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Annual Review of Biomedical Data Science - Early Publication
Reviews in Advance appear online ahead of the full published volume. View expected publication dates for upcoming volumes.
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Mapping the Human Cell Surface Interactome: A Key to Decode Cell-to-Cell Communication
First published online: 09 May 2024More LessProteins on the surfaces of cells serve as physical connection points to bridge one cell with another, enabling direct communication between cells and cohesive structure. As biomedical research makes the leap from characterizing individual cells toward understanding the multicellular organization of the human body, the binding interactions between molecules on the surfaces of cells are foundational both for computational models and for clinical efforts to exploit these influential receptor pathways. To achieve this grander vision, we must assemble the full interactome of ways surface proteins can link together. This review investigates how close we are to knowing the human cell surface protein interactome. We summarize the current state of databases and systematic technologies to assemble surface protein interactomes, while highlighting substantial gaps that remain. We aim for this to serve as a road map for eventually building a more robust picture of the human cell surface protein interactome.
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Centralized and Federated Models for the Analysis of Clinical Data
First published online: 09 May 2024More LessThe progress of precision medicine research hinges on the gathering and analysis of extensive and diverse clinical datasets. With the continued expansion of modalities, scales, and sources of clinical datasets, it becomes imperative to devise methods for aggregating information from these varied sources to achieve a comprehensive understanding of diseases. In this review, we describe two important approaches for the analysis of diverse clinical datasets, namely the centralized model and federated model. We compare and contrast the strengths and weaknesses inherent in each model and present recent progress in methodologies and their associated challenges. Finally, we present an outlook on the opportunities that both models hold for the future analysis of clinical data.
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The Evolutionary Interplay of Somatic and Germline Mutation Rates
First published online: 26 April 2024More LessNovel sequencing technologies are making it increasingly possible to measure the mutation rates of somatic cell lineages. Accurate germline mutation rate measurement technologies have also been available for a decade, making it possible to assess how this fundamental evolutionary parameter varies across the tree of life. Here, we review some classical theories about germline and somatic mutation rate evolution that were formulated using principles of population genetics and the biology of aging and cancer. We find that somatic mutation rate measurements, while still limited in phylogenetic diversity, seem consistent with the theory that selection to preserve the soma is proportional to life span. However, germline and somatic theories make conflicting predictions regarding which species should have the most accurate DNA repair. Resolving this conflict will require carefully measuring how mutation rates scale with time and cell division and achieving a better understanding of mutation rate pleiotropy among cell types.
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Generating Clinical-Grade Gene–Disease Validity Classifications Through the ClinGen Data Platforms
Matt W. Wright, Courtney L. Thaxton, Tristan Nelson, Marina T. DiStefano, Juliann M. Savatt, Matthew H. Brush, Gloria Cheung, Mark E. Mandell, Bryan Wulf, T.J. Ward, Scott Goehringer, Terry O'Neill, Phil Weller, Christine G. Preston, Ingrid M. Keseler, Jennifer L. Goldstein, Natasha T. Strande, Jennifer McGlaughon, Danielle R. Azzariti, Ineke Cordova, Hannah Dziadzio, Lawrence Babb, Kevin Riehle, Aleksandar Milosavljevic, Christa Lese Martin, Heidi L. Rehm, Sharon E. Plon, Jonathan S. Berg, Erin R. Riggs, and Teri E. KleinFirst published online: 25 April 2024More LessClinical genetic laboratories must have access to clinically validated biomedical data for precision medicine. A lack of accessibility, normalized structure, and consistency in evaluation complicates interpretation of disease causality, resulting in confusion in assessing the clinical validity of genes and genetic variants for diagnosis. A key goal of the Clinical Genome Resource (ClinGen) is to fill the knowledge gap concerning the strength of evidence supporting the role of a gene in a monogenic disease, which is achieved through a process known as Gene–Disease Validity curation. Here we review the work of ClinGen in developing a curation infrastructure that supports the standardization, harmonization, and dissemination of Gene–Disease Validity data through the creation of frameworks and the utilization of common data standards. This infrastructure is based on several applications, including the ClinGen GeneTracker, Gene Curation Interface, Data Exchange, GeneGraph, and website.
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Bringing the Genomic Revolution to Comparative Oncology: Human and Dog Cancers
First published online: 22 April 2024More LessDogs are humanity's oldest friend, the first species we domesticated 20,000–40,000 years ago. In this unequaled collaboration, dogs have inadvertently but serendipitously been molded into a potent human cancer model. Unlike many common model species, dogs are raised in the same environment as humans and present with spontaneous tumors with human-like comorbidities, immunocompetency, and heterogeneity. In breast, bladder, blood, and several pediatric cancers, in-depth profiling of dog and human tumors has established the benefits of the dog model. In addition to this clinical and molecular similarity, veterinary studies indicate that domestic dogs have relatively high tumor incidence rates. As a result, there are a plethora of data for analysis, the statistical power of which is bolstered by substantial breed-specific variability. As such, dog tumors provide a unique opportunity to interrogate the molecular factors underpinning cancer and facilitate the modeling of new therapeutic targets. This review discusses the emerging field of comparative oncology, how it complements human and rodent cancer studies, and where challenges remain, given the rapid proliferation of genomic resources. Increasingly, it appears that human's best friend is becoming an irreplaceable component of oncology research.
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Human Genetics and Genomics for Drug Target Identification and Prioritization: Open Targets’ Perspective
First published online: 12 April 2024More LessOpen Targets, a consortium among academic and industry partners, focuses on using human genetics and genomics to provide insights to key questions that build therapeutic hypotheses. Large-scale experiments generate foundational data, and open-source informatic platforms systematically integrate evidence for target–disease relationships and provide dynamic tooling for target prioritization. A locus-to-gene machine learning model uses evidence from genome-wide association studies (GWAS Catalog, UK BioBank, and FinnGen), functional genomic studies, epigenetic studies, and variant effect prediction to predict potential drug targets for complex diseases. These predictions are combined with genetic evidence from gene burden analyses, rare disease genetics, somatic mutations, perturbation assays, pathway analyses, scientific literature, differential expression, and mouse models to systematically build target–disease associations (https://platform.opentargets.org). Scored target attributes such as clinical precedence, tractability, and safety guide target prioritization. Here we provide our perspective on the value and impact of human genetics and genomics for generating therapeutic hypotheses.
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AlphaFold and Protein Folding: Not Dead Yet! The Frontier Is Conformational Ensembles
First published online: 11 April 2024More LessLike the black knight in the classic Monty Python movie, grand scientific challenges such as protein folding are hard to finish off. Notably, AlphaFold is revolutionizing structural biology by bringing highly accurate structure prediction to the masses and opening up innumerable new avenues of research. Despite this enormous success, calling structure prediction, much less protein folding and related problems, “solved” is dangerous, as doing so could stymie further progress. Imagine what the world would be like if we had declared flight solved after the first commercial airlines opened and stopped investing in further research and development. Likewise, there are still important limitations to structure prediction that we would benefit from addressing. Moreover, we are limited in our understanding of the enormous diversity of different structures a single protein can adopt (called a conformational ensemble) and the dynamics by which a protein explores this space. What is clear is that conformational ensembles are critical to protein function, and understanding this aspect of protein dynamics will advance our ability to design new proteins and drugs.
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Biomedical Data Science, Artificial Intelligence, and Ethics: Navigating Challenges in the Face of Explosive Growth
First published online: 10 April 2024More LessAdvances in biomedical data science and artificial intelligence (AI) are profoundly changing the landscape of healthcare. This article reviews the ethical issues that arise with the development of AI technologies, including threats to privacy, data security, consent, and justice, as they relate to donors of tissue and data. It also considers broader societal obligations, including the importance of assessing the unintended consequences of AI research in biomedicine. In addition, this article highlights the challenge of rapid AI development against the backdrop of disparate regulatory frameworks, calling for a global approach to address concerns around data misuse, unintended surveillance, and the equitable distribution of AI's benefits and burdens. Finally, a number of potential solutions to these ethical quandaries are offered. Namely, the merits of advocating for a collaborative, informed, and flexible regulatory approach that balances innovation with individual rights and public welfare, fostering a trustworthy AI-driven healthcare ecosystem, are discussed.
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Computational Approaches to Drug Repurposing: Methods, Challenges, and Opportunities
First published online: 10 April 2024More LessDrug repurposing refers to the inference of therapeutic relationships between a clinical indication and existing compounds. As an emerging paradigm in drug development, drug repurposing enables more efficient treatment of rare diseases, stratified patient populations, and urgent threats to public health. However, prioritizing well-suited drug candidates from among a nearly infinite number of repurposing options continues to represent a significant challenge in drug development. Over the past decade, advances in genomic profiling, database curation, and machine learning techniques have enabled more accurate identification of drug repurposing candidates for subsequent clinical evaluation. This review outlines the major methodologic classes that these approaches comprise, which rely on (a) protein structure, (b) genomic signatures, (c) biological networks, and (d) real-world clinical data. We propose that realizing the full impact of drug repurposing methodologies requires a multidisciplinary understanding of each method's advantages and limitations with respect to clinical practice.
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