Early screening of colorectal cancer based on plasma multi-omics combining with artificial intelligence: a multi-center, prospective study (R-E-C-O-M-M-E-N-D)
Ontology highlight
ABSTRACT:
DISEASE(S): Colorectal Cancer
PROVIDER: 41497 | ecrin-mdr-crc |
REPOSITORIES: ECRIN MDR
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Project description:To evaluate the accuracy and effectiveness of a novel screening method based on plasma multi-omics combining with artificial intelligence in a large prospective cohort for the detection of colorectal cancer and advanced adenomas.
| 2751979 | ecrin-mdr-crc
Project description: Not available
| S-EPMC10025753 | biostudies-literature
Project description:The druggable proteome refers to proteins that can bind to small molecules with appropriate chemical affinity, inducing a favorable clinical response. Predicting druggable proteins through screening and in silico modeling is imperative for drug design. To contribute to this field, we developed an accurate predictive classifier for druggable cancer-driving proteins using amino acid composition descriptors of protein sequences and 13 machine learning linear and non-linear classifiers. The optimal classifier was achieved with the support vector machine method, utilizing 200 tri-amino acid composition descriptors. The high performance of the model is evident from an area under the receiver operating characteristics (AUROC) of 0.975 ± 0.003 and an accuracy of 0.929 ± 0.006 (threefold cross-validation). The machine learning prediction model was enhanced with multi-omics approaches, including the target-disease evidence score, the shortest pathways to cancer hallmarks, structure-based ligandability assessment, unfavorable prognostic protein analysis, and the oncogenic variome. Additionally, we performed a drug repurposing analysis to identify drugs with the highest affinity capable of targeting the best predicted proteins. As a result, we identified 79 key druggable cancer-driving proteins with the highest ligandability, and 23 of them demonstrated unfavorable prognostic significance across 16 TCGA PanCancer types: CDKN2A, BCL10, ACVR1, CASP8, JAG1, TSC1, NBN, PREX2, PPP2R1A, DNM2, VAV1, ASXL1, TPR, HRAS, BUB1B, ATG7, MARK3, SETD2, CCNE1, MUTYH, CDKN2C, RB1, and SMARCA4. Moreover, we prioritized 11 clinically relevant drugs targeting these proteins. This strategy effectively predicts and prioritizes biomarkers, therapeutic targets, and drugs for in-depth studies in clinical trials. Scripts are available at https://github.com/muntisa/machine-learning-for-druggable-proteins .
| S-EPMC11339426 | biostudies-literature
Project description:ObjectiveThis study assesses the concordance in migraine diagnosis between an online, self-administered, Computer-based, Diagnostic Engine (CDE) and semi-structured interview (SSI) by a headache specialist, both using International Classification of Headache Disorders, 3rd edition (ICHD-3) criteria.BackgroundDelay in accurate diagnosis is a major barrier to headache care. Accurate computer-based algorithms may help reduce the need for SSI-based encounters to arrive at correct ICHD-3 diagnosis.MethodsBetween March 2018 and August 2019, adult participants were recruited from three academic headache centers and the community via advertising to our cross-sectional study. Participants completed two evaluations: phone interview conducted by headache specialists using the SSI and a web-based expert questionnaire and analytics, CDE. Participants were randomly assigned to either the SSI followed by the web-based questionnaire or the web-based questionnaire followed by the SSI. Participants completed protocols a few minutes apart. The concordance in migraine/probable migraine (M/PM) diagnosis between SSI and CDE was measured using Cohen's kappa statistics. The diagnostic accuracy of CDE was assessed using the SSI as reference standard.ResultsOf the 276 participants consented, 212 completed both SSI and CDE (study completion rate = 77%; median age = 32 years [interquartile range: 28-40], female:male ratio = 3:1). Concordance in M/PM diagnosis between SSI and CDE was: κ = 0.83 (95% confidence interval [CI]: 0.75-0.91). CDE diagnostic accuracy: sensitivity = 90.1% (118/131), 95% CI: 83.6%-94.6%; specificity = 95.8% (68/71), 95% CI: 88.1%-99.1%. Positive and negative predictive values = 97.0% (95% CI: 91.3%-99.0%) and 86.6% (95% CI: 79.3%-91.5%), respectively, using identified migraine prevalence of 60%. Assuming a general migraine population prevalence of 10%, positive and negative predictive values were 70.3% (95% CI: 43.9%-87.8%) and 98.9% (95% CI: 98.1%-99.3%), respectively.ConclusionThe SSI and CDE have excellent concordance in diagnosing M/PM. Positive CDE helps rule in M/PM, through high specificity and positive likelihood ratio. A negative CDE helps rule out M/PM through high sensitivity and low negative likelihood ratio. CDE that mimics SSI logic is a valid tool for migraine diagnosis.
| S-EPMC9378575 | biostudies-literature
Project description:Background: The emerging field of artificial intelligence (AI) will probably affect the practice for the next generation of doctors. However, the students' views on AI have not been largely investigated. Methods: An anonymous electronic survey on AI was designed for medical and dental students to explore: (1) sources of information about AI, (2) AI applications and concerns, (3) AI status as a topic in medicine, and (4) students' feelings and attitudes. The questionnaire was advertised on social media platforms in 2020. Security measures were employed to prevent fraudulent responses. Mann-Whitney U-test was employed for all comparisons. A sensitivity analysis was also performed by binarizing responses to express disagreement and agreement using the Chi-squared test. Results: Three thousand one hundred thirty-three respondents from 63 countries from all continents were included. Most respondents reported having at least a moderate understanding of the technologies underpinning AI and of their current application, with higher agreement associated with being male (p < 0.0001), tech-savvy (p < 0.0001), pre-clinical student (p < 0.006), and from a developed country (p < 0.04). Students perceive AI as a partner rather than a competitor (72.2%) with a higher agreement for medical students (p = 0.002). The belief that AI will revolutionize medicine and dentistry (83.9%) with greater agreement for students from a developed country (p = 0.0004) was noted. Most students agree that the AI developments will make medicine and dentistry more exciting (69.9%), that AI shall be part of the medical training (85.6%) and they are eager to incorporate AI in their future practice (99%). Conclusion: Currently, AI is a hot topic in medicine and dentistry. Students have a basic understanding of AI principles, a positive attitude toward AI and would like to have it incorporated into their training.
| S-EPMC8739771 | biostudies-literature
Project description:Enzyme research is important for the development of various scientific fields such as medicine and biotechnology. Enzyme databases facilitate this research by providing a wide range of information relevant to research planning and data analysis. Over the years, various databases that cover different aspects of enzyme biology (e.g., kinetic parameters, enzyme occurrence, and reaction mechanisms) have been developed. Most of the databases are curated manually, which improves reliability of the information; however, such curation cannot keep pace with the exponential growth in published data. Lack of data standardization is another obstacle for data extraction and analysis. Improving machine readability of databases is especially important in the light of recent advances in deep learning algorithms that require big training datasets. This review provides information regarding the current state of enzyme databases, especially in relation to the ever-increasing amount of generated research data and recent advancements in artificial intelligence algorithms. Furthermore, it describes several enzyme databases, providing the reader with necessary information for their use.
| S-EPMC10707154 | biostudies-literature
Project description:Researchers increasingly turn to explainable artificial intelligence (XAI) to analyze omics data and gain insights into the underlying biological processes. Yet, given the interdisciplinary nature of the field, many findings have only been shared in their respective research community. An overview of XAI for omics data is needed to highlight promising approaches and help detect common issues. Toward this end, we conducted a systematic mapping study. To identify relevant literature, we queried Scopus, PubMed, Web of Science, BioRxiv, MedRxiv and arXiv. Based on keywording, we developed a coding scheme with 10 facets regarding the studies' AI methods, explainability methods and omics data. Our mapping study resulted in 405 included papers published between 2010 and 2023. The inspected papers analyze DNA-based (mostly genomic), transcriptomic, proteomic or metabolomic data by means of neural networks, tree-based methods, statistical methods and further AI methods. The preferred post-hoc explainability methods are feature relevance (n = 166) and visual explanation (n = 52), while papers using interpretable approaches often resort to the use of transparent models (n = 83) or architecture modifications (n = 72). With many research gaps still apparent for XAI for omics data, we deduced eight research directions and discuss their potential for the field. We also provide exemplary research questions for each direction. Many problems with the adoption of XAI for omics data in clinical practice are yet to be resolved. This systematic mapping study outlines extant research on the topic and provides research directions for researchers and practitioners.
| S-EPMC10729786 | biostudies-literature
Project description:In common medical procedures, the time-consuming and expensive nature of obtaining test results plagues doctors and patients. Digital pathology research allows using computational technologies to manage data, presenting an opportunity to improve the efficiency of diagnosis and treatment. Artificial intelligence (AI) has a great advantage in the data analytics phase. Extensive research has shown that AI algorithms can produce more up-to-date and standardized conclusions for whole slide images. In conjunction with the development of high-throughput sequencing technologies, algorithms can integrate and analyze data from multiple modalities to explore the correspondence between morphological features and gene expression. This review investigates using the most popular image data, hematoxylin-eosin stained tissue slide images, to find a strategic solution for the imbalance of healthcare resources. The article focuses on the role that the development of deep learning technology has in assisting doctors' work and discusses the opportunities and challenges of AI.
| S-EPMC9677480 | biostudies-literature
Project description:We sequenced 8 colorectal cancer patients' PBMC samples, and 6 healthy donors' PBMC samples. These individuals' plasma RNA have been profiled.
2023-09-28 | GSE218999 | GEO
Project description:We sequenced cell-free nucleaic acid (cfNA) for 2 major cancer types (44 samples of colorectal cancer and 36 samples of stomach cancer) and 81 samples of healthy individuals collected in China. Cancer related signaling pathway were identified. Cancer detection and specific classification were achieved through combining both cfRNA and cfDNA reads.
2023-09-28 | GSE186595 | GEO