QIAGEN Collaborates with Allele Frequency Community

A coalition of 13 leading life science and diagnostics organizations today 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 (www.allelefrequencycommunity.org) 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:

• David Goldstein, Columbia University Institute for Genomic Medicine
• Madhuri Hegde, Emory Genetics Laboratory
• Peter van der Spek, Erasmus University Medical Center
• Eric Schadt, Icahn Institute for Genomics and Multiscale Biology at Mount Sinai
• Gustavo Glusman, The Institute for Systems Biology
• Greg Eley & Joe Volckley,Inova Translational Medicine Institute
• Tom Kaminski &Stan LetovsEnlighten Health Genomics, a business of Laboratory Corporation of America® Holdings (LabCorp®)
• Nathan Pearson, New York Genome Center
• Heidi Rehm, Partners Healthcare Personalized Medicine
• Doug Bassett, QIAGEN Bioinformatics
• Phil Hieter, University of British Columbia
• Jay Shendure, University of Washington
• Chris Mason, Weill Cornell Medical College

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 person’s 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.

“The Allele Frequency Community database is more than just a simple repository; it is a dynamic resource that has been designed to grow and become more informative through more use by members of the community,” said Dr. John Niederhuber, M.D., Chief Executive Officer at Inova Translational Medicine Institute. “Large-scale datasets of diverse allele frequency data are critical to advancing personalized medicine, and Inova is pleased to support this important global collaboration. By taking advantage of anonymized pooled data, this project will support patients and clinicians who have struggled to identify the elusive genetic changes that are necessary to diagnose and treat complex diseases.”

The data of the Allele Frequency Community is stored on QIAGEN’s secure, HIPAA and Safe Harbor compliant IT infrastructure and made available for free to registered community members. Researchers can initially explore the data using QIAGEN’s Ingenuity® Variant Analysis™. The data is planned to be accessible via other analysis and data interpretation tools in the future, including QIAGEN’s Ingenuity Clinical decision-support solution currently in development as well as CLC Cancer Research Workbench, CLC Genomics Workbench and other bioinformatics solutions.

“The currently available public allele frequency data does not have the diverse coverage needed for disease research and clinical interpretation. The Allele Frequency Community aims to address this important challenge by encouraging the broad sharing and utility of this information in a privacy-protected way for the benefit of patients,” said Dr. Doug Bassett, Vice President Translational Research & Chief Scientific Officer at QIAGEN Bioinformatics. “QIAGEN is pleased to sponsor this important project, and we look forward to working closely with the Allele Frequency Community to address the pressing need for high-quality, diverse allele frequency information, which is vital to realizing the full potential of personalized healthcare.”

Dr. Bassett will present details on the participation of QIAGEN in the Allele Frequency Community in a seminar at the Advances in Genome Biology and Technology (AGBT) meeting in Marco Island, Florida. AGBT attendees can also participate in a demonstration session on February 26 at 5:15 p.m. Eastern Time.