Database for Parkinson Disease Mutations and Rare Variants
Technical Report,01 Jul 2014,30 Jun 2016
University of Miami Coral Gables United States
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Massive parallel sequencing MPS allows for fast, high-throughput detection of rare variants, greatly increasing the research fields potential to study the common disease, rare variant hypothesis in complex disorders. For Parkinson Disease PD specifically, the variant databases currently available are incomplete, dont assess impact andor are not equipped to deal with massive parallel sequencing data. In this proposal, we set out to create a user-friendly database providing assessment of potential relevance of variants to PD through a ranking score and easy access to summary data of MPS datasets. We combine all information available on sequence variants identified in PD patients, from literature, publically available MPS datasets and MPS datasets from collaborators. Sequence variants are ranked in each of three evidence levels genetic and functional evidence from literature and evidence from in-silico analyses performed in-house. Each variant will then be placed in one of six ranking score categories indicating impact to PD based on the strength of evidence from the three evidence-levels. Currently, variant positions, in-silico analyses data and ranking scores of the literature variants and two major MPS datasets Miami Udall Center and the Progressive Parkinson Biomarker Initiative whole exome sequencing projects have been uploaded to the flexible back-end structure of the database. Scripts for high-throughput analyses and data uploads to the database for future MPS datasets have been developed. All information is available through the Variant Database of Parkinson Disease VarDoPa website allowing for easy sharing of data and quick evaluation of identified sequence variants.
- Medicine and Medical Research