Percorrer por autor "Holt, R."
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- CNVs leading to fusion transcripts in individuals with autism spectrum disorderPublication . Holt, R.; Sykes, N.H.; Conceição, I.C.; Cazier, J.B.; Anney, R.J.; Oliveira, G.; Gallagher, L.; Vicente, A.M.; Monaco, A.P.; Pagnamenta, A.T.There is strong evidence that rare copy number variants (CNVs) have a role in susceptibility to autism spectrum disorders (ASDs). Much research has focused on how CNVs mediate a phenotypic effect by altering gene expression levels. We investigated an alternative mechanism whereby CNVs combine the 5' and 3' ends of two genes, creating a 'fusion gene'. Any resulting mRNA with an open reading frame could potentially alter the phenotype via a gain-of-function mechanism. We examined 2382 and 3096 rare CNVs from 996 individuals with ASD and 1287 controls, respectively, for potential to generate fusion transcripts. There was no increased burden in individuals with ASD; 122/996 cases harbored at least one rare CNV of this type, compared with 179/1287 controls (P=0.89). There was also no difference in the overall frequency distribution between cases and controls. We examined specific examples of such CNVs nominated by case-control analysis and a candidate approach. Accordingly, a duplication involving REEP1-POLR1A (found in 3/996 cases and 0/1287 controls) and a single occurrence CNV involving KIAA0319-TDP2 were tested. However, no fusion transcripts were detected by RT-PCR. Analysis of additional samples based on cell line availability resulted in validation of a MAPKAPK5-ACAD10 fusion transcript in two probands. However, this variant was present in controls at a similar rate and is unlikely to influence ASD susceptibility. In summary, although we find no evidence that fusion-gene generating CNVs lead to ASD susceptibility, discovery of a MAPKAPK5-ACAD10 transcript with an estimated frequency of ∼1/200 suggests that gain-of-function mechanisms should be considered in future CNVs studies.
- Convergence of genes and cellular pathways dysregulated in autism spectrum disordersPublication . Pinto, D.; Delaby, E.; Merico, D.; Barbosa, M.; Merikangas, A.; Klei, L; Thiruvahindrapuram, B.; Xu, X.; Ziman, R.; Wang, Z.; Vorstman, J.A.; Thompson, A.; Regan, R.; Pilorge, M.; Pellecchia, G.; Pagnamenta, A.T.; Oliveira, B.; Marshall, C.R.; Magalhães, T.R.; Lowe, J.K.; Howe, J.L.; Griswold, A.J.; Gilbert, J.; Duketis, E.; Dombroski, B.A.; De Jonge, M.V.; Cuccaro, M.; Crawford, E.L.; Correia, C.T.; Conroy, J.; Conceição, I.C; Chiocchetti, A.G.; Casey, J.P.; Cai, G.; Cabrol, C.; Bolshakova, N.; Bacchelli, E.; Anney, R.; Gallinger, S.; Cotterchio, M.; Casey, G.; Zwaigenbaum, L.; Wittemeyer, K.; Wing, K.; Wallace, S.; van Engeland, H.; Tryfon, A.; Thomson, S.; Soorya, L.; Rogé, B.; Roberts, W.; Poustka, F.; Mouga, S.; Minshew, N.; McInnes, L.A.; McGrew, S.G.; Lord, C.; Leboyer, M.; Le Couteur, A.S.; Kolevzon, A.; Jiménez González, P.; Jacob, S.; Holt, R.; Guter, S.; Green, J.; Green, A.; Gillberg, C.; Fernandez, B.A.; Duque, F.; Delorme, R.; Dawson, G.; Chaste, P.; Café, C.; Brennan, S.; Bourgeron, T.; Bolton, P.F.; Bölte, S.; Bernier, R.; Baird, G.; Bailey, A.J.; Anagnostou, E.; Almeida, J.; Wijsman, E.M.; Vieland, V.J.; Vicente, A.M.; Schellenberg, G.D.; Pericak-Vance, M.; Paterson, A.D.; Parr, J.R.; Oliveira, G.; Nurnberger, J.I.; Monaco, A.P.; Maestrini, E.; Klauck, S.M.; Hakonarson, H.; Haines, J.L.; Geschwind, D.H.; Freitag, C.M.; Folstein, S.E.; Ennis, S.; Coon, H.; Battaglia, A.; Szatmari, P.; Sutcliffe, J.S.; Hallmayer, J.; Gill, M.; Cook, E.H.; Buxbaum, J.D.; Devlin, B.; Gallagher, L.; Betancur, C.Rare copy-number variation (CNV) is an important source of risk for autism spectrum disorders (ASDs). We analyzed 2,446 ASD-affected families and confirmed an excess of genic deletions and duplications in affected versus control groups (1.41-fold, p = 1.0 × 10(-5)) and an increase in affected subjects carrying exonic pathogenic CNVs overlapping known loci associated with dominant or X-linked ASD and intellectual disability (odds ratio = 12.62, p = 2.7 × 10(-15), ∼3% of ASD subjects). Pathogenic CNVs, often showing variable expressivity, included rare de novo and inherited events at 36 loci, implicating ASD-associated genes (CHD2, HDAC4, and GDI1) previously linked to other neurodevelopmental disorders, as well as other genes such as SETD5, MIR137, and HDAC9. Consistent with hypothesized gender-specific modulators, females with ASD were more likely to have highly penetrant CNVs (p = 0.017) and were also overrepresented among subjects with fragile X syndrome protein targets (p = 0.02). Genes affected by de novo CNVs and/or loss-of-function single-nucleotide variants converged on networks related to neuronal signaling and development, synapse function, and chromatin regulation.
- Functional impact of global rare copy number variation in autism spectrum disordersPublication . Pinto, D.; Pagnamenta, A.T.; Klei, L.; Anney, R.; Merico, D.; Regan, R.; Conroy, J.; Magalhaes, T.R.; Correia, C.; Abrahams, B.S.; Almeida, J.; Bacchelli, E.; Bader, G.D.; Bailey, A.J.; Baird, G.; Battaglia, A.; Berney, T.; Bolshakova, N.; Bölte, S.; Bolton, P.F.; Bourgeron, T.; Brennan, S.; Brian, J.; Bryson, S.E.; Carson, A.R.; Casallo, G.; Casey, J.; Chung, B.H.; Cochrane, L.; Corsello, C.; Crawford, E.L.; Crossett, A.; Cytrynbaum, C.; Dawson, G.; de Jonge, M.; Delorme, R.; Drmic, I.; Duketis, E.; Duque, F.; Estes, A.; Farrar, P.; Fernandez, B.A.; Folstein, S.E.; Fombonne, E.; Freitag, C.M.; Gilbert, J.; Gillberg, C.; Glessner, J.T.; Goldberg, J.; Green, A.; Green, J.; Guter, S.J.; Hakonarson, H.; Heron, E.A.; Hill, M.; Holt, R.; Howe, J.L.; Hughes, G.; Hus, V.; Igliozzi, R.; Kim, C.; Klauck, S.M.; Kolevzon, A.; Korvatska, O.; Kustanovich, V.; Lajonchere, C.M.; Lamb, J.A.; Laskawiec, M.; Leboyer, M.; Le Couteur, A.; Leventhal, B.L.; Lionel, A.C.; Liu, X.Q.; Lord, C.; Lotspeich, L.; Lund, S.C.; Maestrini, E.; Mahoney, W.; Mantoulan, C.; Marshall, C.R.; McConachie, H.; McDougle, C.J.; McGrath, J.; McMahon, W.M.; Merikangas, A.; Migita, O.; Minshew, N.J.; Mirza, G.K.; Munson, J.; Nelson, S.F.; Noakes, C.; Noor, A.; Nygren, G.; Oliveira, G.; Papanikolaou, K.; Parr, J.R.; Parrini, B.; Paton, T.; Pickles, A.; Pilorge, M.; Piven, J.; Ponting, C.P.; Posey, D.J.; Poustka, A.; Poustka, F.; Prasad, A.; Ragoussis, J.; Renshaw, K.; Rickaby, J.; Roberts, W.; Roeder, K.; Roge, B.; Rutter, M.L.; Bierut, L.J.; Rice, J.P.; Salt, J.; Sansom, K.; Sato, D.; Segurado, R.; Sequeira, A.F.; Senman, L.; Shah, N.; Sheffield, V.C.; Soorya, L.; Sousa, I.; Stein, O.; Sykes, N.; Stoppioni, V.; Strawbridge, C.; Tancredi, R.; Tansey, K.; Thiruvahindrapduram, B.; Thompson, A.P.; Thomson, S.; Tryfon, A.; Tsiantis, J.; Van Engeland, H.; Vincent, J.B.; Volkmar, F.; Wallace, S.; Wang, K.; Wang, Z.; Wassink, T.H.; Webber, C.; Weksberg, R.; Wing, K.; Wittemeyer, K.; Wood, S.; Wu, J.; Yaspan, B.L.; Zurawiecki, D.; Zwaigenbaum, L.; Buxbaum, J.D.; Cantor, R.M.; Cook, E.H.; Coon, H.; Cuccaro, M.L.; Devlin, B.; Ennis, S.; Gallagher, L.; Geschwind, D.H.; Gill, M.; Haines, J.L.; Hallmayer, J.; Miller, J.; Monaco, A.P.; Nurnberger Jr, J.I.; Paterson, A.D.; Pericak-Vance, M.A.; Schellenberg, G.D.; Szatmari, P.; Vicente, A.M.; Vieland, V.J.; Wijsman, E.M.; Scherer, S.W.; Sutcliffe, J.S.; Betancur, C.The autism spectrum disorders (ASDs) are a group of conditions characterized by impairments in reciprocal social interaction and communication, and the presence of restricted and repetitive behaviours. Individuals with an ASD vary greatly in cognitive development, which can range from above average to intellectual disability. Although ASDs are known to be highly heritable ( approximately 90%), the underlying genetic determinants are still largely unknown. Here we analysed the genome-wide characteristics of rare (<1% frequency) copy number variation in ASD using dense genotyping arrays. When comparing 996 ASD individuals of European ancestry to 1,287 matched controls, cases were found to carry a higher global burden of rare, genic copy number variants (CNVs) (1.19 fold, P = 0.012), especially so for loci previously implicated in either ASD and/or intellectual disability (1.69 fold, P = 3.4 x 10(-4)). Among the CNVs there were numerous de novo and inherited events, sometimes in combination in a given family, implicating many novel ASD genes such as SHANK2, SYNGAP1, DLGAP2 and the X-linked DDX53-PTCHD1 locus. We also discovered an enrichment of CNVs disrupting functional gene sets involved in cellular proliferation, projection and motility, and GTPase/Ras signalling. Our results reveal many new genetic and functional targets in ASD that may lead to final connected pathways.
- Gene-ontology enrichment analysis in two independent family-based samples highlights biologically plausible processes for autism spectrum disordersPublication . Anney, R.J.; Kenny, E.M.; O'Dushlaine, C.; Parkhomenka, E.; Buxbaum, J.D.; Sutcliffe, J.; Gill, M.; Gallagher, L.; Bailey, A.J.; Fernandez, B.A.; Szatmari, P.; Nurnberger Jr, J.I.; McDougle, C.J.; Posey, D.J.; Lord, C.; Corsello, C.; Hus, V.; Buxbaum, J.D.; Kolevzon, A.; Soorya, L.; Parkhomenko, E.; Scherer, S.W.; Leventhal, B.L.; Dawson, G.; Vieland, V.J.; Hakonarson, H.; Glessner, J.T.; Kim, C.; Wang, K.; Schellenberg, G.D.; Devlin, B.; Klei, L.; Patterson, A.; Minshew, N.; Sutcliffe, J.S.; Haines, J.L.; Lund, S.C.; Thomson, S.; Yaspan, B.L.; Coon, H.; Miller, J.; McMahon, W.M.; Munson, J.; Marshall, C.R.; Estes, A.; Wijsman, EM.; The Autism Genome Project; Pinto, D.; Vincent, J.B.; Fombonne, E.; Betancur, C.; Delorme, R.; Leboyer, M.; Bourgeron, T.; Mantoulan, C.; Roge, B.; Tauber, M.; Freitag, C.M.; Poustka, F.; Duketis, E.; Klauck, S.M.; Poustka, A.; Papanikolaou, K.; Tsiantis, J.; Gallagher, L.; Gill, M.; Anney, R.; Bolshakova, N.; Brennan, S.; Hughes, G.; McGrath, J.; Merikangas, A.; Ennis, S.; Green, A.; Casey, J.P.; Conroy, J.M.; Regan, R.; Shah, N.; Maestrini, E.; Bacchelli, E.; Minopoli, F.; Stoppioni, V.; Battaglia, A.; Igliozzi, R.; Parrini, B.; Tancredi, R.; Oliveira, G.; Almeida, J.; Duque, F.; Vicente, A.M.; Correia, C.; Magalhaes, T.R.; Gillberg, C.; Nygren, G.; Jonge, M.D.; Van Engeland, H.; Vorstman, J.A.; Wittemeyer, K.; Baird, G.; Bolton, P.F; Rutter, M.L.; Green, J.; Lamb, J.A.; Pickles, A.; Parr, J.R.; Couteur, A.L.; Berney, T.; McConachie, H.; Wallace, S.; Coutanche, M.; Foley, S.; White, K.; Monaco, A.P.; Holt, R.; Farrar, P.; Pagnamenta, A.T.; Mirza, G.K.; Ragoussis, J.; Sousa, I.; Sykes, N.; Wing, K.; Hallmayer, J.; Cantor, R.M.; Nelson, S.F.; Geschwind, D.H.; Abrahams, B.S.; Volkmar, F.; Pericak-Vance, M.A.; Cuccaro, M.L.; Gilbert, J.; Cook, E.H.; Guter, S.J.; Jacob, S.Recent genome-wide association studies (GWAS) have implicated a range of genes from discrete biological pathways in the aetiology of autism. However, despite the strong influence of genetic factors, association studies have yet to identify statistically robust, replicated major effect genes or SNPs. We apply the principle of the SNP ratio test methodology described by O'Dushlaine et al to over 2100 families from the Autism Genome Project (AGP). Using a two-stage design we examine association enrichment in 5955 unique gene-ontology classifications across four groupings based on two phenotypic and two ancestral classifications. Based on estimates from simulation we identify excess of association enrichment across all analyses. We observe enrichment in association for sets of genes involved in diverse biological processes, including pyruvate metabolism, transcription factor activation, cell-signalling and cell-cycle regulation. Both genes and processes that show enrichment have previously been examined in autistic disorders and offer biologically plausibility to these findings.
- Genetic and Functional Analyses of SHANK2 Mutations Suggest a Multiple Hit Model of Autism Spectrum DisordersPublication . Leblond, C.S.; Heinrich, J.; Delorme, R.; Proepper, C.; Betancur, C.; Huguet, G.; Konyukh, M.; Chaste, P.; Ey, E.; Rastam, M.; Anckarsäter, H.; Nygren, G.; Gillberg, I.C.; Melke, J.; Toro, R.; Regnault, B.; Fauchereau, F.; Mercati, O.; Lemière, N.; Skuse, D.; Poot, M.; Holt, R.; Monaco, A.P.; Järvelä, I.; Kantojärvi, K.; Vanhala, R.; Curran, S.; Collier, D.A.; Bolton, P.; Chiocchetti, A; Klauck, S.M.; Poustka, F.; Freitag, C.M.; Waltes, R.; Kopp, M.; Duketis, E.; Bacchelli, E.; Minopoli, F.; Ruta, L.; Battaglia, A.; Mazzone, L.; Maestrini, E.; Sequeira, A.F.; Oliveira, B.; Vicente, A.M.; Oliveira, G.; Pinto, D.; Scherer, S.W.; Zelenika, D.; Delepine, M.; Lathrop, M.; Bonneau, D.; Guinchat, V.; Devillard, F.; Assouline, B.; Mouren, M.C.; Leboyer, M.; Gillberg, C.; Boeckers, T.M.Autism spectrum disorders (ASD) are a heterogeneous group of neurodevelopmental disorders with a complex inheritance pattern. While many rare variants in synaptic proteins have been identified in patients with ASD, little is known about their effects at the synapse and their interactions with other genetic variations. Here, following the discovery of two de novo SHANK2 deletions by the Autism Genome Project, we identified a novel 421 kb de novo SHANK2 deletion in a patient with autism. We then sequenced SHANK2 in 455 patients with ASD and 431 controls and integrated these results with those reported by Berkel et al. 2010 (n = 396 patients and n = 659 controls). We observed a significant enrichment of variants affecting conserved amino acids in 29 of 851 (3.4%) patients and in 16 of 1,090 (1.5%) controls (P = 0.004, OR = 2.37, 95% CI = 1.23-4.70). In neuronal cell cultures, the variants identified in patients were associated with a reduced synaptic density at dendrites compared to the variants only detected in controls (P = 0.0013). Interestingly, the three patients with de novo SHANK2 deletions also carried inherited CNVs at 15q11-q13 previously associated with neuropsychiatric disorders. In two cases, the nicotinic receptor CHRNA7 was duplicated and in one case the synaptic translation repressor CYFIP1 was deleted. These results strengthen the role of synaptic gene dysfunction in ASD but also highlight the presence of putative modifier genes, which is in keeping with the "multiple hit model" for ASD. A better knowledge of these genetic interactions will be necessary to understand the complex inheritance pattern of ASD.
- A genome-wide scan for common alleles affecting risk for autismPublication . Anney, R.; Klei, L.; Pinto, D.; Regan, R.; Conroy, J.; Magalhaes, T.R.; Correia, C.; Abrahams, B.S.; Sykes, N.; Pagnamenta, A.T.; Almeida, J.; Bacchelli, E.; Bailey, A.J.; Baird, G.; Battaglia, A.; Berney, T.; Bolshakova, N.; Bölte, S.; Bolton, P.F.; Bourgeron, T.; Brennan, S.; Brian, J.; Carson, A.R.; Casallo, G.; Casey, J.; Chu, S.H.; Cochrane, L.; Corsello, C.; Crawford, E.L.; Crossett, A.; Dawson, G.; de Jonge, M.; Delorme, R.; Drmic, I.; Duketis, E.; Duque, F.; Estes, A.; Farrar, P.; Fernandez, B.A.; Folstein, S.E.; Fombonne, E.; Freitag, C.M.; Gilbert, J.; Gillberg, C.; Glessner, J.T.; Goldberg, J.; Green, J.; Guter, S.J.; Hakonarson, H.; Heron, E.A.; Hill, M.; Holt, R.; Howe, J.L.; Hughes, G.; Hus, V.; Igliozzi, R.; Kim, C.; Klauck, S.M.; Kolevzon, A.; Korvatska, O.; Kustanovich, V.; Lajonchere, C.M.; Lamb, J.A.; Laskawiec, M.; Leboyer, M.; Le Couteur, A.; Leventhal, B.L.; Lionel, A.C.; Liu, X.Q.; Lord, C.; Lotspeich, L.; Lund, S.C.; Maestrini, E.; Mahoney, W.; Mantoulan, C.; Marshall, C.R.; McConachie, H.; McDougle, C.J.; McGrath, J.; McMahon, W.M.; Melhem, N.M.; Merikangas, A.; Migita, O.; Minshew, N.J.; Mirza, G.K.; Munson, J.; Nelson, S.F.; Noakes, C.; Noor, A.; Nygren, G.; Oliveira, G.; Papanikolaou, K.; Parr, J.R.; Parrini, B.; Paton, T.; Pickles, A.; Piven, J.; Posey, D.J.; Poustka, A.; Poustka, F.; Prasad, A.; Ragoussis, J.; Renshaw, K.; Rickaby, J.; Roberts, W.; Roeder, K.; Roge, B.; Rutter, M.L.; Bierut, L.J.; Rice, J.P.; Salt, J.; Sansom, K.; Sato, D.; Segurado, R.; Senman, L.; Shah, N.; Sheffield, V.C.; Soorya, L.; Sousa, I.; Stoppioni, V.; Strawbridge, C.; Tancredi, R.; Tansey, K.; Thiruvahindrapduram, B.; Thompson, A.P.; Thomson, S.; Tryfon, A.; Tsiantis, J.; Van Engeland, H.; Vincent, J.B.; Volkmar, F.; Wallace, S.; Wang, K.; Wang, Z.; Wassink, T.H.; Wing, K.; Wittemeyer, K.; Wood, S.; Yaspan, B.L.; Zurawiecki, D.; Zwaigenbaum, L.; Betancur, C.; Buxbaum, J.D.; Cantor, R.M.; Cook, E.H.; Coon, H.; Cuccaro, M.L.; Gallagher, L.; Geschwind, D.H.; Gill, M.; Haines, J.L.; Miller, J.; Monaco, A.P.; Nurnberger Jr, J.I.; Paterson, A.D.; Pericak-Vance, M.A.; Schellenberg, G.D.; Scherer, S.W.; Sutcliffe, J.S.; Szatmari, P.; Vicente, A.M.; Vieland, V.J.; Wijsman, E.M.; Devlin, B.; Ennis, S.; Hallmayer, J.Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10(-8). When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10(-8) threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.
- Individual common variants exert weak effects on the risk for autism spectrum disorderspiPublication . Anney, R.; Klei, L.; Pinto, D.; Almeida, J.; Bacchelli, E.; Baird, G.; Bolshakova, N.; Bölte, S.; Bolton, P.F.; Bourgeron, T.; Brennan, S.; Brian, J.; Casey, J.; Conroy, J.; Correia, C.; Corsello, C.; Crawford, E.L.; de Jonge, M.; Delorme, R.; Duketis, E.; Duque, F.; Estes, A.; Farrar, P.; Fernandez, B.A.; Folstein, S.E.; Fombonne, E.; Gilbert, J.; Gillberg, C.; Glessner, J.T.; Green, A.; Green, J.; Guter, S.J.; Heron, E.A.; Holt, R.; Howe, J.L.; Hughes, G.; Hus, V.; Igliozzi, R.; Jacob, S.; Kenny, G.P.; Kim, C.; Kolevzon, A.; Kustanovich, V.; Lajonchere, C.M.; Lamb, J.A.; Law-Smith, M.; Leboyer, M.; Le Couteur, A.; Leventhal, B.L.; Liu, X.Q.; Lombard, F.; Lord, C.; Lotspeich, L.; Lund, S.C.; Magalhaes, T.R.; Mantoulan, C.; McDougle, C.J.; Melhem, N.M.; Merikangas, A.; Minshew, N.J.; Mirza, G.K.; Munson, J.; Noakes, C.; Nygren, G.; Papanikolaou, K.; Pagnamenta, A.T.; Parrini, B.; Paton, T.; Pickles, A.; Posey, D.J.; Poustka, F.; Ragoussis, J.; Regan, R.; Roberts, W.; Roeder, K.; Roge, B.; Rutter, M.L.; Schlitt, S.; Shah, N.; Sheffield, V.C.; Soorya, L.; Sousa, I.; Stoppioni, V.; Sykes, N.; Tancredi, R.; Thompson, A.P.; Thomson, S.; Tryfon, A.; Tsiantis, J.; Van Engeland, H.; Vincent, J.B.; Volkmar, F.; Vorstman, J.; Wallace, S.; Wing, K.; Wittemeyer, K.; Wood, S.; Zurawiecki, D.; Zwaigenbaum, L.; Bailey, AJ; Battaglia, A.; Cantor, R.M.; Coon, H.; Cuccaro, M.L.; Dawson, G.; Ennis, S.; Freitag, C.M.; Geschwind, D.H.; Haines, J.L.; Klauck, S.M.; McMahon, W.M.; Maestrini, E.; Miller, J.; Monaco, A.P.; Nelson, S.F.; Nurnberger Jr, J.I.; Oliveira, G.; Parr, J.R.; Pericak-Vance, M.A.; Piven, J.; Schellenberg, G.D.; Scherer, S.W.; Vicente, A.M.; Wassink, T.H.; Wijsman, E.M.; Betancur, C.; Buxbaum, J.D.; Cook, E.H.; Gallagher, L.; Gill, M.; Hallmayer, J.; Paterson, A.D.; Sutcliffe, J.S.; Szatmari, P.; Vieland, V.J.; Hakonarson, H.; Devlin, B.While it is apparent that rare variation can play an important role in the genetic architecture of autism spectrum disorders (ASDs), the contribution of common variation to the risk of developing ASD is less clear. To produce a more comprehensive picture, we report Stage 2 of the Autism Genome Project genome-wide association study, adding 1301 ASD families and bringing the total to 2705 families analysed (Stages 1 and 2). In addition to evaluating the association of individual single nucleotide polymorphisms (SNPs), we also sought evidence that common variants, en masse, might affect the risk. Despite genotyping over a million SNPs covering the genome, no single SNP shows significant association with ASD or selected phenotypes at a genome-wide level. The SNP that achieves the smallest P-value from secondary analyses is rs1718101. It falls in CNTNAP2, a gene previously implicated in susceptibility for ASD. This SNP also shows modest association with age of word/phrase acquisition in ASD subjects, of interest because features of language development are also associated with other variation in CNTNAP2. In contrast, allele scores derived from the transmission of common alleles to Stage 1 cases significantly predict case status in the independent Stage 2 sample. Despite being significant, the variance explained by these allele scores was small (Vm< 1%). Based on results from individual SNPs and their en masse effect on risk, as inferred from the allele score results, it is reasonable to conclude that common variants affect the risk for ASD but their individual effects are modest.
- A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorderPublication . Casey, J.P.; Magalhaes, T.; Conroy, J.M.; Regan, R.; Shah, N.; Anney, R.; Shields, D.C.; Abrahams, B.S.; Almeida, J.; Bacchelli, E.; Bailey, A.J.; Piven, J.; Posey, D.J.; Poustka, A.; Poustka, F.; Ragoussis, J.; Roge, B.; Rutter, M.L.; Sequeira, A.F.; Soorya, L.; Sousa, I.; Wittemeyer, K.; Sykes, N.; Stoppioni, V.; Tancredi, R.; Tauber, M.; Thompson, A.P.; Thomson, S.; Tsiantis, J.; Van Engeland, H.; Vincent, J.B.; Volkmar, F.; Yaspan, B.L.; Vorstman, J.A.; Wallace, S.; Wang, K.; Wassink, T.H.; White, K.; Wing, K.; Zwaigenbaum, L.; Betancur, C.; Buxbaum, J.D.; Cantor, R.M.; Cook, E.H.; Coon, H.; Cuccaro, M.L.; Geschwind, D.H.; Baird, G.; Haines, J.L.; Hallmayer, J.; Monaco, A.P.; Nurnberger, J.I. Jr; Pericak-Vance, M.A.; Schellenberg, G.D.; Scherer, S.W.; Sutcliffe, J.S.; Szatmari, P.; Vieland, V.J.; Battaglia, A.; Wijsman, E.M.; Green, A.; Gill, M.; Gallagher, L.; Vicente, A.M.; Ennis, S.; Berney, T.; Bolshakova, N.; Bolton, P.F.; Bourgeron, T.; Brennan, S.; Cali, P.; Correia, C.; Corsello, C.; Coutanche, M.; Dawson, G.; de Jonge, M.; Delorme, R.; Duketis, E.; Duque, F.; Estes, A.; Farrar, P.; Fernandez, B.A.; Folstein, S.E.; Foley, S.; Fombonne, E.; Freitag, C.M.; Gilbert, J.; Gillberg, C.; Glessner, J.T.; Green, J.; Guter, S.J.; Hakonarson, H.; Holt, R.; Hughes, G.; Hus, V.; Igliozzi, R.; Kim, C.; Klauck, S.M.; Kolevzon, A.; Lamb, J.A.; Leboyer, M.; Le Couteur, A.; Leventhal, B.L.; Lord, C.; Lund, S.C.; Maestrini, E.; Mantoulan, C.; Marshall, C.R.; McConachie, H.; McDougle, C.J.; McGrath, J.; McMahon, W.M.; Merikangas, A.; Miller, J.; Minopoli, F.; Mirza, G.K.; Munson, J.; Nelson, S.F.; Nygren, G.; Oliveira, G.; Pagnamenta, A.T.; Papanikolaou, K.; Parr, J.R.; Parrini, B.; Pickles, A.; Pinto, D.Autism spectrum disorder (ASD) is a highly heritable disorder of complex and heterogeneous aetiology. It is primarily characterized by altered cognitive ability including impaired language and communication skills and fundamental deficits in social reciprocity. Despite some notable successes in neuropsychiatric genetics, overall, the high heritability of ASD (~90%) remains poorly explained by common genetic risk variants. However, recent studies suggest that rare genomic variation, in particular copy number variation, may account for a significant proportion of the genetic basis of ASD. We present a large scale analysis to identify candidate genes which may contain low-frequency recessive variation contributing to ASD while taking into account the potential contribution of population differences to the genetic heterogeneity of ASD. Our strategy, homozygous haplotype (HH) mapping, aims to detect homozygous segments of identical haplotype structure that are shared at a higher frequency amongst ASD patients compared to parental controls. The analysis was performed on 1,402 Autism Genome Project trios genotyped for 1 million single nucleotide polymorphisms (SNPs). We identified 25 known and 1,218 novel ASD candidate genes in the discovery analysis including CADM2, ABHD14A, CHRFAM7A, GRIK2, GRM3, EPHA3, FGF10, KCND2, PDZK1, IMMP2L and FOXP2. Furthermore, 10 of the previously reported ASD genes and 300 of the novel candidates identified in the discovery analysis were replicated in an independent sample of 1,182 trios. Our results demonstrate that regions of HH are significantly enriched for previously reported ASD candidate genes and the observed association is independent of gene size (odds ratio 2.10). Our findings highlight the applicability of HH mapping in complex disorders such as ASD and offer an alternative approach to the analysis of genome-wide association data.