaessen, A., Maurer, U., Lyytinen, H., Peyrard-Janvid, M., Leppänen, P. H. T., Brandeis, D., Bonte, M., Stein, J. F., Talcott, J. B., Fauchereau, F., Wilcke, A., Francks, C., Bourgeron, T., Monaco, A. P., Ramus, F., Landerl, K., Kere, J., Scerri, T. S., Paracchini, S., Fisher, S. E., Schumacher, J., Nöthen, M. M., Müller-Myhsok, B., & Schulte-Körne, G. (2019). Genome-wide association scan identifies new variants associated with a cognitive predictor of dyslexia. Translational Psychiatry, 9(1): 77. doi:10.1038/s41398-019-0402-0.

    Abstract

    Developmental dyslexia (DD) is one of the most prevalent learning disorders, with high impact on school and psychosocial development and high comorbidity with conditions like attention-deficit hyperactivity disorder (ADHD), depression, and anxiety. DD is characterized by deficits in different cognitive skills, including word reading, spelling, rapid naming, and phonology. To investigate the genetic basis of DD, we conducted a genome-wide association study (GWAS) of these skills within one of the largest studies available, including nine cohorts of reading-impaired and typically developing children of European ancestry (N = 2562–3468). We observed a genome-wide significant effect (p < 1 × 10−8) on rapid automatized naming of letters (RANlet) for variants on 18q12.2, within MIR924HG (micro-RNA 924 host gene; rs17663182 p = 4.73 × 10−9), and a suggestive association on 8q12.3 within NKAIN3 (encoding a cation transporter; rs16928927, p = 2.25 × 10−8). rs17663182 (18q12.2) also showed genome-wide significant multivariate associations with RAN measures (p = 1.15 × 10−8) and with all the cognitive traits tested (p = 3.07 × 10−8), suggesting (relational) pleiotropic effects of this variant. A polygenic risk score (PRS) analysis revealed significant genetic overlaps of some of the DD-related traits with educational attainment (EDUyears) and ADHD. Reading and spelling abilities were positively associated with EDUyears (p ~ [10−5–10−7]) and negatively associated with ADHD PRS (p ~ [10−8−10−17]). This corroborates a long-standing hypothesis on the partly shared genetic etiology of DD and ADHD, at the genome-wide level. Our findings suggest new candidate DD susceptibility genes and provide new insights into the genetics of dyslexia and its comorbities.
  • De Kovel, C. G. F., Carrion Castillo, A., & Francks, C. (2019). A large-scale population study of early life factors influencing left-handedness. Scientific Reports, 9: 584. doi:10.1038/s41598-018-37423-8.

    Abstract

    Hand preference is a conspicuous variation in human behaviour, with a worldwide proportion of around 90% of people preferring to use the right hand for many tasks, and 10% the left hand. We used the large cohort of the UK biobank (~500,000 participants) to study possible relations between early life factors and adult hand preference. The probability of being left-handed was affected by the year and location of birth, likely due to cultural effects. In addition, hand preference was affected by birthweight, being part of a multiple birth, season of birth, breastfeeding, and sex, with each effect remaining significant after accounting for all others. Analysis of genome-wide genotype data showed that left-handedness was very weakly heritable, but shared no genetic basis with birthweight. Although on average left-handers and right-handers differed for a number of early life factors, all together these factors had only a minimal predictive value for individual hand preference.

    Additional information

    Supplementary information
  • De Kovel, C. G. F., Aftanas, L., Aleman, A., Alexander-Bloch, A. F., Baune, B. T., Brack, I., Bülow, R., Filho, G. B., Carballedo, A., Connolly, C. G., Cullen, K. R., Dannlowski, U., Davey, C. G., Dima, D., Dohm, K., Erwin-Grabner, T., Frodl, T., Fu, C. H., Hall, G. B., Glahn, D. C. and 58 moreDe Kovel, C. G. F., Aftanas, L., Aleman, A., Alexander-Bloch, A. F., Baune, B. T., Brack, I., Bülow, R., Filho, G. B., Carballedo, A., Connolly, C. G., Cullen, K. R., Dannlowski, U., Davey, C. G., Dima, D., Dohm, K., Erwin-Grabner, T., Frodl, T., Fu, C. H., Hall, G. B., Glahn, D. C., Godlewska, B., Gotlib, I. H., Goya-Maldonado, R., Grabe, H. J., Groenewold, N. A., Grotegerd, D., Gruber, O., Harris, M. A., Harrison, B. J., Hatton, S. N., Hickie, I. B., Ho, T. C., Jahanshad, N., Kircher, T., Krämer, B., Krug, A., Lagopoulos, J., Leehr, E. J., Li, M., MacMaster, F. P., MacQueen, G., McIntosh, A. M., McLellan, Q., Medland, S. E., Mueller, B. A., Nenadic, I., Osipov, E., Papmeyer, M., Portella, M. J., Reneman, L., Rosa, P. G., Sacchet, M. D., Schnell, K., Schrantee, A., Sim, K., Simulionyte, E., Sindermann, L., Singh, A., Stein, D. J., Ubani, B. N., der Wee, N. J. V., der Werff, S. J. V., Veer, I. M., Vives-Gilabert, Y., Völzke, H., Walter, H., Walter, M., Schreiner, M. W., Whalley, H., Winter, N., Wittfeld, K., Yang, T. T., Yüksel, D., Zaremba, D., Thompson, P. M., Veltman, D. J., Schmaal, L., & Francks, C. (2019). No alterations of brain structural asymmetry in major depressive disorder: An ENIGMA consortium analysis. American Journal of Psychiatry, 176(12), 1039-1049. doi:10.1176/appi.ajp.2019.18101144.

    Abstract

    Objective:

    Asymmetry is a subtle but pervasive aspect of the human brain, and it may be altered in several psychiatric conditions. MRI studies have shown subtle differences of brain anatomy between people with major depressive disorder and healthy control subjects, but few studies have specifically examined brain anatomical asymmetry in relation to this disorder, and results from those studies have remained inconclusive. At the functional level, some electroencephalography studies have indicated left fronto-cortical hypoactivity and right parietal hypoactivity in depressive disorders, so aspects of lateralized anatomy may also be affected. The authors used pooled individual-level data from data sets collected around the world to investigate differences in laterality in measures of cortical thickness, cortical surface area, and subcortical volume between individuals with major depression and healthy control subjects.
    Methods:

    The authors investigated differences in the laterality of thickness and surface area measures of 34 cerebral cortical regions in 2,256 individuals with major depression and 3,504 control subjects from 31 separate data sets, and they investigated volume asymmetries of eight subcortical structures in 2,540 individuals with major depression and 4,230 control subjects from 32 data sets. T1-weighted MRI data were processed with a single protocol using FreeSurfer and the Desikan-Killiany atlas. The large sample size provided 80% power to detect effects of the order of Cohen’s d=0.1.
    Results:

    The largest effect size (Cohen’s d) of major depression diagnosis was 0.085 for the thickness asymmetry of the superior temporal cortex, which was not significant after adjustment for multiple testing. Asymmetry measures were not significantly associated with medication use, acute compared with remitted status, first episode compared with recurrent status, or age at onset.
    Conclusions:

    Altered brain macro-anatomical asymmetry may be of little relevance to major depression etiology in most cases.
  • De Kovel, C. G. F., & Francks, C. (2019). The molecular genetics of hand preference revisited. Scientific Reports, 9: 5986. doi:10.1038/s41598-019-42515-0.

    Abstract

    Hand preference is a prominent behavioural trait linked to human brain asymmetry. A handful of genetic variants have been reported to associate with hand preference or quantitative measures related to it. Most of these reports were on the basis of limited sample sizes, by current standards for genetic analysis of complex traits. Here we performed a genome-wide association analysis of hand preference in the large, population-based UK Biobank cohort (N = 331,037). We used gene-set enrichment analysis to investigate whether genes involved in visceral asymmetry are particularly relevant to hand preference, following one previous report. We found no evidence supporting any of the previously suggested variants or genes, nor that genes involved in visceral laterality have a role in hand preference. It remains possible that some of the previously reported genes or pathways are relevant to hand preference as assessed in other ways, or else are relevant within specific disorder populations. However, some or all of the earlier findings are likely to be false positives, and none of them appear relevant to hand preference as defined categorically in the general population. Our analysis did produce a small number of novel, significant associations, including one implicating the microtubule-associated gene MAP2 in handedness.
  • Postema, M., Van Rooij, D., Anagnostou, E., Arango, C., Auzias, G., Behrmann, M., Busatto Filho, G., Calderoni, S., Calvo, R., Daly, E., Deruelle, C., Di Martino, A., Dinstein, I., Duran, F. L. S., Durston, S., Ecker, C., Ehrlich, S., Fair, D., Fedor, J., Feng, X. and 38 morePostema, M., Van Rooij, D., Anagnostou, E., Arango, C., Auzias, G., Behrmann, M., Busatto Filho, G., Calderoni, S., Calvo, R., Daly, E., Deruelle, C., Di Martino, A., Dinstein, I., Duran, F. L. S., Durston, S., Ecker, C., Ehrlich, S., Fair, D., Fedor, J., Feng, X., Fitzgerald, J., Floris, D. L., Freitag, C. M., Gallagher, L., Glahn, D. C., Gori, I., Haar, S., Hoekstra, L., Jahanshad, N., Jalbrzikowski, M., Janssen, J., King, J. A., Kong, X., Lazaro, L., Lerch, J. P., Luna, B., Martinho, M. M., McGrath, J., Medland, S. E., Muratori, F., Murphy, C. M., Murphy, D. G. M., O'Hearn, K., Oranje, B., Parellada, M., Puig, O., Retico, A., Rosa, P., Rubia, K., Shook, D., Taylor, M., Tosetti, M., Wallace, G. L., Zhou, F., Thompson, P., Fisher, S. E., Buitelaar, J. K., & Francks, C. (2019). Altered structural brain asymmetry in autism spectrum disorder in a study of 54 datasets. Nature Communications, 10: 4958. doi:10.1038/s41467-019-13005-8.
  • Satizabal, C. L., Adams, H. H. H., Hibar, D. P., White, C. C., Knol, M. J., Stein, J. L., Scholz, M., Sargurupremraj, M., Jahanshad, N., Roshchupkin, G. V., Smith, A. V., Bis, J. C., Jian, X., Luciano, M., Hofer, E., Teumer, A., Van der Lee, S. J., Yang, J., Yanek, L. R., Lee, T. V. and 271 moreSatizabal, C. L., Adams, H. H. H., Hibar, D. P., White, C. C., Knol, M. J., Stein, J. L., Scholz, M., Sargurupremraj, M., Jahanshad, N., Roshchupkin, G. V., Smith, A. V., Bis, J. C., Jian, X., Luciano, M., Hofer, E., Teumer, A., Van der Lee, S. J., Yang, J., Yanek, L. R., Lee, T. V., Li, S., Hu, Y., Koh, J. Y., Eicher, J. D., Desrivières, S., Arias-Vasquez, A., Chauhan, G., Athanasiu, L., Renteria, M. E., Kim, S., Höhn, D., Armstrong, N. J., Chen, Q., Holmes, A. J., Den Braber, A., Kloszewska, I., Andersson, M., Espeseth, T., Grimm, O., Abramovic, L., Alhusaini, S., Milaneschi, Y., Papmeyer, M., Axelsson, T., Ehrlich, S., Roiz-Santiañez, R., Kraemer, B., Håberg, A. K., Jones, H. J., Pike, G. B., Stein, D. J., Stevens, A., Bralten, J., Vernooij, M. W., Harris, T. B., Filippi, I., Witte, A. V., Guadalupe, T., Wittfeld, K., Mosley, T. H., Becker, J. T., Doan, N. T., Hagenaars, S. P., Saba, Y., Cuellar-Partida, G., Amin, N., Hilal, S., Nho, K., Karbalai, N., Arfanakis, K., Becker, D. M., Ames, D., Goldman, A. L., Lee, P. H., Boomsma, D. I., Lovestone, S., Giddaluru, S., Le Hellard, S., Mattheisen, M., Bohlken, M. M., Kasperaviciute, D., Schmaal, L., Lawrie, S. M., Agartz, I., Walton, E., Tordesillas-Gutierrez, D., Davies, G. E., Shin, J., Ipser, J. C., Vinke, L. N., Hoogman, M., Jia, T., Burkhardt, R., Klein, M., Crivello, F., Janowitz, D., Carmichael, O., Haukvik, U. K., Aribisala, B. S., Schmidt, H., Strike, L. T., Cheng, C.-Y., Risacher, S. L., Pütz, B., Fleischman, D. A., Assareh, A. A., Mattay, V. S., Buckner, R. L., Mecocci, P., Dale, A. M., Cichon, S., Boks, M. P., Matarin, M., Penninx, B. W. J. H., Calhoun, V. D., Chakravarty, M. M., Marquand, A., Macare, C., Masouleh, S. K., Oosterlaan, J., Amouyel, P., Hegenscheid, K., Rotter, J. I., Schork, A. J., Liewald, D. C. M., De Zubicaray, G. I., Wong, T. Y., Shen, L., Sämann, P. G., Brodaty, H., Roffman, J. L., De Geus, E. J. C., Tsolaki, M., Erk, S., Van Eijk, K. R., Cavalleri, G. L., Van der Wee, N. J. A., McIntosh, A. M., Gollub, R. L., Bulayeva, K. B., Bernard, M., Richards, J. S., Himali, J. J., Loeffler, M., Rommelse, N., Hoffmann, W., Westlye, L. T., Valdés Hernández, M. C., Hansell, N. K., Van Erp, T. G. M., Wolf, C., Kwok, J. B. J., Vellas, B., Heinz, A., Olde Loohuis, L. M., Delanty, N., Ho, B.-C., Ching, C. R. K., Shumskaya, E., Singh, B., Hofman, A., Van der Meer, D., Homuth, G., Psaty, B. M., Bastin, M., Montgomery, G. W., Foroud, T. M., Reppermund, S., Hottenga, J.-J., Simmons, A., Meyer-Lindenberg, A., Cahn, W., Whelan, C. D., Van Donkelaar, M. M. J., Yang, Q., Hosten, N., Green, R. C., Thalamuthu, A., Mohnke, S., Hulshoff Pol, H. E., Lin, H., Jack Jr., C. R., Schofield, P. R., Mühleisen, T. W., Maillard, P., Potkin, S. G., Wen, W., Fletcher, E., Toga, A. W., Gruber, O., Huentelman, M., Smith, G. D., Launer, L. J., Nyberg, L., Jönsson, E. G., Crespo-Facorro, B., Koen, N., Greve, D., Uitterlinden, A. G., Weinberger, D. R., Steen, V. M., Fedko, I. O., Groenewold, N. A., Niessen, W. J., Toro, R., Tzourio, C., Longstreth Jr., W. T., Ikram, M. K., Smoller, J. W., Van Tol, M.-J., Sussmann, J. E., Paus, T., Lemaître, H., Schroeter, M. L., Mazoyer, B., Andreassen, O. A., Holsboer, F., Depondt, C., Veltman, D. J., Turner, J. A., Pausova, Z., Schumann, G., Van Rooij, D., Djurovic, S., Deary, I. J., McMahon, K. L., Müller-Myhsok, B., Brouwer, R. M., Soininen, H., Pandolfo, M., Wassink, T. H., Cheung, J. W., Wolfers, T., Martinot, J.-L., Zwiers, M. P., Nauck, M., Melle, I., Martin, N. G., Kanai, R., Westman, E., Kahn, R. S., Sisodiya, S. M., White, T., Saremi, A., Van Bokhoven, H., Brunner, H. G., Völzke, H., Wright, M. J., Van 't Ent, D., Nöthen, M. M., Ophoff, R. A., Buitelaar, J. K., Fernández, G., Sachdev, P. S., Rietschel, M., Van Haren, N. E. M., Fisher, S. E., Beiser, A. S., Francks, C., Saykin, A. J., Mather, K. A., Romanczuk-Seiferth, N., Hartman, C. A., DeStefano, A. L., Heslenfeld, D. J., Weiner, M. W., Walter, H., Hoekstra, P. J., Nyquist, P. A., Franke, B., Bennett, D. A., Grabe, H. J., Johnson, A. D., Chen, C., Van Duijn, C. M., Lopez, O. L., Fornage, M., Wardlaw, J. A., Schmidt, R., DeCarli, C., De Jager, P. L., Villringer, A., Debette, S., Gudnason, V., Medland, S. E., Shulman, J. M., Thompson, P. M., Seshadri, S., & Ikram, M. A. (2019). Genetic architecture of subcortical brain structures in 38,854 individuals worldwide. Nature Genetics, 51, 1624-1636. doi:10.1038/s41588-019-0511-y.

    Abstract

    Subcortical brain structures are integral to motion, consciousness, emotions and learning. We identified common genetic variation related to the volumes of the nucleus accumbens, amygdala, brainstem, caudate nucleus, globus pallidus, putamen and thalamus, using genome-wide association analyses in almost 40,000 individuals from CHARGE, ENIGMA and UK Biobank. We show that variability in subcortical volumes is heritable, and identify 48 significantly associated loci (40 novel at the time of analysis). Annotation of these loci by utilizing gene expression, methylation and neuropathological data identified 199 genes putatively implicated in neurodevelopment, synaptic signaling, axonal transport, apoptosis, inflammation/infection and susceptibility to neurological disorders. This set of genes is significantly enriched for Drosophila orthologs associated with neurodevelopmental phenotypes, suggesting evolutionarily conserved mechanisms. Our findings uncover novel biology and potential drug targets underlying brain development and disease.
  • Truong, D. T., Adams, A. K., Paniagua, S., Frijters, J. C., Boada, R., Hill, D. E., Lovett, M. W., Mahone, E. M., Willcutt, E. G., Wolf, M., Defries, J. C., Gialluisi, A., Francks, C., Fisher, S. E., Olson, R. K., Pennington, B. F., Smith, S. D., Bosson-Heenan, J., & Gruen, J. R. (2019). Multivariate genome-wide association study of rapid automatised naming and rapid alternating stimulus in Hispanic American and African–American youth. Journal of Medical Genetics, 56(8), 557-566. doi:10.1136/jmedgenet-2018-105874.

    Abstract

    Background Rapid automatised naming (RAN) and rapid alternating stimulus (RAS) are reliable predictors of reading disability. The underlying biology of reading disability is poorly understood. However, the high correlation among RAN, RAS and reading could be attributable to shared genetic factors that contribute to common biological mechanisms.

    Objective To identify shared genetic factors that contribute to RAN and RAS performance using a multivariate approach.

    Methods We conducted a multivariate genome-wide association analysis of RAN Objects, RAN Letters and RAS Letters/Numbers in a sample of 1331 Hispanic American and African–American youth. Follow-up neuroimaging genetic analysis of cortical regions associated with reading ability in an independent sample and epigenetic examination of extant data predicting tissue-specific functionality in the brain were also conducted.

    Results Genome-wide significant effects were observed at rs1555839 (p=4.03×10−8) and replicated in an independent sample of 318 children of European ancestry. Epigenetic analysis and chromatin state models of the implicated 70 kb region of 10q23.31 support active transcription of the gene RNLS in the brain, which encodes a catecholamine metabolising protein. Chromatin contact maps of adult hippocampal tissue indicate a potential enhancer–promoter interaction regulating RNLS expression. Neuroimaging genetic analysis in an independent, multiethnic sample (n=690) showed that rs1555839 is associated with structural variation in the right inferior parietal lobule.

    Conclusion This study provides support for a novel trait locus at chromosome 10q23.31 and proposes a potential gene–brain–behaviour relationship for targeted future functional analysis to understand underlying biological mechanisms for reading disability.

    Additional information

    Supplementary data
  • Carrion Castillo, A., Maassen, B., Franke, B., Heister, A., Naber, M., Van der Leij, A., Francks, C., & Fisher, S. E. (2017). Association analysis of dyslexia candidate genes in a Dutch longitudinal sample. European Journal of Human Genetics, 25(4), 452-460. doi:10.1038/ejhg.2016.194.

    Abstract

    Dyslexia is a common specific learning disability with a substantive genetic component. Several candidate genes have been proposed to be implicated in dyslexia susceptibility, such as DYX1C1, ROBO1, KIAA0319, and DCDC2. Associations with variants in these genes have also been reported with a variety of psychometric measures tapping into the underlying processes that might be impaired in dyslexic people. In this study, we first conducted a literature review to select single nucleotide polymorphisms (SNPs) in dyslexia candidate genes that had been repeatedly implicated across studies. We then assessed the SNPs for association in the richly phenotyped longitudinal data set from the Dutch Dyslexia Program. We tested for association with several quantitative traits, including word and nonword reading fluency, rapid naming, phoneme deletion, and nonword repetition. In this, we took advantage of the longitudinal nature of the sample to examine if associations were stable across four educational time-points (from 7 to 12 years). Two SNPs in the KIAA0319 gene were nominally associated with rapid naming, and these associations were stable across different ages. Genetic association analysis with complex cognitive traits can be enriched through the use of longitudinal information on trait development.
  • Chen, X. S., Reader, R. H., Hoischen, A., Veltman, J. A., Simpson, N. H., Francks, C., Newbury, D. F., & Fisher, S. E. (2017). Next-generation DNA sequencing identifies novel gene variants and pathways involved in specific language impairment. Scientific Reports, 7: 46105. doi:10.1038/srep46105.

    Abstract

    A significant proportion of children have unexplained problems acquiring proficient linguistic skills despite adequate intelligence and opportunity. Developmental language disorders are highly heritable with substantial societal impact. Molecular studies have begun to identify candidate loci, but much of the underlying genetic architecture remains undetermined. We performed whole-exome sequencing of 43 unrelated probands affected by severe specific language impairment, followed by independent validations with Sanger sequencing, and analyses of segregation patterns in parents and siblings, to shed new light on aetiology. By first focusing on a pre-defined set of known candidates from the literature, we identified potentially pathogenic variants in genes already implicated in diverse language-related syndromes, including ERC1, GRIN2A, and SRPX2. Complementary analyses suggested novel putative candidates carrying validated variants which were predicted to have functional effects, such as OXR1, SCN9A and KMT2D. We also searched for potential “multiple-hit” cases; one proband carried a rare AUTS2 variant in combination with a rare inherited haplotype affecting STARD9, while another carried a novel nonsynonymous variant in SEMA6D together with a rare stop-gain in SYNPR. On broadening scope to all rare and novel variants throughout the exomes, we identified biological themes that were enriched for such variants, including microtubule transport and cytoskeletal regulation.
  • Gialluisi, A., Guadalupe, T., Francks, C., & Fisher, S. E. (2017). Neuroimaging genetic analyses of novel candidate genes associated with reading and language. Brain and Language, 172, 9-15. doi:10.1016/j.bandl.2016.07.002.

    Abstract

    Neuroimaging measures provide useful endophenotypes for tracing genetic effects on reading and language. A recent Genome-Wide Association Scan Meta-Analysis (GWASMA) of reading and language skills (N = 1862) identified strongest associations with the genes CCDC136/FLNC and RBFOX2. Here, we follow up the top findings from this GWASMA, through neuroimaging genetics in an independent sample of 1275 healthy adults. To minimize multiple-testing, we used a multivariate approach, focusing on cortical regions consistently implicated in prior literature on developmental dyslexia and language impairment. Specifically, we investigated grey matter surface area and thickness of five regions selected a priori: middle temporal gyrus (MTG); pars opercularis and pars triangularis in the inferior frontal gyrus (IFG-PO and IFG-PT); postcentral parietal gyrus (PPG) and superior temporal gyrus (STG). First, we analysed the top associated polymorphisms from the reading/language GWASMA: rs59197085 (CCDC136/FLNC) and rs5995177 (RBFOX2). There was significant multivariate association of rs5995177 with cortical thickness, driven by effects on left PPG, right MTG, right IFG (both PO and PT), and STG bilaterally. The minor allele, previously associated with reduced reading-language performance, showed negative effects on grey matter thickness. Next, we performed exploratory gene-wide analysis of CCDC136/FLNC and RBFOX2; no other associations surpassed significance thresholds. RBFOX2 encodes an important neuronal regulator of alternative splicing. Thus, the prior reported association of rs5995177 with reading/language performance could potentially be mediated by reduced thickness in associated cortical regions. In future, this hypothesis could be tested using sufficiently large samples containing both neuroimaging data and quantitative reading/language scores from the same individuals.

    Additional information

    mmc1.docx
  • Guadalupe, T., Mathias, S. R., Van Erp, T. G. M., Whelan, C. D., Zwiers, M. P., Abe, Y., Abramovic, L., Agartz, I., Andreassen, O. A., Arias-Vásquez, A., Aribisala, B. S., Armstrong, N. J., Arolt, V., Artiges, E., Ayesa-Arriola, R., Baboyan, V. G., Banaschewski, T., Barker, G., Bastin, M. E., Baune, B. T. and 141 moreGuadalupe, T., Mathias, S. R., Van Erp, T. G. M., Whelan, C. D., Zwiers, M. P., Abe, Y., Abramovic, L., Agartz, I., Andreassen, O. A., Arias-Vásquez, A., Aribisala, B. S., Armstrong, N. J., Arolt, V., Artiges, E., Ayesa-Arriola, R., Baboyan, V. G., Banaschewski, T., Barker, G., Bastin, M. E., Baune, B. T., Blangero, J., Bokde, A. L., Boedhoe, P. S., Bose, A., Brem, S., Brodaty, H., Bromberg, U., Brooks, S., Büchel, C., Buitelaar, J., Calhoun, V. D., Cannon, D. M., Cattrell, A., Cheng, Y., Conrod, P. J., Conzelmann, A., Corvin, A., Crespo-Facorro, B., Crivello, F., Dannlowski, U., De Zubicaray, G. I., De Zwarte, S. M., Deary, I. J., Desrivières, S., Doan, N. T., Donohoe, G., Dørum, E. S., Ehrlich, S., Espeseth, T., Fernández, G., Flor, H., Fouche, J.-P., Frouin, V., Fukunaga, M., Gallinat, J., Garavan, H., Gill, M., Suarez, A. G., Gowland, P., Grabe, H. J., Grotegerd, D., Gruber, O., Hagenaars, S., Hashimoto, R., Hauser, T. U., Heinz, A., Hibar, D. P., Hoekstra, P. J., Hoogman, M., Howells, F. M., Hu, H., Hulshoff Pol, H. E.., Huyser, C., Ittermann, B., Jahanshad, N., Jönsson, E. G., Jurk, S., Kahn, R. S., Kelly, S., Kraemer, B., Kugel, H., Kwon, J. S., Lemaitre, H., Lesch, K.-P., Lochner, C., Luciano, M., Marquand, A. F., Martin, N. G., Martínez-Zalacaín, I., Martinot, J.-L., Mataix-Cols, D., Mather, K., McDonald, C., McMahon, K. L., Medland, S. E., Menchón, J. M., Morris, D. W., Mothersill, O., Maniega, S. M., Mwangi, B., Nakamae, T., Nakao, T., Narayanaswaamy, J. C., Nees, F., Nordvik, J. E., Onnink, A. M. H., Opel, N., Ophoff, R., Martinot, M.-L.-P., Orfanos, D. P., Pauli, P., Paus, T., Poustka, L., Reddy, J. Y., Renteria, M. E., Roiz-Santiáñez, R., Roos, A., Royle, N. A., Sachdev, P., Sánchez-Juan, P., Schmaal, L., Schumann, G., Shumskaya, E., Smolka, M. N., Soares, J. C., Soriano-Mas, C., Stein, D. J., Strike, L. T., Toro, R., Turner, J. A., Tzourio-Mazoyer, N., Uhlmann, A., Valdés Hernández, M., Van den Heuvel, O. A., Van der Meer, D., Van Haren, N. E.., Veltman, D. J., Venkatasubramanian, G., Vetter, N. C., Vuletic, D., Walitza, S., Walter, H., Walton, E., Wang, Z., Wardlaw, J., Wen, W., Westlye, L. T., Whelan, R., Wittfeld, K., Wolfers, T., Wright, M. J., Xu, J., Xu, X., Yun, J.-Y., Zhao, J., Franke, B., Thompson, P. M., Glahn, D. C., Mazoyer, B., Fisher, S. E., & Francks, C. (2017). Human subcortical asymmetries in 15,847 people worldwide reveal effects of age and sex. Brain Imaging and Behavior, 11(5), 1497-1514. doi:10.1007/s11682-016-9629-z.

    Abstract

    The two hemispheres of the human brain differ functionally and structurally. Despite over a century of research, the extent to which brain asymmetry is influenced by sex, handedness, age, and genetic factors is still controversial. Here we present the largest ever analysis of subcortical brain asymmetries, in a harmonized multi-site study using meta-analysis methods. Volumetric asymmetry of seven subcortical structures was assessed in 15,847 MRI scans from 52 datasets worldwide. There were sex differences in the asymmetry of the globus pallidus and putamen. Heritability estimates, derived from 1170 subjects belonging to 71 extended pedigrees, revealed that additive genetic factors influenced the asymmetry of these two structures and that of the hippocampus and thalamus. Handedness had no detectable effect on subcortical asymmetries, even in this unprecedented sample size, but the asymmetry of the putamen varied with age. Genetic drivers of asymmetry in the hippocampus, thalamus and basal ganglia may affect variability in human cognition, including susceptibility to psychiatric disorders.

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    11682_2016_9629_MOESM1_ESM.pdf
  • Hibar, D. P., Adams, H. H. H., Jahanshad, N., Chauhan, G., Stein, J. L., Hofer, E., Rentería, M. E., Bis, J. C., Arias-Vasquez, A., Ikram, M. K., Desrivieres, S., Vernooij, M. W., Abramovic, L., Alhusaini, S., Amin, N., Andersson, M., Arfanakis, K., Aribisala, B. S., Armstrong, N. J., Athanasiu, L. and 312 moreHibar, D. P., Adams, H. H. H., Jahanshad, N., Chauhan, G., Stein, J. L., Hofer, E., Rentería, M. E., Bis, J. C., Arias-Vasquez, A., Ikram, M. K., Desrivieres, S., Vernooij, M. W., Abramovic, L., Alhusaini, S., Amin, N., Andersson, M., Arfanakis, K., Aribisala, B. S., Armstrong, N. J., Athanasiu, L., Axelsson, T., Beecham, A. H., Beiser, A., Bernard, M., Blanton, S. H., Bohlken, M. M., Boks, M. P., Bralten, J., Brickman, A. M., Carmichael, O., Chakravarty, M. M., Chen, Q., Ching, C. R. K., Chouraki, V., Cuellar-Partida, G., Crivello, F., den Brabander, A., Doan, N. T., Ehrlich, S., Giddaluru, S., Goldman, A. L., Gottesman, R. F., Grimm, O., Griswold, M. E., Guadalupe, T., Gutman, B. A., Hass, J., Haukvik, U. K., Hoehn, D., Holmes, A. J., Hoogman, M., Janowitz, D., Jia, T., Jørgensen, K. N., Mirza-Schreiber, N., Kasperaviciute, D., Kim, S., Klein, M., Krämer, B., Lee, P. H., Liewald, D. C. M., Lopez, L. M., Luciano, M., Macare, C., Marquand, A. F., Matarin, M., Mather, K. A., Mattheisen, M., McKay, D. R., Milaneschi, Y., Maniega, S. M., Nho, K., Nugent, A. C., Nyquist, P., Olde Loohuis, L. M., Oosterlaan, J., Papmeyer, M., Pirpamer, L., Pütz, B., Ramasamy, A., Richards, J. S., Risacher, S., Roiz-Santiañez, R., Rommelse, N., Ropele, S., Rose, E., Royle, N. A., Rundek, T., Sämann, P. G., Saremi, A., Satizabal, C. L., Schmaal, L., Schork, A. J., Shen, L., Shin, J., Shumskaya, E., Smith, A. V., Sprooten, E., Strike, L. T., Teumer, A., Tordesillas-Gutierrez, D., Toro, R., Trabzuni, D., Trompet, S., Vaidya, D., Van der Grond, J., Van der Lee, S. J., Van der Meer, D., Van Donkelaar, M. M. J., Van Eijk, K. R., van Erp, T. G. M., Van Rooij, D., Walton, E., Westlye, L. T., Whelan, C. D., Windham, B. G., Winkler, A. M., Wittfeld, K. M., Woldehawariat, G., Wolf, C., Wolfers, T., Yanek, L. R., Yang, J., Zijdenbos, A., Zwiers, M. P., Agartz, I., Almasy, L., Ames, D., Amouyel, P., Andreassen, O. A., Arepalli, S., Assareh, A. A., Barral, S., Bastin, M. E., Becker, D. M., Becker, J. T., Bennett, D. A., Blangero, J., Van Bokhoven, H., Boomsma, D. I., Brodaty, H., Brouwer, R. M., Brunner, H. G., Buckner, R. L., Buitelaar, J. K., Bulayeva, K. B., Cahn, W., Calhoun, V. D., Cannon, D. M., Cavalleri, G. L., Cheng, C.-Y., Cichon, S., Cookson, M. R., Corvin, A., Crespo-Facorro, B., Curran, J. E., Czisch, M., Dale, A. M., Davies, G. E., De Craen, A. J. M., De Geus, E. J. C., De Jager, P. L., De Zubicaray, G. i., Deary, I. J., Debette, S., DeCarli, C., Delanty, N., Depondt, C., DeStefano, A., Dillman, A., Djurovic, S., Donohoe, G., Drevets, W. C., Duggirala, R., Dyer, T. D., Enzinger, C., Erk, S., Espeseth, T., Fedko, I. O., Fernández, G., Ferrucci, L., Fisher, S. E., Fleischman, D. A., Ford, I., Fornage, M., Foroud, T. M., Fox, P. T., Francks, C., Fukunaga, M., Gibbs, J. R., Glahn, D. C., Gollub, R. L., Göring, H. H. H., Green, R. C., Gruber, O., Gudnason, V., Guelfi, S., Haberg, A. K., Hansell, N. K., Hardy, J., Hartman, C. A., Hashimoto, R., Hegenscheid, K., Heinz, A., Le Hellard, S., Hernandez, D. G., Heslenfeld, D. J., Ho, B.-C., Hoekstra, P. J., Hoffmann, W., Hofman, A., Holsboer, F., Homuth, G., Hosten, N., Hottenga, J.-J., Huentelman, M., Pol, H. E. H., Ikeda, M., Jack Jr., C. R., Jenkinson, M., Johnson, R., Jonsson, E. G., Jukema, J. W., Kahn, R. S., Kanai, R., Kloszewska, I., Knopman, D. S., Kochunov, P., Kwok, J. B., Lawrie, S. M., Lemaître, H., Liu, X., Longo, D. L., Lopez, O. L., Lovestone, S., Martinez, O., Martinot, J.-L., Mattay, V. S., McDonald, C., Mcintosh, A. M., McMahon, F., McMahon, K. L., Mecocci, P., Melle, I., Meyer-Lindenberg, A., Mohnke, S., Montgomery, G. W., Morris, D. W., Mosley, T. H., Mühleisen, T. W., Müller-Myhsok, B., Nalls, M. A., Nauck, M., Nichols, T. E., Niessen, W. J., Nöthen, M. M., Nyberg, L., Ohi, K., Olvera, R. L., Ophoff, R. A., Pandolfo, M., Paus, T., Pausova, Z., Penninx, B. W. J. H., Pike, G. B., Potkin, S. G., Psaty, B. M., Reppermund, S., Rietschel, M., Roffman, J. L., Romanczuk-Seiferth, N., Rotter, J. I., Ryten, M., Sacco, R. L., Sachdev, P. S., Saykin, A. J., Schmidt, R., Schmidt, H., Schofield, P. R., Sigursson, S., Simmons, A., Singleton, A., Sisodiya, S. M., Smith, C., Smoller, J. W., Soininen, H., Steen, V. M., Stott, D. J., Sussmann, J. E., Thalamuthu, A., Toga, A. W., Traynor, B. J., Troncoso, J., Tsolaki, M., Tzourio, C., Uitterlinden, A. G., Hernández, M. C. V., Van der Brug, M., Van der Lugt, A., Van der Wee, N. J. A., Van Haren, N. E. M., Van Tol, M.-J., Vardarajan, B. N., Vellas, B., Veltman, D. J., Völzke, H., Walter, H., Wardlaw, J. M., Wassink, T. H., Weale, M. e., Weinberger, D. R., Weiner, M., Wen, W., Westman, E., White, T., Wong, T. Y., Wright, C. B., Zielke, R. H., Zonderman, A. B., Martin, N. G., Van Duijn, C. M., Wright, M. J., Longstreth, W. W. T., Schumann, G., Grabe, H. J., Franke, B., Launer, L. J., Medland, S. E., Seshadri, S., Thompson, P. M., & Ikram, A. (2017). Novel genetic loci associated with hippocampal volume. Nature Communications, 8: 13624. doi:10.1038/ncomms13624.

    Abstract

    The hippocampal formation is a brain structure integrally involved in episodic memory, spatial navigation, cognition and stress responsiveness. Structural abnormalities in hippocampal volume and shape are found in several common neuropsychiatric disorders. To identify the genetic underpinnings of hippocampal structure here we perform a genome-wide association study (GWAS) of 33,536 individuals and discover six independent loci significantly associated with hippocampal volume, four of them novel. Of the novel loci, three lie within genes (ASTN2, DPP4 and MAST4) and one is found 200 kb upstream of SHH. A hippocampal subfield analysis shows that a locus within the MSRB3 gene shows evidence of a localized effect along the dentate gyrus, subiculum, CA1 and fissure. Further, we show that genetic variants associated with decreased hippocampal volume are also associated with increased risk for Alzheimer’s disease (rg=−0.155). Our findings suggest novel biological pathways through which human genetic variation influences hippocampal volume and risk for neuropsychiatric illness.

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    ncomms13624-s1.pdf ncomms13624-s2.xlsx
  • Kavaklioglu, T., Guadalupe, T., Zwiers, M., Marquand, A. F., Onnink, M., Shumskaya, E., Brunner, H., Fernandez, G., Fisher, S. E., & Francks, C. (2017). Structural asymmetries of the human cerebellum in relation to cerebral cortical asymmetries and handedness. Brain Structure and Function, 22, 1611-1623. doi:10.1007/s00429-016-1295-9.

    Abstract

    There is evidence that the human cerebellum is involved not only in motor control but also in other cognitive functions. Several studies have shown that language-related activation is lateralized toward the right cerebellar hemisphere in most people, in accordance with leftward cerebral cortical lateralization for language and a general contralaterality of cerebral–cerebellar activations. In terms of behavior, hand use elicits asymmetrical activation in the cerebellum, while hand preference is weakly associated with language lateralization. However, it is not known how, or whether, these functional relations are reflected in anatomy. We investigated volumetric gray matter asymmetries of cerebellar lobules in an MRI data set comprising 2226 subjects. We tested these cerebellar asymmetries for associations with handedness, and for correlations with cerebral cortical anatomical asymmetries of regions important for language or hand motor control, as defined by two different automated image analysis methods and brain atlases, and supplemented with extensive visual quality control. No significant associations of cerebellar asymmetries to handedness were found. Some significant associations of cerebellar lobular asymmetries to cerebral cortical asymmetries were found, but none of these correlations were greater than 0.14, and they were mostly method-/atlas-dependent. On the basis of this large and highly powered study, we conclude that there is no overt structural manifestation of cerebellar functional lateralization and connectivity, in respect of hand motor control or language laterality
  • De Kovel, C. G. F., Lisgo, S., Karlebach, G., Ju, J., Cheng, G., Fisher, S. E., & Francks, C. (2017). Left-right asymmetry of maturation rates in human embryonic neural development. Biological Psychiatry, 82(3), 204-212. doi:10.1016/j.biopsych.2017.01.016.

    Abstract

    Background

    Left-right asymmetry is a fundamental organizing feature of the human brain, and neuro-psychiatric disorders such as schizophrenia sometimes involve alterations of brain asymmetry. As early as 8 weeks post conception, the majority of human fetuses move their right arms more than their left arms, but because nerve fibre tracts are still descending from the forebrain at this stage, spinal-muscular asymmetries are likely to play an important developmental role.
    Methods

    We used RNA sequencing to measure gene expression levels in the left and right spinal cords, and left and right hindbrains, of 18 post-mortem human embryos aged 4-8 weeks post conception. Genes showing embryonic lateralization were tested for an enrichment of signals in genome-wide association data for schizophrenia.
    Results

    The left side of the embryonic spinal cord was found to mature faster than the right side. Both sides transitioned from transcriptional profiles associated with cell division and proliferation at earlier stages, to neuronal differentiation and function at later stages, but the two sides were not in synchrony (p = 2.2 E-161). The hindbrain showed a left-right mirrored pattern compared to the spinal cord, consistent with the well-known crossing over of function between these two structures. Genes that showed lateralization in the embryonic spinal cord were enriched for association signals with schizophrenia (p = 4.3 E-05).
    Conclusions
    These are the earliest-stage left-right differences of human neural development ever reported. Disruption of the lateralised developmental programme may play a role in the genetic susceptibility to schizophrenia.

    Additional information

    mmc1.pdf
  • Ocklenburg, S., Schmitz, J., Moinfar, Z., Moser, D., Klose, R., Lor, S., Kunz, G., Tegenthoff, M., Faustmann, P., Francks, C., Epplen, J. T., Kumsta, R., & Güntürkün, O. (2017). Epigenetic regulation of lateralized fetal spinal gene expression underlies hemispheric asymmetries. eLife, 6: e22784. doi:10.7554/eLife.22784.001.

    Abstract

    Lateralization is a fundamental principle of nervous system organization but its molecular determinants are mostly unknown. In humans, asymmetric gene expression in the fetal cortex has been suggested as the molecular basis of handedness. However, human fetuses already show considerable asymmetries in arm movements before the motor cortex is functionally linked to the spinal cord, making it more likely that spinal gene expression asymmetries form the molecular basis of handedness. We analyzed genome-wide mRNA expression and DNA methylation in cervical and anterior thoracal spinal cord segments of five human fetuses and show development-dependent gene expression asymmetries. These gene expression asymmetries were epigenetically regulated by miRNA expression asymmetries in the TGF-β signaling pathway and lateralized methylation of CpG islands. Our findings suggest that molecular mechanisms for epigenetic regulation within the spinal cord constitute the starting point for handedness, implying a fundamental shift in our understanding of the ontogenesis of hemispheric asymmetries in humans
  • Thompson, P. M., Andreassen, O. A., Arias-Vasquez, A., Bearden, C. E., Boedhoe, P. S., Brouwer, R. M., Buckner, R. L., Buitelaar, J. K., Bulaeva, K. B., Cannon, D. M., Cohen, R. A., Conrod, P. J., Dale, A. M., Deary, I. J., Dennis, E. L., De Reus, M. A., Desrivieres, S., Dima, D., Donohoe, G., Fisher, S. E. and 51 moreThompson, P. M., Andreassen, O. A., Arias-Vasquez, A., Bearden, C. E., Boedhoe, P. S., Brouwer, R. M., Buckner, R. L., Buitelaar, J. K., Bulaeva, K. B., Cannon, D. M., Cohen, R. A., Conrod, P. J., Dale, A. M., Deary, I. J., Dennis, E. L., De Reus, M. A., Desrivieres, S., Dima, D., Donohoe, G., Fisher, S. E., Fouche, J.-P., Francks, C., Frangou, S., Franke, B., Ganjgahi, H., Garavan, H., Glahn, D. C., Grabe, H. J., Guadalupe, T., Gutman, B. A., Hashimoto, R., Hibar, D. P., Holland, D., Hoogman, M., Pol, H. E. H., Hosten, N., Jahanshad, N., Kelly, S., Kochunov, P., Kremen, W. S., Lee, P. H., Mackey, S., Martin, N. G., Mazoyer, B., McDonald, C., Medland, S. E., Morey, R. A., Nichols, T. E., Paus, T., Pausova, Z., Schmaal, L., Schumann, G., Shen, L., Sisodiya, S. M., Smit, D. J., Smoller, J. W., Stein, D. J., Stein, J. L., Toro, R., Turner, J. A., Van den Heuvel, M., Van den Heuvel, O. A., Van Erp, T. G., Van Rooij, D., Veltman, D. J., Walter, H., Wang, Y., Wardlaw, J. M., Whelan, C. D., Wright, M. J., & Ye, J. (2017). ENIGMA and the Individual: Predicting Factors that Affect the Brain in 35 Countries Worldwide. NeuroImage, 145, 389-408. doi:10.1016/j.neuroimage.2015.11.057.
  • Adams, H. H. H., Hibar, D. P., Chouraki, V., Stein, J. L., Nyquist, P., Renteria, M. E., Trompet, S., Arias-Vasquez, A., Seshadri, S., Desrivières, S., Beecham, A. H., Jahanshad, N., Wittfeld, K., Van der Lee, S. J., Abramovic, L., Alhusaini, S., Amin, N., Andersson, M., Arfanakis, K. A., Aribisala, B. S. and 322 moreAdams, H. H. H., Hibar, D. P., Chouraki, V., Stein, J. L., Nyquist, P., Renteria, M. E., Trompet, S., Arias-Vasquez, A., Seshadri, S., Desrivières, S., Beecham, A. H., Jahanshad, N., Wittfeld, K., Van der Lee, S. J., Abramovic, L., Alhusaini, S., Amin, N., Andersson, M., Arfanakis, K. A., Aribisala, B. S., Armstrong, N. J., Athanasiu, L., Axelsson, T., Beiser, A., Bernard, M., Bis, J. C., Blanken, L. M. E., Blanton, S. H., Bohlken, M. M., Boks, M. P., Bralten, J., Brickman, A. M., Carmichael, O., Chakravarty, M. M., Chauhan, G., Chen, Q., Ching, C. R. K., Cuellar-Partida, G., Den Braber, A., Doan, N. T., Ehrlich, S., Filippi, I., Ge, T., Giddaluru, S., Goldman, A. L., Gottesman, R. F., Greven, C. U., Grimm, O., Griswold, M. E., Guadalupe, T., Hass, J., Haukvik, U. K., Hilal, S., Hofer, E., Höhn, D., Holmes, A. J., Hoogman, M., Janowitz, D., Jia, T., Karbalai, N., Kasperaviciute, D., Kim, S., Klein, M., Krämer, B., Lee–, P. H., Liao, J., Liewald, D. C. M., Lopez, L. M., Luciano, M., Macare, C., Marquand, A., Matarin, M., Mather, K. A., Mattheisen, M., Mazoyer, B., McKay, D. R., McWhirter, R., Milaneschi, Y., Muetzel, R. L., Muñoz Maniega, S., Nho, K., Nugent, A. C., Olde Loohuis, L. M., Oosterlaan, J., Papmeyer, M., Pappa, I., Pirpamer, L., Pudas, S., Pütz, B., Rajan, K. B., Ramasamy, A., Richards, J. S., Risacher, S. L., Roiz-Santiañez, R., Rommelse, N., Rose, E. J., Royle, N. A., Rundek, T., Sämann, P. G., Satizabal, C. L., Schmaal, L., Schork, A. J., Shen, L., Shin, J., Shumskaya, E., Smith, A. V., Sprooten, E., Strike, L. T., Teumer, A., Thomson, R., Tordesillas-Gutierrez, D., Toro, R., Trabzuni, D., Vaidya, D., Van der Grond, J., Van der Meer, D., Van Donkelaar, M. M. J., Van Eijk, K. R., VanErp, T. G. M., Van Rooij, D., Walton, E., Westlye, L. T., Whelan, C. D., Windham, B. G., Winkler, A. M., Woldehawariat, G., Wolf, C., Wolfers, T., Xu, B., Yanek, L. R., Yang, J., Zijdenbos, A., Zwiers, M. P., Agartz, I., Aggarwal, N. T., Almasy, L., Ames, D., Amouyel, P., Andreassen, O. A., Arepalli, S., Assareh, A. A., Barral, S., Bastin, M. E., Becker, J. T., Becker, D. M., Bennett, D. A., Blangero, J., Van Bokhoven, H., Boomsma, D. I., Brodaty, H., Brouwer, R. M., Brunner, H. G., Buckner, R. L., Buitelaar, J. K., Bulayeva, K. B., Cahn, W., Calhoun, V. D., Cannon, D. M., Cavalleri, G. L., Chen, C., Cheng, C.-Y., Cichon, S., Cookson, M. R., Corvin, A., Crespo-Facorro, B., Curran, J. E., Czisch, M., Dale, A. M., Davies, G. E., De Geus, E. J. C., De Jager, P. L., De Zubicaray, G. I., Delanty, N., Depondt, C., DeStefano, A., Dillman, A., Djurovic, S., Donohoe, G., Drevets, W. C., Duggirala, R., Dyer, T. D., Erk, S., Espeseth, T., Evans, D. A., Fedko, I. O., Fernández, G., Ferrucci, L., Fisher, S. E., Fleischman, D. A., Ford, I., Foroud, T. M., Fox, P. T., Francks, C., Fukunaga, M., Gibbs, J. R., Glahn, D. C., Gollub, R. L., Göring, H. H. H., Grabe, H. J., Green, R. C., Gruber, O., Guelfi, S., Hansell, N. K., Hardy, J., Hartman, C. A., Hashimoto, R., Hegenscheid, K., Heinz, A., Le Hellard, S., Hernandez, D. G., Heslenfeld, D. J., Ho, B.-C., Hoekstra, P. J., Hoffmann, W., Hofman, A., Holsboer, F., Homuth, G., Hosten, N., Hottenga, J.-J., Hulshoff Pol, H. E., Ikeda, M., Ikram, M. K., Jack Jr, C. R., Jenkinson, M., Johnson, R., Jönsson, E. G., Jukema, J. W., Kahn, R. S., Kanai, R., Kloszewska, I., Knopman, D. S., Kochunov, P., Kwok, J. B., Launer, L. J., Lawrie, S. M., Lemaître, H., Liu, X., Longo, D. L., Longstreth Jr, W. T., Lopez, O. L., Lovestone, S., Martinez, O., Martinot, J.-L., Mattay, V. S., McDonald, C., McIntosh, A. M., McMahon, F. J., McMahon, K. L., Mecocci, P., Melle, I., Meyer-Lindenberg, A., Mohnke, S., Montgomery, G. W., Morris, D. W., Mosley, T. H., Mühleisen, T. W., Müller-Myhsok, B., Nalls, M. A., Nauck, M., Nichols, T. E., Niessen, W. J., Nöthen, M. M., Nyberg, L., Ohi, K., Olvera, R. L., Ophoff, R. A., Pandolfo, M., Paus, T., Pausova, Z., Penninx, B. W. J. H., Pike, G. B., Potkin, S. G., Psaty, B. M., Reppermund, S., Rietschel, M., Roffman, J. L., Romanczuk-Seiferth, N., Rotter, J. I., Ryten, M., Sacco, R. L., Sachdev, P. S., Saykin, A. J., Schmidt, R., Schofield, P. R., Sigursson, S., Simmons, A., Singleton, A., Sisodiya, S. M., Smith, C., Smoller, J. W., Soininen, H., Srikanth, V., Steen, V. M., Stott, D. J., Sussmann, J. E., Thalamuthu, A., Tiemeier, H., Toga, A. W., Traynor, B., Troncoso, J., Turner, J. A., Tzourio, C., Uitterlinden, A. G., Valdés Hernández, M. C., Van der Brug, M., Van der Lugt, A., Van der Wee, N. J. A., Van Duijn, C. M., Van Haren, N. E. M., Van 't Ent, D., Van Tol, M.-J., Vardarajan, B. N., Veltman, D. J., Vernooij, M. W., Völzke, H., Walter, H., Wardlaw, J. M., Wassink, T. H., Weale, M. E., Weinberger, D. R., Weiner, M. W., Wen, W., Westman, E., White, T., Wong, T. Y., Wright, C. B., Zielke, R. H., Zonderman, A. B., the Alzheimer's Disease Neuroimaging Initiative, EPIGEN, IMAGEN, SYS, Deary, I. J., DeCarli, C., Schmidt, H., Martin, N. G., De Craen, A. J. M., Wright, M. J., Gudnason, V., Schumann, G., Fornage, M., Franke, B., Debette, S., Medland, S. E., Ikram, M. A., & Thompson, P. M. (2016). Novel genetic loci underlying human intracranial volume identified through genome-wide association. Nature Neuroscience, 19, 1569-1582. doi:10.1038/nn.4398.

    Abstract

    Intracranial volume reflects the maximally attained brain size during development, and remains stable with loss of tissue in late
    life. It is highly heritable, but the underlying genes remain largely undetermined. In a genome-wide association study of 32,438
    adults, we discovered five previously unknown loci for intracranial volume and confirmed two known signals. Four of the loci were
    also associated with adult human stature, but these remained associated with intracranial volume after adjusting for height.
    We found a high genetic correlation with child head circumference (genetic = 0.748), which indicates a similar genetic
    background and allowed us to identify four additional loci through meta-analysis (Ncombined = 37,345). Variants for intracranial
    volume were also related to childhood and adult cognitive function, and Parkinson’s disease, and were enriched near genes
    involved in growth pathways, including PI3K-AKT signaling. These findings identify the biological underpinnings of intracranial
    volume and provide genetic support for theories on brain reserve and brain overgrowth.
  • Becker, M., Guadalupe, T., Franke, B., Hibar, D. P., Renteria, M. E., Stein, J. L., Thompson, P. M., Francks, C., Vernes, S. C., & Fisher, S. E. (2016). Early developmental gene enhancers affect subcortical volumes in the adult human brain. Human Brain Mapping, 37(5), 1788-1800. doi:10.1002/hbm.23136.

    Abstract

    Genome-wide association screens aim to identify common genetic variants contributing to the phenotypic variability of complex traits, such as human height or brain morphology. The identified genetic variants are mostly within noncoding genomic regions and the biology of the genotype–phenotype association typically remains unclear. In this article, we propose a complementary targeted strategy to reveal the genetic underpinnings of variability in subcortical brain volumes, by specifically selecting genomic loci that are experimentally validated forebrain enhancers, active in early embryonic development. We hypothesized that genetic variation within these enhancers may affect the development and ultimately the structure of subcortical brain regions in adults. We tested whether variants in forebrain enhancer regions showed an overall enrichment of association with volumetric variation in subcortical structures of >13,000 healthy adults. We observed significant enrichment of genomic loci that affect the volume of the hippocampus within forebrain enhancers (empirical P = 0.0015), a finding which robustly passed the adjusted threshold for testing of multiple brain phenotypes (cutoff of P < 0.0083 at an alpha of 0.05). In analyses of individual single nucleotide polymorphisms (SNPs), we identified an association upstream of the ID2 gene with rs7588305 and variation in hippocampal volume. This SNP-based association survived multiple-testing correction for the number of SNPs analyzed but not for the number of subcortical structures. Targeting known regulatory regions offers a way to understand the underlying biology that connects genotypes to phenotypes, particularly in the context of neuroimaging genetics. This biology-driven approach generates testable hypotheses regarding the functional biology of identified associations.
  • Carrion Castillo, A., van Bergen, E., Vino, A., van Zuijen, T., de Jong, P. F., Francks, C., & Fisher, S. E. (2016). Evaluation of results from genome-wide studies of language and reading in a novel independent dataset. Genes, Brain and Behavior, 15(6), 531-541. doi:10.1111/gbb.12299.

    Abstract

    Recent genome wide association scans (GWAS) for reading and language abilities have pin-pointed promising new candidate loci. However, the potential contributions of these loci remain to be validated. In the present study, we tested 17 of the most significantly associated single nucleotide polymorphisms (SNPs) from these GWAS studies (p < 10−6 in the original studies) in a new independent population dataset from the Netherlands: known as FIOLA (Familial Influences On Literacy Abilities). This dataset comprised 483 children from 307 nuclear families, plus 505 adults (including parents of participating children), and provided adequate statistical power to detect the effects that were previously reported. The following measures of reading and language performance were collected: word reading fluency, nonword reading fluency, phonological awareness, and rapid automatized naming. Two SNPs (rs12636438, rs7187223) were associated with performance in multivariate and univariate testing, but these did not remain significant after correction for multiple testing. Another SNP (rs482700) was only nominally associated in the multivariate test. For the rest of the SNPs we did not find supportive evidence of association. The findings may reflect differences between our study and the previous investigations in respects such as the language of testing, the exact tests used, and the recruitment criteria. Alternatively, most of the prior reported associations may have been false positives. A larger scale GWAS meta-analysis than those previously performed will likely be required to obtain robust insights into the genomic architecture underlying reading and language.
  • Franke, B., Stein, J. L., Ripke, S., Anttila, V., Hibar, D. P., Van Hulzen, K. J. E., Arias-Vasquez, A., Smoller, J. W., Nichols, T. E., Neale, M. C., McIntosh, A. M., Lee, P., McMahon, F. J., Meyer-Lindenberg, A., Mattheisen, M., Andreassen, O. A., Gruber, O., Sachdev, P. S., Roiz-Santiañez, R., Saykin, A. J. and 17 moreFranke, B., Stein, J. L., Ripke, S., Anttila, V., Hibar, D. P., Van Hulzen, K. J. E., Arias-Vasquez, A., Smoller, J. W., Nichols, T. E., Neale, M. C., McIntosh, A. M., Lee, P., McMahon, F. J., Meyer-Lindenberg, A., Mattheisen, M., Andreassen, O. A., Gruber, O., Sachdev, P. S., Roiz-Santiañez, R., Saykin, A. J., Ehrlich, S., Mather, K. A., Turner, J. A., Schwarz, E., Thalamuthu, A., Yao, Y., Ho, Y. Y. W., Martin, N. G., Wright, M. J., Guadalupe, T., Fisher, S. E., Francks, C., Schizophrenia Working Group of the Psychiatric Genomics Consortium, ENIGMA Consortium, O’Donovan, M. C., Thompson, P. M., Neale, B. M., Medland, S. E., & Sullivan, P. F. (2016). Genetic influences on schizophrenia and subcortical brain volumes: large-scale proof of concept. Nature Neuroscience, 19, 420-431. doi:10.1038/nn.4228.

    Abstract

    Schizophrenia is a devastating psychiatric illness with high heritability. Brain structure and function differ, on average, between people with schizophrenia and healthy individuals. As common genetic associations are emerging for both schizophrenia and brain imaging phenotypes, we can now use genome-wide data to investigate genetic overlap. Here we integrated results from common variant studies of schizophrenia (33,636 cases, 43,008 controls) and volumes of several (mainly subcortical) brain structures (11,840 subjects). We did not find evidence of genetic overlap between schizophrenia risk and subcortical volume measures either at the level of common variant genetic architecture or for single genetic markers. These results provide a proof of concept (albeit based on a limited set of structural brain measures) and define a roadmap for future studies investigating the genetic covariance between structural or functional brain phenotypes and risk for psychiatric disorders

    Additional information

    Franke_etal_2016_supp1.pdf
  • Gialluisi, A., Visconti, A., Wilcutt, E. G., Smith, S., Pennington, B., Falchi, M., DeFries, J., Olson, R., Francks, C., & Fisher, S. E. (2016). Investigating the effects of copy number variants on reading and language performance. Journal of Neurodevelopmental Disorders, 8: 17. doi:10.1186/s11689-016-9147-8.

    Abstract

    Background

    Reading and language skills have overlapping genetic bases, most of which are still unknown. Part of the missing heritability may be caused by copy number variants (CNVs).
    Methods

    In a dataset of children recruited for a history of reading disability (RD, also known as dyslexia) or attention deficit hyperactivity disorder (ADHD) and their siblings, we investigated the effects of CNVs on reading and language performance. First, we called CNVs with PennCNV using signal intensity data from Illumina OmniExpress arrays (~723,000 probes). Then, we computed the correlation between measures of CNV genomic burden and the first principal component (PC) score derived from several continuous reading and language traits, both before and after adjustment for performance IQ. Finally, we screened the genome, probe-by-probe, for association with the PC scores, through two complementary analyses: we tested a binary CNV state assigned for the location of each probe (i.e., CNV+ or CNV−), and we analyzed continuous probe intensity data using FamCNV.
    Results

    No significant correlation was found between measures of CNV burden and PC scores, and no genome-wide significant associations were detected in probe-by-probe screening. Nominally significant associations were detected (p~10−2–10−3) within CNTN4 (contactin 4) and CTNNA3 (catenin alpha 3). These genes encode cell adhesion molecules with a likely role in neuronal development, and they have been previously implicated in autism and other neurodevelopmental disorders. A further, targeted assessment of candidate CNV regions revealed associations with the PC score (p~0.026–0.045) within CHRNA7 (cholinergic nicotinic receptor alpha 7), which encodes a ligand-gated ion channel and has also been implicated in neurodevelopmental conditions and language impairment. FamCNV analysis detected a region of association (p~10−2–10−4) within a frequent deletion ~6 kb downstream of ZNF737 (zinc finger protein 737, uncharacterized protein), which was also observed in the association analysis using CNV calls.
    Conclusions

    These data suggest that CNVs do not underlie a substantial proportion of variance in reading and language skills. Analysis of additional, larger datasets is warranted to further assess the potential effects that we found and to increase the power to detect CNV effects on reading and language.
  • Kavaklioglu, T., Ajmal, M., Hameed, A., & Francks, C. (2016). Whole exome sequencing for handedness in a large and highly consanguineous family. Neuropsychologia, 93, part B, 342-349. doi:10.1016/j.neuropsychologia.2015.11.010.

    Abstract

    Pinpointing genes involved in non-right-handedness has the potential to clarify developmental contributions to human brain lateralization. Major-gene models have been considered for human handedness which allow for phenocopy and reduced penetrance, i.e. an imperfect correspondence between genotype and phenotype. However, a recent genome-wide association scan did not detect any common polymorphisms with substantial genetic effects. Previous linkage studies in families have also not yielded significant findings. Genetic heterogeneity and/or polygenicity are therefore indicated, but it remains possible that relatively rare, or even unique, major-genetic effects may be detectable in certain extended families with many non-right-handed members. Here we applied whole exome sequencing to 17 members from a single, large consanguineous family from Pakistan. Multipoint linkage analysis across all autosomes did not yield clear candidate genomic regions for involvement in the trait and single-point analysis of exomic variation did not yield clear candidate mutations/genes. Any genetic contribution to handedness in this unusual family is therefore likely to have a complex etiology, as at the population level.

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