The paper introduces Cat-VRS, a framework for computable representation of genomic variant categories to improve data interoperability and clinical interpretation.

bioRxiv · Apr 30, 2026 · PreprintGenomics

The Clinical Genomic Variation Landscape

Wesley Goar, Daniel Puthawala, Kori Kuzma, Anastasia Bratulin, Austin A. Antoniou, Jeremy A. Arbesfeld, Lawrence J. Babb, Kyle Ferriter, Terry O’Neill, James Stevenson, Kathryn Perry, Matthew Cannon, Jiachen Liu, Xue‐Lu Liu, Brian Walsh, , Alex Handler Wagner

The paper evaluates challenges in genomic variant representation across resources and develops normalization methods to improve clinical outcome associations.

medRxiv · Nov 4, 2025 · PreprintGenetic & Genomic Medicine

Development and application of a computable genotype model in the GA4GH Variation Representation Specification

Wesley Goar, Lawrence J. Babb, Srikar Chamala, Melissa Cline, Robert R. Freimuth, Reece K. Hart, Kori Kuzma, Jennifer Lee, Tristan H. Nelson, Andreas Prlić, Kevin P. Riehle, Anastasia L. Smith, Kathryn Stahl, Andrew D. Yates, Heidi L. Rehm, Alex Handler Wagner

The paper develops and applies a computable genotype model within the GA4GH Variation Representation Specification to enable precise and interoperable representation of genomic variation data.

Pacific Symposium on Biocomputing (PSB) · Nov 1, 2022Peer-reviewedBioinformatics

The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine

Julius O.B. Jacobsen, Michael Baudis, Gareth S Baynam, Jacques Samuel Beckmann, Sergi Beltrán, Orion J. Buske, Tiffany J. Callahan, Christopher G. Chute, Mélanie Courtot, Daniel Daniš, Olivier Elemento, Andrea Essenwanger, Robert R. Freimuth, Michael A. Gargano, Tudor Groza, , Peter N. Robinson

The paper introduces the GA4GH Phenopacket schema to standardize the exchange of phenotypic data for precision medicine applications.

Nature Biotechnology · Jun 1, 2022Peer-reviewedGenetic & Genomic Medicine

The Gene Curation Coalition: A global effort to harmonize gene-disease evidence resources

Marina T. DiStefano, Scott R. Goehringer, Lawrence J. Babb, Fowzan Sami Alkuraya, Joanna S. Amberger, Mutaz Amin, Christina Anne Austin-Tse, Marie Balzotti, Jonathan S. Berg, Ewan Birney, Carol A. Bocchini, Elspeth A. Bruford, Alison J. Coffey, Heather Collins, Fiona M Cunningham, , Heidi L. Rehm

The paper describes the formation of the Gene Curation Coalition to standardize gene-disease validity terminology and create a unified database for curated gene-disease assertions.

Genetics in Medicine · May 4, 2022Peer-reviewedGenetic & Genomic Medicine

seqr: a web-based analysis and collaboration tool for rare disease genomics

Lynn S. Pais, Hana Snow, Ben Weisburd, Shifa Zhang, Samantha M. Baxter, Stephanie P. DiTroia, Emily O’Heir, Eleina M. England, Katherine R. Chao, Gabrielle Lemire, Ikeoluwa Osei‐Owusu, Grace E. VanNoy, Michael W. Wilson, Kevin K. Nguyen, Harindra Arachchi, , Anne O’Donnell‐Luria

seqr is a web-based tool for analyzing rare disease genomic data, enabling variant filtering, annotation, and collaboration, with over 10,000 families analyzed and 300 novel disease genes discovered.

Human Mutation · Mar 10, 2022Peer-reviewedGenetic & Genomic Medicine

ClinGen Variant Curation Interface: A Variant Classification Platform for the Application of Evidence Criteria from ACMG/AMP Guidelines

Christine G. Preston, Matt W. Wright, Rao Madhavrao, Steven M. Harrison, Jennifer Goldstein, Xi Luo, Hannah Wand, Bryan Wulf, Gloria Cheung, Mark E. Mandell, Howard Tong, Shaung Cheng, Michael A. Iacocca, Arturo López Pineda, Alice B. Popejoy, , Helio A. Costa

The paper introduces the ClinGen Variant Curation Interface, a platform for applying ACMG/AMP guidelines to classify genetic variants, enabling collaboration and standardization in clinical variant interpretation.

Genome Medicine · Jan 17, 2022Peer-reviewedGenetic & Genomic Medicine

The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation

Alex Handler Wagner, Lawrence J. Babb, Gil Alterovitz, Michael Baudis, Matthew Brush, Daniel Cameron, Melissa Cline, Malachi Griffith, Obi L. Griffith, Sarah E Hunt, David Kreda, Jennifer Lee, Stephanie Li, Javier Lopez, Eric Moyer, , Reece K. Hart

The paper introduces the GA4GH Variation Representation Specification (VRS), a framework for precise and federated representation of molecular variation, with a reference implementation and community resources available online.

Cell Genomics · Nov 1, 2021Peer-reviewedBioinformatics

Neptune: An environment for the delivery of genomic medicine

Eric Venner, Victoria Yi, David R. Murdock, Sara E. Kalla, Tsung-Jung Wu, Aniko Sabo, Shoudong Li, Qingchang Meng, Tian Xia, Mullai Murugan, Michelle L. Cohen, Christie Kovar, Wei‐Qi Wei, Wendy K. Chung, Chunhua Weng, , Andrea L. Hartzler

Neptune delivers structured genomic data to EHR systems through customizable reports and variant reanalysis, supporting over 15,000 clinical reports.

Genetics in Medicine · Jul 13, 2021Peer-reviewedBioinformatics

Genomic Considerations for FHIR; eMERGE Implementation Lessons

Mullai Murugan, Lawrence J. Babb, Casey Overby Taylor, Luke V. Rasmussen, Robert R. Freimuth, Eric Venner, Fei Yan, Victoria Yi, Stephen J. Granite, Hana Zouk, Samuel Aronson, Kevin Power, Alex Fedotov, David R. Crosslin, David A. Fasel, , Richard A. Gibbs

This paper describes the implementation of HL7 FHIR standards for representing clinical genomics results in the eMERGE Networks, improving interoperability for genetic data management.

Journal of Biomedical Informatics · Apr 28, 2021Peer-reviewedGenomics