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h1: Mining shared evidence documents and data for variants
p: The shift from genetic testing of individual genes to exome and genome sequencing has been accompanied by new challenges in genome interpretation. The American College of Medical Genetics and Genomics and the Association for Molecular Pathology have published Standards and Guidelines for the Interpretation of Sequence Variants. To enable wide application of these and related standards and the development of collective knowledge by the community, ClinGen has developed ClinGen Pathogenicity Calculator. ClinGen Pathogenicity Calculator enables evaluation of pathogenicity according to the ACMG/ACP Guidelines. Pathogenicity Calculator also allows easy storing and sharing of collected evidence and generated assertions. </br> </br>
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h1: Data-linking and Pathogenicity Calculator
p: Several evidence of allele being benign or pathogenic, can be generated automatically. This can be based on computational methods as well as mining public resources like Exome Aggregation Consortium, ClinVar, Leiden Open Variation Database (LOVD), myvariant.info. However, these resources store data as a function of different identifiers/different representation of alleles. With the help of allele registry, three key resources providing evidence for pathogenicity of variants were linked: ClinVar ClinVar, ExAC and myvariant.info. Data from ExAC and myvariant.info where converted to ACMG based evidence tags (BA1, PM3, PP3, BP4), while the ClinVar data is displayed in visually intuitive manner in the Pathogenicity Calculator. The tags are supported using the links to original resources. The publicly accessible version of calculator also hosts evidence generated from CSER bake off experiment. <br><br>
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h1: What is there in public resources?
p: Currently, the data-linking efforts were undertaken for ACMG 56 genes and auto-generated evidence tags are accessible through publicly accessible version of the Pathogenicity Calculator. For en example variant click here. Currently the Pathogenicity Calculator hosts data for 54,236 documents with at least one ACMG evidence tag and 34,931 ClinVar records for ACMG 56 genes. Although the database contains most data from these resoruces not all data is accessible through Pathogenicity Calculator <br><br>
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