HEALTHCARE SECTOR and Bioinformatics - Suggested reading by the EMA Board – THE BIOS PROJECT -
Guglielmo M. Trovato MD, PhD, FRCP (Lon)
Director: European Medical Association (EMA); Expert at the European Cooperation in Science & Technology COST association Prof. of Internal Medicine & former Director: the Postgrad. School of e-learning & ICT UNICT Italy
The presentation and the links refers to several issues present in the second and third module of the BioS Course.
Module 2. Computational Statistics for clinical doctors
? Basic statistical techniques, including: descriptive statistics, elements of probability, hypothesis testing, nonparametric methods, correlation analysis, and linear regression
? How to choose appropriate statistical tests and how to assess statistical significance
? How data can be visualized and tested within the R language environment, e.g. how variants can be identified from sequencing data
We list below few articles, which are itemized by their main contents and concepts, and referenced choosing exclusively full free open access texts easily reachable in the web and downloadable in the most usual ways.
If accessed through the vpn of any European Teaching Institution, as most trainees will probably be able to do, for instance in their condition of medical under- or post-graduate students or through Eduroam, other articles, not listed here, can be read and downloaded as well.
We arranged an interactive overview addressing computational statistics which is available at https://www.dhirubhai.net/pulse/erasmus-plus-bios-project-bioinformatics-literacy-guglielmo-m-
The use and management of big data in the “real world” is a topic strongly and plainly addressed in several uploaded articles:
1. Five ways to fix statistics https://media.nature.com/original/magazine-assets/d41586-017-07522-z/d41586-017-07522-z.pdf
2. Building reliable evidence from real-world data Needs, methods, cautions. A very Challenging and comprehensive article. https://ebph.it/article/download/8981/8192
3. It is particularly interesting the article of the New England Journal of Medicine, “The Primary Outcome Is Positive”, challenging some of the pivotal topics of clinical trials and computational statistics.
https://www.nejm.org/doi/pdf/10.1056/NEJMra1601511?articleTools=true
Several contributions in Nature were subsequently provided, and are a useful source of ideas and debate:
4. No publication without confirmation https://www.nature.com/news/no-publicationwithoutconfirmation-1.21509
5. Scientists rise up against statistical significance https://www.nature.com/articles/d41586-019-00857-9
6. Blind analysis_ Hide results to seek the truth https://www.nature.com/news/blind-analysis-hideresultsto-seek-the-truth-1.18510
7. Crowdsourced research_ Many hands make tight work https://www.nature.com/articles/526189a
8. Reproducibility A tragedy of errors https://www.nature.com/news/reproducibility-a-tragedy-oferrors1.19264
Some articles in Italian are focused to topics, which are fruitfully managed by computational statistics:
9. Il cancro, dal modello istologico a quello mutazionale https://www.quotidianosanita.it/scienza-e-farmaci/articolo.php?articolo_id=72642
10. Malattie cardiovascolari. Solo 1 paziente su 2 segue le terapie https://www.quotidianosanita.it/scienzaefarmaci/articolo.php?articolo_id=11866
11. La bravura di un medico_ è inversamente proporzionale al numero di esami che prescrive (by Guglielmo Trovato) https://www.quotidianosanita.it/lavoro-eprofessioni/articolo.php?articolo_id=26620
12. Telemedicina, App, robotica, hi tech e bioinformatica:gli ospedali dell’Usl Toscana centro https://www.quotidianosanita.it/toscana/articolo.php?articolo_id=72124
Module 3. Commercial personalized genomics services in patient care
? SNPs and their role in health and disease
? Disease risk related statistics and their interpretation
? Overview of reports from services such as 23andMe, deCODE, Gene by Gene
? Translating example reports to non-disease phenotypes with selected example traits, e.g. bitter taste perception
? Translating example reports to disease risks with selected example diseases, e.g. asthma ?
Translating example reports to drug response traits with relevant examples, e.g. Warfarin sensitivity
We list below few articles, which are itemized by their main contents and concepts, and referenced choosing exclusively full free open access texts easily reachable in the web and downloadable in the most usual ways.
If accessed through the vpn of a European Teaching Institution, as most trainees will probably be able to do, for instance in their condition of medical under- or post-graduate students or through Eduroam, other articles, not listed here, can be read and downloaded as well.
1. Our material contributed to this module begins with Predictive, Preventive and Personalised Medicine as the hardcore of ‘Horizon 2020’EPMA position paper. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985551/
Committed Medical Associations, being at the forefront of the global efforts, promote integrative and innovative concepts among health care stakeholders, governmental institutions, educators, funding bodies, patient organizations and in the public domain.
Reviews with some topics integrative with those dealt in this module, published in top-ranked Journals are:
2. An evolution from genetic counselling to genomic counselling, which is particularly relevant for the perspectives which are opened in a plain way.
https://www.sciencedirect.com/science/article/pii/S1769721219302514?via%3Dihub
3. A framework for identification of on- and off-target transcriptional responses to drug treatment, combining promoter expression profiling after drug treatment with gene perturbation of the primary drug target. https://www.nature.com/articles/s41598-019-54180-4.pdf
4. Bioinformatic: Big Data Versus the Big C – where Big C stands for Cancer – is a clear, brief and easy to follow overview.
https://www.nature.com/articles/509S66a.pdf
5. Multiomic patterns in body fluids is a special article, contributed by EMA “MULTIOMIC PATTERNS IN BODY FLUIDS: TECHNOLOGICAL CHALLENGE WITH A GREAT POTENTIAL TO IMPLEMENT THE ADVANCED
PARADIGM OF 3P MEDICINE. https://onlinelibrary.wiley.com/doi/pdf/10.1002/mas.21612
Moreover, two articles with a plain presentation of very relevant and challenging themes in oncology are included – in Italian, the first delivered by the greatest professional medical journal in Italy with more than 300.000 subscribers and readers, the second by Scientific American:
6. Bioinformatics also in other approaches and fields: SEPSIS. Educational and Best Practice Frontiers. Beyond the Boundaries of Fatality, Enhancing Clinical Skills and Precision Medicine.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7024868/pdf/tcrm-16-87.pdf
7. Non-alcoholic fatty liver disease and Atherosclerosis at a crossroad: The overlap of a theory of change and bioinformatics. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7226912/pdf/WJGP-11-57.pdf
8. The 4emedicine: Emergency, Environmental, Electronics and Extreme medicine. Overview of the available and on‐going related controlled trials with a survey on the overlap areas and on the use of bioinformatics. https://faseb.onlinelibrary.wiley.com/doi/abs/10.1096/fasebj.2020.34.s1.02723
WEBINARS AND INTERVIEWS
Medical, legal and managerial professionalism in Zurich at the VI Fleming Conference on regulatory compliance and big data sharing, privacy and transparency in the pharmaceutical and healthcare sectors. https://www.youtube.com/watch?v=Ho2F7KIlJWE
Acknowledgment and disclaimer: This article is written by Guglielmo Trovato, MD, Professor of Medicine, Director at EMA for Media, e-Learning and e-Medicine. The European Commission even indirect support for the production of this publication does not constitute an endorsement of the contents which reflect the views only of the author, and the Commission cannot be held responsible for any use which may be made of the information contained therein.