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Hatamikia S, Nougaret S, Panico C, Avesani G, Nero C, Boldrini L, Sala E, Woitek R. Ovarian cancer beyond imaging: integration of AI and multiomics biomarkers. Eur Radiol Exp 2023; 7:50. [PMID: 37700218 PMCID: PMC10497482 DOI: 10.1186/s41747-023-00364-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 06/19/2023] [Indexed: 09/14/2023] Open
Abstract
High-grade serous ovarian cancer is the most lethal gynaecological malignancy. Detailed molecular studies have revealed marked intra-patient heterogeneity at the tumour microenvironment level, likely contributing to poor prognosis. Despite large quantities of clinical, molecular and imaging data on ovarian cancer being accumulated worldwide and the rise of high-throughput computing, data frequently remain siloed and are thus inaccessible for integrated analyses. Only a minority of studies on ovarian cancer have set out to harness artificial intelligence (AI) for the integration of multiomics data and for developing powerful algorithms that capture the characteristics of ovarian cancer at multiple scales and levels. Clinical data, serum markers, and imaging data were most frequently used, followed by genomics and transcriptomics. The current literature proves that integrative multiomics approaches outperform models based on single data types and indicates that imaging can be used for the longitudinal tracking of tumour heterogeneity in space and potentially over time. This review presents an overview of studies that integrated two or more data types to develop AI-based classifiers or prediction models.Relevance statement Integrative multiomics models for ovarian cancer outperform models using single data types for classification, prognostication, and predictive tasks.Key points• This review presents studies using multiomics and artificial intelligence in ovarian cancer.• Current literature proves that integrative multiomics outperform models using single data types.• Around 60% of studies used a combination of imaging with clinical data.• The combination of genomics and transcriptomics with imaging data was infrequently used.
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Affiliation(s)
- Sepideh Hatamikia
- Research Center for Medical Image Analysis and AI (MIAAI), Danube Private University, Krems, Austria.
- Austrian Center for Medical Innovation and Technology (ACMIT), Wiener Neustadt, Austria.
| | - Stephanie Nougaret
- Department of Radiology, Montpellier Cancer Institute, University of Montpellier, Montpellier, France
| | - Camilla Panico
- Dipartimento di Diagnostica Per Immagini, Radioterapia Oncologica Ed Ematologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giacomo Avesani
- Dipartimento di Diagnostica Per Immagini, Radioterapia Oncologica Ed Ematologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Camilla Nero
- Scienze Della Salute Della Donna, del bambino e Di Sanità Pubblica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Luca Boldrini
- Dipartimento di Diagnostica Per Immagini, Radioterapia Oncologica Ed Ematologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Evis Sala
- Dipartimento di Diagnostica Per Immagini, Radioterapia Oncologica Ed Ematologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Ramona Woitek
- Research Center for Medical Image Analysis and AI (MIAAI), Danube Private University, Krems, Austria
- Department of Radiology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
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Zheng B, Liu J, Gu J, Du J, Wang L, Gu S, Cheng J, Yang J, Lu H. Classification of Benign and Malignant Thyroid Nodules Using a Combined Clinical Information and Gene Expression Signatures. PLoS One 2016; 11:e0164570. [PMID: 27776138 PMCID: PMC5077123 DOI: 10.1371/journal.pone.0164570] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 09/27/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND A key challenge in thyroid carcinoma is preoperatively diagnosing malignant thyroid nodules. A novel diagnostic test that measures the expression of a 3-gene signature (DPP4, SCG5 and CA12) has demonstrated promise in thyroid carcinoma assessment. However, more reliable prediction methods combining clinical features with genomic signatures with high accuracy, good stability and low cost are needed. METHODOLOGY/PRINCIPAL FINDINGS 25 clinical information were recorded in 771 patients. Feature selection and validation were conducted using random forest. Thyroid samples and clinical data were obtained from 142 patients at two different hospitals, and expression of the 3-gene signature was measured using quantitative PCR. The predictive abilities of three models (based on the selected clinical variables, the gene expression profile, and integrated gene expression and clinical information) were compared. Seven clinical characteristics were selected based on a training set (539 patients) and tested in three test sets, yielding predictive accuracies of 82.3% (n = 232), 81.4% (n = 70), and 81.9% (n = 72). The predictive sensitivity, specificity, and accuracy were 72.3%, 80.5% and 76.8% for the model based on the gene expression signature, 66.2%, 81.8% and 74.6% for the model based on the clinical data, and 83.1%, 84.4% and 83.8% for the combined model in a 10-fold cross-validation (n = 142). CONCLUSIONS These findings reveal that the integrated model, which combines clinical data with the 3-gene signature, is superior to models based on gene expression or clinical data alone. The integrated model appears to be a reliable tool for the preoperative diagnosis of thyroid tumors.
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Affiliation(s)
- Bing Zheng
- Shanghai Institute of Medical Genetics, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai, China
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Liu
- Department of Otolaryngology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Department of Otolaryngology-Head and Neck Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
- Ear Institute, Shanghai Jiaotong University, Shanghai, China
| | - Jianlei Gu
- Shanghai Institute of Medical Genetics, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Molecular Embryology, Ministry of Health and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Jing Du
- Department of Ultrasonography, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lin Wang
- Department of Ultrasonography, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shengli Gu
- Department of Ultrasonography, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Juan Cheng
- Department of Ultrasonography, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Yang
- Department of Otolaryngology-Head and Neck Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
- Ear Institute, Shanghai Jiaotong University, Shanghai, China
| | - Hui Lu
- Shanghai Institute of Medical Genetics, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Molecular Embryology, Ministry of Health and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
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Ray B, Henaff M, Ma S, Efstathiadis E, Peskin ER, Picone M, Poli T, Aliferis CF, Statnikov A. Information content and analysis methods for multi-modal high-throughput biomedical data. Sci Rep 2014; 4:4411. [PMID: 24651673 PMCID: PMC3961740 DOI: 10.1038/srep04411] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 02/27/2014] [Indexed: 01/30/2023] Open
Abstract
The spectrum of modern molecular high-throughput assaying includes diverse technologies such as microarray gene expression, miRNA expression, proteomics, DNA methylation, among many others. Now that these technologies have matured and become increasingly accessible, the next frontier is to collect "multi-modal" data for the same set of subjects and conduct integrative, multi-level analyses. While multi-modal data does contain distinct biological information that can be useful for answering complex biology questions, its value for predicting clinical phenotypes and contributions of each type of input remain unknown. We obtained 47 datasets/predictive tasks that in total span over 9 data modalities and executed analytic experiments for predicting various clinical phenotypes and outcomes. First, we analyzed each modality separately using uni-modal approaches based on several state-of-the-art supervised classification and feature selection methods. Then, we applied integrative multi-modal classification techniques. We have found that gene expression is the most predictively informative modality. Other modalities such as protein expression, miRNA expression, and DNA methylation also provide highly predictive results, which are often statistically comparable but not superior to gene expression data. Integrative multi-modal analyses generally do not increase predictive signal compared to gene expression data.
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Affiliation(s)
- Bisakha Ray
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY, USA
| | - Mikael Henaff
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY, USA
- Department of Computer Science, New York University, NY, USA
| | - Sisi Ma
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY, USA
| | - Efstratios Efstathiadis
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY, USA
| | - Eric R. Peskin
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY, USA
| | - Marco Picone
- Department of Information Engineering, University of Parma, Parma, Italy
- MultiMed Srl, Cremona, Italy
| | - Tito Poli
- Maxillofacial Surgery Section of the Head and Neck Department, University Hospital of Parma, Parma, Italy
| | - Constantin F. Aliferis
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY, USA
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Alexander Statnikov
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY, USA
- Department of Medicine, New York University School of Medicine, New York, NY, USA
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Gormley M, Dampier W, Ertel A, Karacali B, Tozeren A. Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets. BMC Bioinformatics 2007; 8:415. [PMID: 17963508 PMCID: PMC2211325 DOI: 10.1186/1471-2105-8-415] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Accepted: 10/26/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Independently derived expression profiles of the same biological condition often have few genes in common. In this study, we created populations of expression profiles from publicly available microarray datasets of cancer (breast, lymphoma and renal) samples linked to clinical information with an iterative machine learning algorithm. ROC curves were used to assess the prediction error of each profile for classification. We compared the prediction error of profiles correlated with molecular phenotype against profiles correlated with relapse-free status. Prediction error of profiles identified with supervised univariate feature selection algorithms were compared to profiles selected randomly from a) all genes on the microarray platform and b) a list of known disease-related genes (a priori selection). We also determined the relevance of expression profiles on test arrays from independent datasets, measured on either the same or different microarray platforms. RESULTS Highly discriminative expression profiles were produced on both simulated gene expression data and expression data from breast cancer and lymphoma datasets on the basis of ER and BCL-6 expression, respectively. Use of relapse-free status to identify profiles for prognosis prediction resulted in poorly discriminative decision rules. Supervised feature selection resulted in more accurate classifications than random or a priori selection, however, the difference in prediction error decreased as the number of features increased. These results held when decision rules were applied across-datasets to samples profiled on the same microarray platform. CONCLUSION Our results show that many gene sets predict molecular phenotypes accurately. Given this, expression profiles identified using different training datasets should be expected to show little agreement. In addition, we demonstrate the difficulty in predicting relapse directly from microarray data using supervised machine learning approaches. These findings are relevant to the use of molecular profiling for the identification of candidate biomarker panels.
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Affiliation(s)
- Michael Gormley
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, USA.
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