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Browsing by Author "Anney, R.J."

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  • CNVs leading to fusion transcripts in individuals with autism spectrum disorder
    Publication . 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.
    2012-05-02Journal article Restricted access Show more
  • Gene-ontology enrichment analysis in two independent family-based samples highlights biologically plausible processes for autism spectrum disorders
    Publication . 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.
    2011-04-27Journal article Restricted access Show more
  • Oxytocin receptor (OXTR) does not play a major role in the aetiology of autism: genetic and molecular studies
    Publication . Tansey, K.E.; Brookes, K.J.; Hill, M.J.; Cochrane, L.E.; Gill, M.; Skuse, D.; Correia, C.; Vicente, A.M.; Kent, L.; Gallagher, L.; Anney, R.J.
    Oxytocin (OXT) has been hypothesized to play a role in aetiology of autism based on a demonstrated involvement in the regulation of social behaviours. It is postulated that OXT reduces activation of the amygdala, inhibiting social anxiety, indicating a neural mechanism for the effects of OXT in social cognition. Genetic variation at the oxytocin receptor gene (OXTR) has been reported to be associated with autism. We examined 18 SNPs at the OXTR gene for association in three independent autism samples from Ireland, Portugal and the United Kingdom. We investigated cis-acting genetic effects on OXTR expression in lymphocytes and amygdala region of the brain using an allelic expression imbalance (AEI) assay and by investigating the correlation between RNA levels and genotype in the amygdala region. No marker survived multiple correction for association with autism in any sample or in a combined sample (n=436). Results from the AEI assay performed in the lymphoblast cell lines highlighted two SNPs associated with relative allelic abundance in OXTR (rs237897 and rs237895). Two SNPs were found to be effecting cis-acting variation through AEI in the amygdala. One was weakly correlated with total gene expression (rs13316193) and the other was highlighted in the lymphoblast cell lines (rs237895). Data presented here does not support the role of common genetic variation in OXTR in the aetiology of autism spectrum disorders in Caucasian samples.
    2010-05-03Journal article Restricted access Show more
  • The Autism Simplex Collection: an international, expertly phenotyped autism sample for genetic and phenotypic analyses
    Publication . Buxbaum, J.D.; Bolshakova, N.; Brownfeld, J.M.; Anney, R.J.; Bender, P.; Bernier, R.; Cook, E.H.; Coon, H.; Cuccaro, M.; Freitag, C.M.; Hallmayer, J.; Geschwind, D; Klauck, S.M.; Nurnberger, J.I.; Oliveira, G.; Pinto, D.; Poustka, F.; Scherer, W.S.; Shih, A.; Sutcliffe, J.S.; Szatmari, P.; Vicente, A.M.; Vieland, V.; Gallagher, L.
    BACKGROUND: There is an urgent need for expanding and enhancing autism spectrum disorder (ASD) samples, in order to better understand causes of ASD. METHODS: In a unique public-private partnership, 13 sites with extensive experience in both the assessment and diagnosis of ASD embarked on an ambitious, 2-year program to collect samples for genetic and phenotypic research and begin analyses on these samples. The program was called The Autism Simplex Collection (TASC). TASC sample collection began in 2008 and was completed in 2010, and included nine sites from North America and four sites from Western Europe, as well as a centralized Data Coordinating Center. RESULTS: Over 1,700 trios are part of this collection, with DNA from transformed cells now available through the National Institute of Mental Health (NIMH). Autism Diagnostic Interview-Revised (ADI-R) and Autism Diagnostic Observation Schedule-Generic (ADOS-G) measures are available for all probands, as are standardized IQ measures, Vineland Adaptive Behavioral Scales (VABS), the Social Responsiveness Scale (SRS), Peabody Picture Vocabulary Test (PPVT), and physical measures (height, weight, and head circumference). At almost every site, additional phenotypic measures were collected, including the Broad Autism Phenotype Questionnaire (BAPQ) and Repetitive Behavior Scale-Revised (RBS-R), as well as the non-word repetition scale, Communication Checklist (Children's or Adult), and Aberrant Behavior Checklist (ABC). Moreover, for nearly 1,000 trios, the Autism Genome Project Consortium (AGP) has carried out Illumina 1 M SNP genotyping and called copy number variation (CNV) in the samples, with data being made available through the National Institutes of Health (NIH). Whole exome sequencing (WES) has been carried out in over 500 probands, together with ancestry matched controls, and this data is also available through the NIH. Additional WES is being carried out by the Autism Sequencing Consortium (ASC), where the focus is on sequencing complete trios. ASC sequencing for the first 1,000 samples (all from whole-blood DNA) is complete and data will be released in 2014. Data is being made available through NIH databases (database of Genotypes and Phenotypes (dbGaP) and National Database for Autism Research (NDAR)) with DNA released in Dist 11.0. Primary funding for the collection, genotyping, sequencing and distribution of TASC samples was provided by Autism Speaks and the NIH, including the National Institute of Mental Health (NIMH) and the National Human Genetics Research Institute (NHGRI). CONCLUSIONS: TASC represents an important sample set that leverages expert sites. Similar approaches, leveraging expert sites and ongoing studies, represent an important path towards further enhancing available ASD samples.
    2014-05-20Journal article Open access Show more