Publications by authors named "Tom Berney"

7 Publications

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Psychometric properties of questionnaires and diagnostic measures for autism spectrum disorders in adults: A systematic review.

Autism 2019 02 13;23(2):287-305. Epub 2018 Feb 13.

1 Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.

Accurately diagnosing autism spectrum disorders in adulthood can be challenging. Structured questionnaires and diagnostic measures are frequently used to assist case recognition and diagnosis. This study reviewed research evidence on structured questionnaires and diagnostic measures published since the National Institute for Health and Care Excellence evidence update. The Cochrane library, Medline, Embase and PsycINFO were searched. In all, 20 studies met inclusion criteria. Sensitivity and specificity of structured questionnaires were best for individuals with previously confirmed autism spectrum disorder diagnoses and reduced in participants referred for diagnostic assessments, with discrimination of autism spectrum disorder from mental health conditions especially limited. For adults with intellectual disability, diagnostic accuracy increased when a combination of structured questionnaires were used. Evidence suggests some utility of diagnostic measures in identifying autism spectrum disorder among clinic referrals, although specificity for diagnosis was relatively low. In mental health settings, the use of a single structured questionnaire is unlikely to accurately identify adults without autism spectrum disorder or differentiate autism spectrum disorder from mental health conditions. This is important as adults seeking an autism spectrum disorder diagnostic assessment are likely to have co-existing mental health conditions. Robust autism spectrum disorder assessment tools specifically for use in adult diagnostic health services in the presence of co-occurring mental health and neurodevelopmental disorders are a research priority.
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http://dx.doi.org/10.1177/1362361317748245DOI Listing
February 2019

A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder.

Hum Genet 2012 Apr 14;131(4):565-79. Epub 2011 Oct 14.

School of Medicine and Medical Science University College, Dublin, Ireland.

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.
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http://dx.doi.org/10.1007/s00439-011-1094-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303079PMC
April 2012

Rare familial 16q21 microdeletions under a linkage peak implicate cadherin 8 (CDH8) in susceptibility to autism and learning disability.

J Med Genet 2011 Jan 23;48(1):48-54. Epub 2010 Oct 23.

Wellcome Trust Centre for Human Genetics, University of Oxford, UK.

Background: Autism spectrum disorder (ASD) is characterised by impairments in social communication and by a pattern of repetitive behaviours, with learning disability (LD) typically seen in up to 70% of cases. A recent study using the PPL statistical framework identified a novel region of genetic linkage on chromosome 16q21 that is limited to ASD families with LD.

Methods: In this study, two families with autism and/or LD are described which harbour rare >1.6 Mb microdeletions located within this linkage region. The deletion breakpoints are mapped at base-pair resolution and segregation analysis is performed using a combination of 1M single nucleotide polymorphism (SNP) technology, array comparative genomic hybridisation (CGH), long-range PCR, and Sanger sequencing. The frequency of similar genomic variants in control subjects is determined through analysis of published SNP array data. Expression of CDH8, the only gene disrupted by these microdeletions, is assessed using reverse transcriptase PCR and in situ hybridisation analysis of 9 week human embryos.

Results: The deletion of chr16: 60 025 584-61 667 839 was transmitted to three of three boys with autism and LD and none of four unaffected siblings, from their unaffected mother. In a second family, an overlapping deletion of chr16: 58 724 527-60 547 472 was transmitted to an individual with severe LD from his father with moderate LD. No copy number variations (CNVs) disrupting CDH8 were observed in 5023 controls. Expression analysis indicates that the two CDH8 isoforms are present in the developing human cortex.

Conclusion: Rare familial 16q21 microdeletions and expression analysis implicate CDH8 in susceptibility to autism and LD.
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http://dx.doi.org/10.1136/jmg.2010.079426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3003876PMC
January 2011

A genome-wide scan for common alleles affecting risk for autism.

Hum Mol Genet 2010 Oct 27;19(20):4072-82. Epub 2010 Jul 27.

Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland.

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.
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http://dx.doi.org/10.1093/hmg/ddq307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2947401PMC
October 2010

Functional impact of global rare copy number variation in autism spectrum disorders.

Nature 2010 Jul 9;466(7304):368-72. Epub 2010 Jun 9.

The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada.

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.
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http://dx.doi.org/10.1038/nature09146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3021798PMC
July 2010

The Science and Fiction of Autism.

Authors:
Tom Berney

Child Adolesc Ment Health 2007 May;12(2):102-103

University of Newcastle upon Tyne.

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http://dx.doi.org/10.1111/j.1475-3588.2007.00450_11.xDOI Listing
May 2007

Mapping autism risk loci using genetic linkage and chromosomal rearrangements.

Nat Genet 2007 Mar 18;39(3):319-28. Epub 2007 Feb 18.

Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.

Autism spectrum disorders (ASDs) are common, heritable neurodevelopmental conditions. The genetic architecture of ASDs is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASDs by using Affymetrix 10K SNP arrays and 1,181 [corrected] families with at least two affected individuals, performing the largest linkage scan to date while also analyzing copy number variation in these families. Linkage and copy number variation analyses implicate chromosome 11p12-p13 and neurexins, respectively, among other candidate loci. Neurexins team with previously implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for contributing to ASDs.
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http://dx.doi.org/10.1038/ng1985DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4867008PMC
March 2007