AutDB: A gene reference resource for autism research

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Nucleic Acids Research (Impact Factor: 9.11). 12/2008; 37(Database issue):D832-6. DOI: 10.1093/nar/gkn835
Source: PubMed


Recent advances in studies of Autism Spectrum Disorders (ASD) has uncovered many new candidate genes and continues to do so at an accelerated pace. To address the genetic complexity of ASD, we have developed AutDB (, a publicly available web-portal for on-going collection, manual annotation and visualization of genes linked to the disorder. We present a disease-driven database model in AutDB where all genes connected to ASD are collected and classified according to their genetic variation: candidates identified from genetic association studies, rare single gene mutations and genes linked to syndromic autism. Gene entries are richly annotated for their relevance to autism, along with an in-depth view of their molecular functions. The content of AutDB originates entirely from the published scientific literature and is organized to optimize its use by the research community. The main focus of this resource is to provide an up-to-date, annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder. Our model for consolidated knowledge representation in genetically complex disorders could be replicated to study other such disorders.

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Available from: Sharmila Banerjee-Basu, Oct 07, 2015
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    • "Copy-number alterations in the nephronophthisis 1 gene (NPHP1; NM_000272.3) which is located in the 2q13 region have been associated with ASD [5]-[9]. The genomic region that surrounds NPHP1 is flanked by two inverted low-copy repeats (LCRs), which include 45-kb direct repeats; therefore, deletion or duplication can easily occur in this region via non-allelic homologous recombination, which results in NPHP1 copy-number changes [10]. "
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    ABSTRACT: Autism spectrum disorder is a neurodevelopmental disorder characterized by impairments in social interactions, reduced verbal communication abilities, stereotyped repetitive behaviors, and restricted interests. It is a complex condition caused by genetic and environmental factors; the high heritability of this disorder supports the presence of a significant genetic contribution. Many studies have suggested that copy-number variants contribute to the etiology of autism spectrum disorder. Recently, copy-number variants of the nephronophthisis 1 gene have been reported in patients with autism spectrum disorder. To the best of our knowledge, only six autism spectrum disorder cases with duplications of the nephronophthisis 1 gene have been reported. These patients exhibited intellectual dysfunction, including verbal dysfunction in one patient, below-average verbal intellectual ability in one patient, and intellectual disability in four patients. In this study, we identified nephronophthisis 1 duplications in two unrelated Japanese patients with autism spectrum disorder using a high-resolution single-nucleotide polymorphism array. This report is the first to describe a nephronophthisis 1 duplication in an autism spectrum disorder patient with an average verbal intelligence quotient and an average performance intelligence quotient. However, the second autism spectrum disorder patient with a nephronophthisis 1 duplication had a below-average performance intelligence quotient. Neither patient exhibited physical dysfunction, motor developmental delay, or neurological abnormalities. This study supports the clinical observation of nephronophthisis 1 duplication in autism spectrum disorder cases and might contribute to our understanding of the clinical phenotype that arises from this duplication.
    Annals of General Psychiatry 08/2014; 13(1):22. DOI:10.1186/s12991-014-0022-2 · 1.40 Impact Factor
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    • "This is consistent with our unpublished observations showing decreased levels of myelin proteins in post mortem prefrontal cortex tissue in other psychiatric disorders, such as schizophrenia, bipolar and major depressive disorder. Furthermore, dysregulation of synaptic proteins may reflect alterations in synaptic density and a comparison with published data confirms the alterations of STX1A, STXBP1 and SYN2 in autism at the mRNA level [43]. In addition, SRM-MS showed an approximate 70% increase in the levels of CKB in the prefrontal cortex with a small non-significant decrease of this protein in the cerebellum. "
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    ABSTRACT: Background Autism is a neurodevelopmental disorder characterized by impaired language, communication and social skills. Although genetic studies have been carried out in this field, none of the genes identified have led to an explanation of the underlying causes. Here, we have investigated molecular alterations by proteomic profiling of post mortem brain samples from autism patients and controls. The analysis focussed on prefrontal cortex and cerebellum as previous studies have found that these two brain regions are structurally and functionally connected, and they have been implicated in autism. Methods Post mortem prefrontal cortex and cerebellum samples from autism patients and matched controls were analysed using selected reaction monitoring mass spectrometry (SRM-MS). The main objective was to identify significantly altered proteins and biological pathways and to compare these across these two brain regions. Results Targeted SRM-MS resulted in identification of altered levels of proteins related to myelination, synaptic vesicle regulation and energy metabolism. This showed decreased levels of the immature astrocyte marker vimentin in both brain regions, suggesting a decrease in astrocyte precursor cells. Also, decreased levels of proteins associated with myelination and increased synaptic and energy-related proteins were found in the prefrontal cortex, indicative of increased synaptic connectivity. Finally, opposite directional changes were found for myelination and synaptic proteins in the cerebellum. Conclusion These findings suggest altered structural and/or functional connectivity in the prefrontal cortex and cerebellum in autism patients, as shown by opposite effects on proteins involved in myelination and synaptic function. Further investigation of these findings could help to increase our understanding of the mechanisms underlying autism relating to brain connectivity, with the ultimate aim of facilitating novel therapeutic approaches.
    Molecular Autism 07/2014; 5(1):41. DOI:10.1186/2040-2392-5-41 · 5.41 Impact Factor
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    • "Accordingly, curated disease-specific databases have proven a welcome development over the past decade [17] and have been embraced by their respective research fields. Such is the case, for instance, for the AlzGene database for Alzheimer’s disease [18], AutDB for autism [19] and the T1Dbase for type-1 diabetes [20]. "
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    ABSTRACT: Inherited haemoglobinopathies are the most common monogenic diseases, with millions of carriers and patients worldwide. At present, we know several hundred disease-causing mutations on the globin gene clusters, in addition to numerous clinically important trans-acting disease modifiers encoded elsewhere and a multitude of polymorphisms with relevance for advanced diagnostic approaches. Moreover, new disease-linked variations are discovered every year that are not included in traditional and often functionally limited locus-specific databases. This paper presents IthaGenes, a new interactive database of haemoglobin variations, which stores information about genes and variations affecting haemoglobin disorders. In addition, IthaGenes organises phenotype, relevant publications and external links, while embedding the NCBI Sequence Viewer for graphical representation of each variation. Finally, IthaGenes is integrated with the companion tool IthaMaps for the display of corresponding epidemiological data on distribution maps. IthaGenes is incorporated in the ITHANET community portal and is free and publicly available at
    PLoS ONE 07/2014; 9(7):e103020. DOI:10.1371/journal.pone.0103020 · 3.23 Impact Factor
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