SCA-LSVD: A repeat-oriented locus-specific variation database for genotype to phenotype correlations in spinocerebellar ataxias

Authors

  • Mohammed Faruq,

    1. Genomics and Molecular Medicine, Institute of Genomics and Integrative Biology–Council of Scientific and Industrial Research (IGIB-CSIR), Delhi, India
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    • Mohammed Faruq and Vinod Scaria contributed equally to this work.

  • Vinod Scaria,

    1. GN Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology–Council of Scientific and Industrial Research (IGIB-CSIR), Delhi, India
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    • Mohammed Faruq and Vinod Scaria contributed equally to this work.

  • Inder Singh,

    1. Neuroscience Centre, All India Institute of Medical Sciences (AIIMS), New Delhi, India
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  • Shivani Tyagi,

    1. Genomics and Molecular Medicine, Institute of Genomics and Integrative Biology–Council of Scientific and Industrial Research (IGIB-CSIR), Delhi, India
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  • Achal K. Srivastava,

    1. Neuroscience Centre, All India Institute of Medical Sciences (AIIMS), New Delhi, India
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  • Mitali Mukerji

    Corresponding author
    1. Genomics and Molecular Medicine, Institute of Genomics and Integrative Biology–Council of Scientific and Industrial Research (IGIB-CSIR), Delhi, India
    • Genomics and Molecular medicine, Institute of Genomics and Integrative Biology, Mall Road, Delhi-110 007, India
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  • Communicated by Alastair F. Brown

Abstract

Repeat expansion has been implicated in 10 out of 17 candidate genes identified for autosomal dominant cerebellar ataxias (ADCAs)—commonly referred as spinocerebellar ataxias (SCAs). Though genetically distinct, the SCAs share a large number of features that confound their clinical classification. In addition, there is a difference in the prevalence and phenotypic expression of ataxias between different ethnic groups. We have created a new SCA-locus-specific variation database (LSVD) that aims to catalog and integrate information on SCAs associated with trinucleotide repeat expansion (SCA1, SCA 2, SCA 3, SCA 6, SCA 7, SCA 8, SCA 12, SCA 17, Friedreich's ataxia [FRDA], and dentatorubral-pallidoluysian atrophy [DRPLA]) from all over the world. The database has been developed using the Leiden Open (source) Variation Database (LOVD) software (Leiden University Medical Center, Leiden, the Netherlands). The database houses detailed information on clinical features, such as age and symptom at onset, mode of inheritance, and genotype information, pertaining to the SCA patients from more than 400 families across India. All the compiled genotype data conforms to the HGVS Nomenclature guidelines. This would be a very useful starting point for understanding the molecular correlates of phenotypes in ataxia—a multilocus disease in which related molecular mechanisms converge to overlapping phenotypes. The database is accessible online at http://miracle.igib.res.in/ataxia. Hum Mutat 30:1–6, 2009. © 2009 Wiley-Liss, Inc.

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