Abstract
BackgroundTo date, 35 human diseases, some of which also exhibit anticipation, have been associated with unstable repeats. Anticipation has been reported in a number of diseases in which repeat expansion may have a role in etiology. Despite the growing importance of unstable repeats in disease, currently no resource exists for the prioritization of repeats. Here we present Satellog, a database that catalogs all pure 1–16 repeat unit satellite repeats in the human genome along with supplementary data. Satellog analyzes each pure repeat in UniGene clusters for evidence of repeat polymorphism.ResultsA total of 5,546 such repeats were identified, providing the first indication of many novel polymorphic sites in the genome. Overall, polymorphic repeats were over-represented within 3'-UTR sequence relative to 5'-UTR and coding sequence. Interestingly, we observed that repeat polymorphism within coding sequence is restricted to trinucleotide repeats whereas UTR sequence tolerated a wider range of repeat period polymorphisms. For each pure repeat we also calculate its repeat length percentile rank, its location either within or adjacent to EnsEMBL genes, and its expression profile in normal tissues according to the GeneNote database.ConclusionSatellog provides the ability to dynamically prioritize repeats based on any of their characteristics (i.e. repeat unit, class, period, length, repeat length percentile rank, genomic co-ordinates), polymorphism profile within UniGene, proximity to or presence within gene regions (i.e. cds, UTR, 15 kb upstream etc.), metadata of the genes they are detected within and gene expression profiles within normal human tissues. Unstable repeats associated with 31 diseases were analyzed in Satellog to evaluate their common repeat properties. The utility of Satellog was highlighted by prioritizing repeats for Huntington's disease and schizophrenia. Satellog is available online at .
Highlights
To date, 35 human diseases, some of which exhibit anticipation, have been associated with unstable repeats
For each pure repeat Satellog can calculate the percentile rank of its length relative to other repeats of the same class in the genome, its polymorphism within UniGene clusters [40], its location relative to known genes [41], and its expression profile in normal tissues according to the GeneNote database [42]
Summary statistics A total of 8,357,425 pure repeats were detected by Tandem Repeats Finder (TRF) in the human genome and were stored in Satellog
Summary
35 human diseases, some of which exhibit anticipation, have been associated with unstable repeats. CAG-type expansion disorders include spinal and bulbar muscular atrophy (SBMA) [4], dentatorubral-pallidoluysian atrophy (DRPLA) [6], Huntington disease (HD) [7] and a range of spinocerebellar ataxias (SCAs) including SCA1 [8], SCA2 [9], SCA3 [10], SCA6 [11], and SCA7 [12] In these diseases, an expanded poly-glutamine tract results in a toxic gain of function causing either neuronal degeneration [13], or in mouse models of spinocerebellar ataxia (SCA), neuronal dysfunction due to Purkinje cell abnormalities [14]. Neuronal inclusion bodies are observable on autopsy [14]
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