A key challenge in genome interpretation and precision medicine is the lack of an extensive, high quality, ethnically-diverse collection of human genomes as a reference set. A prospective disease-causing variant that appears to be “rare” based on publicly available sequence may in fact be a polymorphism in an ethnic population under-represented in public databases. Resources such as the Exome Variant Server, the 1000 Genomes Project, and the Exome Aggregation Consortium have been immensely valuable to the community, and Kaviar combines such datasets into integrated allele frequencies, but public databases have not been funded to provide broad and deep ethnic representation.
QIAGEN’s Ingenuity Variant Analysis™ genome interpretation solution has been used to interpret hundreds of thousands of ethnically diverse human sequencing samples. However, these NGS datasets are private and most are never publicly released. Labs often collect their own private allele frequency libraries, but infrastructure and incentives have historically not existed for integrating these resources into a freely-available community asset.
The Allele Frequency Community has been formed to address this interpretation need. Founding members have pooled extensive human exome- and genome-wide variant call datasets in a secure, anonymized, pooled fashion to create the largest integrated, freely-accessible, hosted community database of allele frequencies ever available. To enable this community resource to grow over time, users have the opportunity to opt-in to join the Allele Frequency Community and benefit from the extensive database, agreeing in return to allow their sequences to contribute to the database. Only anonymous, pooled allele frequencies are provided, protecting patient privacy. QIAGEN Bioinformatics agreed to host the content and make it available free of charge via its HIPAA and Safe Harbor compliant genome interpretation ecosystem, which includes QIAGEN’s Ingenuity Variant Analysis, Biomedical Genomics Workbench and QIAGEN Clinical Insight offerings.
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