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

Implementing Integrated Genomic Risk Assessments for Breast Cancer: Lessons Learned from the eMERGE Study

Cong Liu, Katherine D. Crew, Jennifer Morse, Jodell E. Linder, Antonis C. Antoniou, Tim J. Carver, Josh B. Cortopassi, Josh F. Peterson, Casey Ta, Christin Hoell, Cynthia A. Prows, Eimear E. Kenny, Emily Miller, Emma F. Perez, Gail Pairitz Jarvik, , Georgia L. Wiesner

The paper develops a pipeline for integrated breast cancer risk assessment using polygenic risk scores and other factors in the eMERGE study, showing high concordance between API and UI results.

medRxiv · May 22, 2025 · PreprintGenetic & Genomic Medicine

Selection, optimization, and validation of ten chronic disease polygenic risk scores for clinical implementation in diverse populations

Niall J. Lennon, Leah Claire Kottyan, C. Kachulis, Noura S. Abul‐Husn, Josh Arias, Gillian M. Belbin, Jennifer Elizabeth Below, Sonja I. Berndt, Wendy K. Chung, James J. Cimino, Ellen Wright Clayton, John J. Connolly, David R. Crosslin, Ozan Dikilitas, Digna R. Velez Edwards, , Eimear E. Kenny

The paper selects and validates ten polygenic risk scores for clinical use in diverse populations, focusing on chronic diseases and addressing disparities in predictive performance.

medRxiv · May 25, 2023 · PreprintGenetic & Genomic Medicine

Quantifying factors that affect polygenic risk score performance across diverse ancestries and age groups for body mass index

Daniel J. Hui, Brenda Xiao, Ozan Dikilitas, Robert R. Freimuth, Marguerite R. Irvin, Gail Pairitz Jarvik, Leah Claire Kottyan, Iftikhar Kullo, Nita A. Limdi, Cong Liu, Yuan Luo, Bahram Namjou, Megan J. Puckelwartz, Daniel J. Schaid, Hemant K. Tiwari, , Marylyn DeRiggi Ritchie

This study evaluates how ancestry, GWAS sample size, and LD reference panels affect BMI PRS performance across different age groups and ancestries.

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

A harmonized meta-knowledgebase of clinical interpretations of cancer genomic variants

Alex Handler Wagner, Brian Walsh, Georgia Mayfield, David Tamborero, Dmitriy Sonkin, Kilannin Krysiak, Jordi Deu-Pons, Ryan P. Duren, Jianjiong Gao, Julie A. McMurry, Sara E. Patterson, Catherine Del Vecchio Fitz, Beth A. Pitel, Osman Uğur Sezerman, Kyle Ellrott, , Adam A. Margolin

The paper harmonizes clinical interpretations of cancer genomic variants across six knowledgebases, improving overlap and matching with patient cohorts.

Nature Genetics · Apr 1, 2020Peer-reviewedBioinformatics