Applications of artificial intelligence in clinical laboratory genomics.

The transition from analog to digital technologies in clinical laboratory genomics is ushering in an era of "big data" in ways that will exceed human capacity to rapidly and reproducibly analyze those data using conventional approaches. Accurately evaluating complex molecular data to facilitate timely diagnosis and management of genomic disorders will require supportive artificial intelligence methods. These are already being introduced into clinical laboratory genomics to identify variants in DNA sequencing data, predict the effects of DNA variants on protein structure and function to inform clinical interpretation of pathogenicity, link phenotype ontologies to genetic variants identified through exome or genome sequencing to help clinicians reach diagnostic answers faster, correlate genomic data with tumor staging and treatment approaches, utilize natural language processing to identify critical published medical literature during analysis of genomic data, and use interactive chatbots to identify individuals who qualify for genetic testing or to provide pre-test and post-test education. With careful and ethical development and validation of artificial intelligence for clinical laboratory genomics, these advances are expected to significantly enhance the abilities of geneticists to translate complex data into clearly synthesized information for clinicians to use in managing the care of their patients at scale.

Aradhya S ，Facio FM ，Metz H ，Manders T ，Colavin A ，Kobayashi Y ，Nykamp K ，Johnson B ，Nussbaum RL ... -  《-》

Evaluation of an automated genome interpretation model for rare disease routinely used in a clinical genetic laboratory.

The analysis of exome and genome sequencing data for the diagnosis of rare diseases is challenging and time-consuming. In this study, we evaluated an artificial intelligence model, based on machine learning for automating variant prioritization for diagnosing rare genetic diseases in the Baylor Genetics clinical laboratory. The automated analysis model was developed using a supervised learning approach based on thousands of manually curated variants. The model was evaluated on 2 cohorts. The model accuracy was determined using a retrospective cohort comprising 180 randomly selected exome cases (57 singletons, 123 trios); all of which were previously diagnosed and solved through manual interpretation. Diagnostic yield with the modified workflow was estimated using a prospective "production" cohort of 334 consecutive clinical cases. The model accurately pinpointed all manually reported variants as candidates. The reported variants were ranked in top 10 candidate variants in 98.4% (121/123) of trio cases, in 93.0% (53/57) of single proband cases, and 96.7% (174/180) of all cases. The accuracy of the model was reduced in some cases because of incomplete variant calling (eg, copy number variants) or incomplete phenotypic description. The automated model for case analysis assists clinical genetic laboratories in prioritizing candidate variants effectively. The use of such technology may facilitate the interpretation of genomic data for a large number of patients in the era of precision medicine.

Meng L ，Attali R ，Talmy T ，Regev Y ，Mizrahi N ，Smirin-Yosef P ，Vossaert L ，Taborda C ，Santana M ，Machol I ，Xiao R ，Dai H ，Eng C ，Xia F ，Tzur S ... -  《-》

Application of Genomic Data in Translational Medicine During the Big Data Era.

Advances in gene sequencing technology and decreasing costs have resulted in a proliferation of genomic data as an integral component of big data. The availability of vast amounts of genomic data and more sophisticated genomic analysis techniques has facilitated the transition of genomics from the laboratory to clinical settings. More comprehensive and precise DNA sequencing empowers patients to address health issues at the molecular level, facilitating early diagnosis, timely intervention, and personalized healthcare management strategies. Further exploration of disease mechanisms through identification of associated genes may facilitate the discovery of therapeutic targets. The prediction of an individual's disease risk allows for improved stratification and personalized prevention measures. Given the vast amount of genomic data, artificial intelligence, as a burgeoning technology for data analysis, is poised to make a significant impact in genomics.

Zhang Y ，Yu J ，Xie X ，Jiang F ，Wu C ... -  《-》

AI Chatbots in Clinical Laboratory Medicine: Foundations and Trends.

Artificial intelligence (AI) conversational agents, or chatbots, are computer programs designed to simulate human conversations using natural language processing. They offer diverse functions and applications across an expanding range of healthcare domains. However, their roles in laboratory medicine remain unclear, as their accuracy, repeatability, and ability to interpret complex laboratory data have yet to be rigorously evaluated. This review provides an overview of the history of chatbots, two major chatbot development approaches, and their respective advantages and limitations. We discuss the capabilities and potential applications of chatbots in healthcare, focusing on the laboratory medicine field. Recent evaluations of chatbot performance are presented, with a special emphasis on large language models such as the Chat Generative Pre-trained Transformer in response to laboratory medicine questions across different categories, such as medical knowledge, laboratory operations, regulations, and interpretation of laboratory results as related to clinical context. We analyze the causes of chatbots' limitations and suggest research directions for developing more accurate, reliable, and manageable chatbots for applications in laboratory medicine. Chatbots, which are rapidly evolving AI applications, hold tremendous potential to improve medical education, provide timely responses to clinical inquiries concerning laboratory tests, assist in interpreting laboratory results, and facilitate communication among patients, physicians, and laboratorians. Nevertheless, users should be vigilant of existing chatbots' limitations, such as misinformation, inconsistencies, and lack of human-like reasoning abilities. To be effectively used in laboratory medicine, chatbots must undergo extensive training on rigorously validated medical knowledge and be thoroughly evaluated against standard clinical practice.

Yang HS ，Wang F ，Greenblatt MB ，Huang SX ，Zhang Y ... -  《-》

Translating cancer genomics into precision medicine with artificial intelligence: applications, challenges and future perspectives.

Xu J ，Yang P ，Xue S ，Sharma B ，Sanchez-Martin M ，Wang F ，Beaty KA ，Dehan E ，Parikh B ... -  《-》