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Association for Molecular Pathology Issues Guidelines to Promote Genetic Variant Data Sharing

NEW YORK — The Association for Molecular Pathology on Thursday released a series of recommendations to promote the sharing of genetic variant data through the use of public repositories.

The recommendations come as the number of SARS-CoV-2 cases surge globally due to the delta variant, although AMP did not specifically cite the variant as the reason for the new guidance.

"The sharing of data, samples, and other health information is critical for advancing healthcare," in terms of understanding the roles of genetic and genomic variation in disease, the translation of basic research to clinical practice, and the development of vaccines and therapeutics, AMP said in a newly released position statement.

Yet despite the availability of public databases such as the National Institutes of Health's ClinVar, recommendations from scientific organizations, and calls to action, "participation in data sharing among clinical laboratories continues to remain low." At the same time, a lack of population diversity in genetic research literature and commonly used variant databases has proven to be "a disservice to patients," according to AMP.

With the input of a working group, AMP said it identified a number of factors that contribute to a lab's inability or unwillingness to participate in variant data-sharing arrangements. These include insufficient resources to de-identify, standardize, and otherwise prepare data for submission to sharing entities; a desire to maintain ownership of and monetize data; a lack of confidence that in-house databases are curated; and privacy concerns.

To address these issues, AMP drafted a series of variant data-sharing recommendations aimed at different stakeholders.

For organizations, institutions, and companies, the group urges the public endorsement of database contribution, particularly with data representing the diversity of patient populations, as well as the implementation of data-sharing policies that allow lab professionals, and researchers to transfer de-identified variant and phenotypic information to publicly accessible databases.

Clinical labs should assign dedicated personnel to help link shared sequence databases with diagnostic genetic test result platforms, AMP recommends. Clinical labs should also aim to better understand the clinical relevance of variants in different populations and try to use harmonized/standardized test requisition forms for common data elements in order to streamline the data handling across databases and labs. Clinical labs should also publicly acknowledge their participation in data sharing to help normalize the practice.

Operators of public databases, meantime, should work with labs to establish convenient and practical data submission processes to reduce the burden of data sharing, and they should provide support to resource-strained labs that want to contribute, according to AMP. To help build confidence from users, database operators should apply curation processes that remove obvious data outliers, request evidence missing from original submissions, and follow up with those who provide older data in order to confirm its relevance.

AMP also sees a role for policymakers in improving variant data sharing, urging government agencies to work with clinical, academic, and public interest groups to form a standards-setting body to accelerate the harmonization of database elements. Policymakers should also consider incentives for variant data sharing such as reimbursements to offset the costs of data submission and take strides to address barriers for inclusion of underserved populations, both in public sequencing databases and in clinical test utilization including through the use of funding policy reforms.

AMP also calls for policymakers to ensure that intellectual property policies are maintained throughout the data-sharing process so that genetic testing technology development continues without affecting the needs of the broader research community. Doing so would include restricting the ownership of collected genetic information and prevent the patenting of biomarkers and their association with health status.

Lastly, AMP recommends that patients, providers, and researchers help harmonize phenotypic data collection that are essential for variant classification and explore ways in which information generated in a research setting can be more quickly translated for use in clinically focused databases. Additionally, patient groups devoted to health initiatives for underserved populations should collaborate with providers and labs to increase diversity in databases, AMP said.

"AMP is strongly committed to working collaboratively with all relevant stakeholders to meet these recommendations with the goal of establishing data sharing as the expectation and norm," the group said in its position statement. "Today, patient-level clinical data is an optional data element in variant databases."

Beyond its recommendations, AMP said that more attention needs to be placed on the interoperability between variant databases and electronic health systems so that genetic information can be better incorporated into professional practice and patient care. "The contribution of information between variant databases and electronic health systems will facilitate genetic and genomic discoveries into healthcare advances for patients," it stated, adding that it intends to update its recommendation and guidelines in the future to help achieve this goal.