Robert R. Freimuth

Personal Health Data Spaces for precision prevention and continuity of care: integrating genomic, imaging, and clinical data in primary care

Elisa J. Houwink, Robert R. Freimuth

Despite substantial advances in disease prevention, current clinical approaches remain largely anchored in short-term risk estimation models that are dominated by age and conventional risk factors. As a result, individuals with substantial inherited susceptibility, particularly younger patients, are frequently underrecognized until disease …

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The GA4GH Genomic Knowledge Standards for Variant Interpretation

Melissa Cline, Daniel Puthawala, Brendan Reardon, Kori Kuzma et autres

Most observed genetic variants are of uncertain significance, largely due to technical barriers to the precise sharing of knowledge about them. Addressing this challenge, the GA4GH Genomic Knowledge Standards (GKS) Work Stream develops interoperable standards for variant representation and annotation through collaboration …

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The GA4GH Genomic Knowledge Standards for Variant Interpretation

Melissa Cline, Daniel Puthawala, Brendan Reardon, Kori Kuzma et autres

Most observed genetic variants are of uncertain significance, largely due to technical barriers to the precise sharing of knowledge about them. Addressing this challenge, the GA4GH Genomic Knowledge Standards (GKS) Work Stream develops interoperable standards for variant representation and annotation through collaboration …

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Deriving wisdom from data: The value and continued rationale for structured data in the era of artificial intelligence–driven oncology care

Hamid Emamekhoo, Irbaz Riaz, Daniel B. Martin, Peter E. Gabriel et autres

The adoption of electronic health records (EHRs) has transformed health care, improving efficiency and chart accessibility. However, the widespread reliance on unstructured data entry and the lack of standardized documentation frameworks have resulted in significant data fragmentation across health care systems. The …

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The GA4GH Categorical Variation Representation Specification: A Unified Computational Framework for Reasoning over Genomic Variant Categories

Daniel Puthawala, Brendan Reardon, Lawrence Babb, Kori Kuzma et autres

Categorical variants, or sets of genomic alterations constrained by shared properties, are pervasive across clinical, regulatory, and research domains in the biomedical ecosystem, yet their inconsistent and non-computable representation hinders data interoperability and clinical interpretation. We surveyed genomic knowledgebases spanning regulatory approvals …

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

Cong Liu, Katherine D. Crew, Jennifer Morse, Jodell E. Linder et autres

Objective: To develop and implement a pipeline for integrated breast cancer risk assessment using the BOADICEA model within the eMERGE study, incorporating polygenic risk scores (PRS), monogenic variants, family history, and clinical factors. Materials and Methods: A pipeline was deployed across ten …

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Standardization of Genomic Nomenclature across a Diverse Ecosystem of Stakeholders: Evolution and Challenges

Laura K. Conlin, Melissa Landrum, Robert R. Freimuth, Birgit Funke

BACKGROUND: Genetic testing has traditionally been divided into molecular genetics and cytogenetics, originally driven by the use of different assays and their associated limitations. Cytogenetic technologies such as karyotyping, fluorescent in situ hybridization or chromosomal microarrays are used to detect large "megabase …

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65. Creating a common language for categorical variants

Daniel Puthawala, Wesley Goar, Brendan Reardon, Salem Bajjali et autres

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

Niall J. Lennon, Leah C. Kottyan, Christopher Kachulis, Noura S. Abul‐Husn et autres

Polygenic risk scores (PRSs) have improved in predictive performance, but several challenges remain to be addressed before PRSs can be implemented in the clinic, including reduced predictive performance of PRSs in diverse populations, and the interpretation and communication of genetic results to …

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Precision Pharmacogenomics for Assessing hERG-related Cardiotoxicity Bridging Data and Knowledge Gaps: A Neuro-Symbolic AI Approach

Delower Hossain, Nan Huo, Robert R. Freimuth

Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup

Nephi Walton, Radha Nagarajan, Chen Wang, Murat Sincan et autres

OBJECTIVE: Given the importance AI in genomics and its potential impact on human health, the American Medical Informatics Association-Genomics and Translational Biomedical Informatics (GenTBI) Workgroup developed this assessment of factors that can further enable the clinical application of AI in this space. …

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Representing NIH Genetic Test Registry Data in the FHIR Genomic Study Resource

Aly Khalifa, Robert R. Freimuth

The National Institute of Health (NIH) Genetic Testing Registry (GTR) provides a variety of information about genetic tests such as relevant methods, conditions, and performing laboratories. This study mapped a subset of GTR data to the newly developed HL7®-FHIR® Genomic Study resource. …

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