scholarly journals Practicing precision medicine with intelligently integrative clinical and multi-omics data analysis

2020 ◽  
Vol 14 (1) ◽  
Author(s):  
Zeeshan Ahmed
Keyword(s):  
Machine Learning ◽  
Precision Medicine ◽  
Ethical Issues ◽  
Predictive Biomarkers ◽  
Heterogeneous Data ◽  
Prognostic Models ◽  
Omics Data ◽  
Clinical Predictors ◽  
Personalized Care ◽  
Complex Disorders

Abstract Precision medicine aims to empower clinicians to predict the most appropriate course of action for patients with complex diseases like cancer, diabetes, cardiomyopathy, and COVID-19. With a progressive interpretation of the clinical, molecular, and genomic factors at play in diseases, more effective and personalized medical treatments are anticipated for many disorders. Understanding patient’s metabolomics and genetic make-up in conjunction with clinical data will significantly lead to determining predisposition, diagnostic, prognostic, and predictive biomarkers and paths ultimately providing optimal and personalized care for diverse, and targeted chronic and acute diseases. In clinical settings, we need to timely model clinical and multi-omics data to find statistical patterns across millions of features to identify underlying biologic pathways, modifiable risk factors, and actionable information that support early detection and prevention of complex disorders, and development of new therapies for better patient care. It is important to calculate quantitative phenotype measurements, evaluate variants in unique genes and interpret using ACMG guidelines, find frequency of pathogenic and likely pathogenic variants without disease indicators, and observe autosomal recessive carriers with a phenotype manifestation in metabolome. Next, ensuring security to reconcile noise, we need to build and train machine-learning prognostic models to meaningfully process multisource heterogeneous data to identify high-risk rare variants and make medically relevant predictions. The goal, today, is to facilitate implementation of mainstream precision medicine to improve the traditional symptom-driven practice of medicine, and allow earlier interventions using predictive diagnostics and tailoring better-personalized treatments. We strongly recommend automated implementation of cutting-edge technologies, utilizing machine learning (ML) and artificial intelligence (AI) approaches for the multimodal data aggregation, multifactor examination, development of knowledgebase of clinical predictors for decision support, and best strategies for dealing with relevant ethical issues.

scholarly journals Biomarker discovery studies for patient stratification using machine learning analysis of omics data: a scoping review

BMJ Open ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. e053674
Author(s):  
Enrico Glaab ◽  
Armin Rauschenberger ◽  
Rita Banzi ◽  
Chiara Gerardi ◽  
Paula Garcia ◽  
...  
Keyword(s):  
Machine Learning ◽  
Scoping Review ◽  
Biomarker Discovery ◽  
Biomedical Literature ◽  
Molecular Signature ◽  
Biological Knowledge ◽  
Measurement Technology ◽  
Omics Data ◽  
Patient Stratification ◽  
Complex Disorders

ObjectiveTo review biomarker discovery studies using omics data for patient stratification which led to clinically validated FDA-cleared tests or laboratory developed tests, in order to identify common characteristics and derive recommendations for future biomarker projects.DesignScoping review.MethodsWe searched PubMed, EMBASE and Web of Science to obtain a comprehensive list of articles from the biomedical literature published between January 2000 and July 2021, describing clinically validated biomarker signatures for patient stratification, derived using statistical learning approaches. All documents were screened to retain only peer-reviewed research articles, review articles or opinion articles, covering supervised and unsupervised machine learning applications for omics-based patient stratification. Two reviewers independently confirmed the eligibility. Disagreements were solved by consensus. We focused the final analysis on omics-based biomarkers which achieved the highest level of validation, that is, clinical approval of the developed molecular signature as a laboratory developed test or FDA approved tests.ResultsOverall, 352 articles fulfilled the eligibility criteria. The analysis of validated biomarker signatures identified multiple common methodological and practical features that may explain the successful test development and guide future biomarker projects. These include study design choices to ensure sufficient statistical power for model building and external testing, suitable combinations of non-targeted and targeted measurement technologies, the integration of prior biological knowledge, strict filtering and inclusion/exclusion criteria, and the adequacy of statistical and machine learning methods for discovery and validation.ConclusionsWhile most clinically validated biomarker models derived from omics data have been developed for personalised oncology, first applications for non-cancer diseases show the potential of multivariate omics biomarker design for other complex disorders. Distinctive characteristics of prior success stories, such as early filtering and robust discovery approaches, continuous improvements in assay design and experimental measurement technology, and rigorous multicohort validation approaches, enable the derivation of specific recommendations for future studies.

scholarly journals Integrative clinical, genomics and metabolomics data analysis for mainstream precision medicine to investigate COVID-19

2020 ◽  
Vol 7 (1) ◽  
pp. 6-10 ◽  
Author(s):  
Zeeshan Ahmed ◽  
Saman Zeeshan ◽  
David J Foran ◽  
Lawrence C Kleinman ◽  
Fredric E Wondisford ◽  
...  
Keyword(s):  
Machine Learning ◽  
Data Analysis ◽  
Early Detection ◽  
Predictive Biomarkers ◽  
Machine Learning Algorithms ◽  
Prognostic Models ◽  
Genetic Profile ◽  
Metabolomics Data ◽  
Clinical Genomics ◽  
Early Detection And Prevention

Despite significant scientific and medical discoveries, the genetics of novel infectious diseases like COVID-19 remains far from understanding. SARS-CoV-2 is a single-stranded RNA respiratory virus that causes COVID-19 by binding to the ACE2 receptor in the lung and other organs. Understanding its clinical presentation and metabolomic and genetic profile will lead to the discovery of diagnostic, prognostic and predictive biomarkers, which may lead to more effective medical therapy. It is important to investigate correlations and overlap between reported diagnoses of a patient with COVID-19 in clinical data with identified germline and somatic mutations, and highly expressed genes from genomics data analysis. Timely model clinical, genomics and metabolomics data to find statistical patterns across millions of features to identify underlying biological pathways, modifiable risk factors and actionable information that supports early detection and prevention of COVID-19, and development of new therapies for better patient care. Next, ensuring security reconcile noise, need to build and train machine learning prognostic models to find actionable information that supports early detection and prevention of COVID-19. Based on the myriad data, applying appropriate machine learning algorithms to stratify patients, understand scenarios, optimise decision-making, identify high-risk rare variants (including ACE2, TMPRSS2) and making medically relevant predictions. Innovative and intelligent solutions are required to improve the traditional symptom-driven practice, and allow earlier interventions using predictive diagnostics and tailor better personalised treatments, when confronted with the challenges of pandemic situations.

scholarly journals The Future of Health care: Machine Learning

2018 ◽  
Vol 7 (4.6) ◽  
pp. 23 ◽  
Author(s):  
M. A.Jabbar ◽  
Shirina Samreen ◽  
Rajanikanth Aluvalu
Keyword(s):  
Machine Learning ◽  
Health Care ◽  
Decision Support ◽  
Decision Support Systems ◽  
Precision Medicine ◽  
Support Systems ◽  
Personalized Care ◽  
Machine Learning Methods ◽  
Effective Diagnosis ◽  
Change Health Care

Machine learning (ML) is a rising field. Machine learning is to find patterns automatically and reason about data.ML enables personalized care called precision medicine. Machine learning methods have made advances in healthcare domain. This paper discuss about application of machine learning in health care. Machine learning will change health care within a few years. In future ML and AI will transform health care, but quality ML and AI decision support systems (DSS) Should Require to address the problems faced by patients and physicians in effective diagnosis. 

Machine learning for precision medicine forecasts and challenges when incorporating non omics and omics data

2021 ◽  
Vol 15 (1) ◽  
pp. 69-85
Author(s):  
J. Susymary ◽  
P. Deepalakshmi
Keyword(s):  
Machine Learning ◽  
Precision Medicine ◽  
Data Analytics ◽  
Forecast Model ◽  
Biological Knowledge ◽  
Omics Data ◽  
Future Directions ◽  
Hard Data ◽  
Data Limitations ◽  
Future Project

Precision Medicine has emerged as a preventive, diagnostic and treatment tool to approach human diseases in a personalized manner. Since precision medicine incorporates omics data and knowledge in personal health records, people who live in industrially polluted areas have an advantage in the medicinal field. Integration of non-omics data and related biological knowledge in term omics data is a reality. The heterogenic characteristics of non-omics data and high dimensional omics data makes the integration challengeable. Hard data analytics problems create better opportunities in analytics. This review cut across the boundaries of machine learning models for the eventual development of a successful precision medicine forecast model, different strategies for the integration of non-omics data and omics data, limitations and challenges in data integration, and future directions for the precision medicine forecasts. The literature also discusses non-omics data, diseases associated with air pollutants, and omics data. This information gives insight to the integrated data analytics and their application in future project implications. It intends to motivate researchers and precision medicine forecast model developers in a global integrative analytical approach.

Avenues to Precision Oncology

2020 ◽  
pp. 36-45
Author(s):  
Alexander Meisel
Keyword(s):  
Precision Medicine ◽  
Trial Design ◽  
Ad Hoc ◽  
Molecular Targets ◽  
Clinical Trial Design ◽  
Predictive Biomarkers ◽  
Precision Oncology ◽  
Companion Diagnostics ◽  
Bona Fide ◽  
The One

Until recently, the clinical management of cancer heavily relied on anatomical and histopathological criteria, with ad hoc guidelines directing the therapeutic choices in specific indications. In the last years, the development and therapeutic implementation of novel anticancer therapies significantly improved the clinical outcome of cancer patients. Nonetheless, such cutting-edge approaches revealed the limitation of the one-size-fits-all paradigm. The newly discovered molecular targets can be exploited either as bona fide targets for subsequent drug development, or as tools to precision medicine, in the form of prognostic and/or predictive biomarkers. This article provides an overview of some of the most recent advances in precision medicine in oncology, with a focus on novel tissue-agnostic anticancer therapies. The definition and implementation of biomarkers and companion diagnostics in clinical trials and clinical practice are also discussed, as well as the changing landscape in clinical trial design.

scholarly journals Machine Learning Use for Prognostic Purposes in Multiple Sclerosis

Life ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 122
Author(s):  
Ruggiero Seccia ◽  
Silvia Romano ◽  
Marco Salvetti ◽  
Andrea Crisanti ◽  
Laura Palagi ◽  
...  
Keyword(s):  
Machine Learning ◽  
Multiple Sclerosis ◽  
High Impact ◽  
Prognostic Models ◽  
Early Prediction ◽  
Disease Course ◽  
Slow Progression ◽  
Relapsing Remitting ◽  
Long Time ◽  
Effective Drugs

The course of multiple sclerosis begins with a relapsing-remitting phase, which evolves into a secondarily progressive form over an extremely variable period, depending on many factors, each with a subtle influence. To date, no prognostic factors or risk score have been validated to predict disease course in single individuals. This is increasingly frustrating, since several treatments can prevent relapses and slow progression, even for a long time, although the possible adverse effects are relevant, in particular for the more effective drugs. An early prediction of disease course would allow differentiation of the treatment based on the expected aggressiveness of the disease, reserving high-impact therapies for patients at greater risk. To increase prognostic capacity, approaches based on machine learning (ML) algorithms are being attempted, given the failure of other approaches. Here we review recent studies that have used clinical data, alone or with other types of data, to derive prognostic models. Several algorithms that have been used and compared are described. Although no study has proposed a clinically usable model, knowledge is building up and in the future strong tools are likely to emerge.

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