Allele Frequency Community formed to significantly address need to improve the interpretation of DNA findings on disease-causing gene variants and rare diseases

A coalition of 13 leading life science and diagnostics organizations recently announced the formation of the Allele Frequency Community, a landmark initiative that is creating an extensive, high-quality and ethnically diverse collection of human genomes to address a key challenge in interpreting sequencing data for research and clinical applications. The announcement coincides with the start of the 16th annual Advances in Genome Biology and Technology (AGBT) scientific meeting in Marco Island, Florida.

The Allele Frequency Community was recently formed after the 13 organizations agreed to pool their extensive human exome- and genome-wide variant call datasets in a secure, anonymized, pooled fashion to create the most ethnically diverse, freely-accessible, hosted community database of allele frequencies available. Until now, labs often collected their own, private allele frequency libraries, but did not have the infrastructure and incentives to integrate their resources into a freely-available community asset.

Increasing participation in this community-based resource is expected to create greater value over time. In particular, the Allele Frequency Community has the potential to create increasing value for life sciences and clinical research since information on observed allele frequencies can create important benchmarks that significantly increase the accuracy of findings from data generated by molecular analyses, such as Next-Generation Sequencing (NGS).

To enable this resource to grow, users have the opportunity to opt-in to join the Allele Frequency Community and benefit from the extensive database, agreeing in return to contribute statistics from their sequences to the database. Only anonymous, pooled allele frequencies are provided, protecting patient privacy.

The Allele Frequency Community database already holds more than 70,000 variant call datasets including 8,000 whole genomes and has been shown in internal benchmarking studies to generate a 43% average reduction in false positive rates in causal variant identification.

The founding collaborators of the Allele Frequency Community are:

QIAGEN N.V. is one of the founding collaborators of the Allele Frequency Community, and is providing bioinformatics infrastructure and software for the development of this community-based resource.

Over the last few years, access to allele frequency data from large populations has been the most useful resource for the interpretation of human variation, said Dr. Heidi Rehm, Ph.D., Director of the Laboratory for Molecular Medicine at Partners Healthcare Personalized Medicine. The Allele Frequency Community is a really valuable project. I am happy to share data through this new resource and excited that many other people have agreed to do so as well.

An allele is an alternative form of a gene found in a persons DNA. Scientists need diverse, large-scale data on allele frequencies to accurately identify potential disease-causing DNA changes in a population. Information on allele frequency also tells clinicians how common certain changes are within the population, helping to distinguish rare, disease-causing DNA changes from more common variations. A key challenge has been the lack of extensive collections of human genomes as a reference set. A prospective disease-causing variant that appears to be rare based on publicly available data may in fact be more prevalent in an ethnic population under-represented in public databases.

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QIAGEN Collaborates With Allele Frequency Community To Advance Translational Medicine And Clinical Diagnostics