E-learning training modules

1. E-learning training modules related to Genomic Medicine topics, such as: Personalised Medicine, Economics and Health Technology Assessment in Genomics, Nutrigenomics, bioinformatics.

These modules are provided in English, as well as in local languages, where applicable. They are available every trimester and are designed for healthcare professionals and biomedical scientists, who wish to enrich their knowledge on these emerging disciplines and lead to academic Certificates. 

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The following e-learning training modules are currently available:

Introduction to Bioinformatics for clinical genome interpretation

Introduction to Bioinformatics for clinical genome interpretation

Instructor: Dr. Darrol J. Baker; The Golden Helix Foundation, London, UK 

Course overview

This is a practical course in Bioinformatics, which will emphasize how to use the computer as a tool for biomedical research. Prerequisites include a thorough understanding of theoretical and practical aspects of molecular biology, and a medium level of mathematics and statistics, but no prior knowledge of computer programming or computer hardware is necessary.

Bioinformatics has now firmly established itself as a discipline in molecular medicine, and encompasses a wide range of subject areas from structural biology, genomics to gene expression studies and personalised medicine. In this course we will learn how algorithms, databases and popular software tools are used to answer these and many other questions in modern clinical genomic biology as well as applying them to real world whole human genomes experimental datasets for understanding and interpretation. We will take the user from a beginner level understanding to one that can analysis multiple whole human genomes and derive meaningful clinical results using the latest methodologies.

The first part of the course includes an introduction to bioinformatics the discipline of Pharmacogenomics, accompanied by an historical perspective. This part also refers to the analytical methods used in pharmacogenomic testing.

The second part of the course includes a comprehensive overview of databases used within the field of bioinformatics for clinical data understanding and the power of relational databases within this setting. The final part covers algorithms for solving various biological problems along with a handful of programming challenges helping you implement these algorithms using Perl and Python.

The third part of the course will cover algorithms for solving various biological problems along with a handful of programming challenges helping you implement these algorithms in Python. Lasty, this places these techniques in a clinical setting for the understanding of clinical genomes and patient diagnosis.

The fourth part of this course covers more advanced techniques for genome manipulation and understanding that are crucial in personalized medicine and tailoring ones genome understanding within a clinical setting.

The fifth and final part of the course is dedicated to clinical genomics and bioinformatics understanding within a clinical or healthcare settings. Dealing with patient data and presenting clinical findings to clinicians, healthcare workers and patients. Finally, an understanding of data security, ethics and future directions in genome and personalised medicine.

Duration: 3 months

Table of Contents

1.1 The Role of Bioinformatics in Clinical Genomics

1.2 Introducing Clinical Genomics Databases

1.3 Introducing Alignments, BLAST and Perl

1.4 Further Alignment with Perl for the Clinic

1.5 Multiple Sequence Alignments (MSA) and Perl in Clinical Genomics.  

1.6 Clinical Phylogenetic Analysis

1.7 Introduction to Clinical Genomics

1.8 Advanced Clinical Genomics: Microarray Analysis

1.9 Clinical Next Generation Sequencing (NGS)

1.9.1 Loading Sequence

1.9.2 Manipulation and Analysis

1.10 Advance Clinical NGS Analysis

1.10.1 Sequence Variation

1.10.2. Commercial Genomics

1.11 Clinical NGS 1: The importance of ChIP-seq

1.12 Clinical NGS 2: The importance of RNA-seq

1.13 Clinical NGS: Personalised and Stratified Medicine.

1.14 Future Directions in Clinical Medicine

Evaluation

The overall evaluation of the students will be based on the assessment of a task that will be related to the topics discussed in this course. 

Health Economics in Personalised Medicine

Health Economics in Personalised Medicine

Instructors: Vasilis Fragoulakis, PhD; Christina Mitropoulou, MBA, The Golden Helix Foundation, London, UK

Course overview

This e-learning course touches upon the use of health economics in Personalized Medicine. The course begins with the description of the international environment and the basic economic issues which need to be tackled from health economics. Then, an introduction to the notions of human genetics and genomics, Pharmacogenomics and Personalized Medicine is provided, along with their applications, in relation to health economics.

The course continuous with an introduction to health economics, providing and analyzing some aspects of health economics and its relation to the economic science. The course also discusses the decision criteria based on the cost-utility analysis, from which the final decision to adopt or reject a new technology, new therapy, or innovative drug, is derived. In addition, the various ways of assessing the quality of life in cost-utility analysis and utility estimation methods. This section ends with the summary of the disadvantages and the assumptions of the cost-utility analysis. The notion of pricing and reimbursement is also addressed in this course and the means of performing this analysis in different countries, always related to Personalized Medicine. Most importantly,the step-by-step methodology of the economic evaluation is outlined, combined with examples of application in medical practice. In particular, the methodology includes an introduction to the method of economic evaluation, the various aspects of cost-effectiveness analysis with regard to alternative approaches, accompanied by specific examples in medical practice, the appropriate measure of cost-effectiveness analysis and the evaluation criteria that are used in health. In this course, the principles of economic analysis in personalized medicine are thoroughly analyzed, particularly the various economic models used in personalized medicine, both in prospective and in retrospective studies. Finally, the challenges of the economic assessment in the field of personalized medicine and the future perspectives of this discipline are summarized.

Evaluation

The overall evaluation of the students will be based on the assessment of a task that will be related to the topics discussed in this course. 

Course duration: 3 months

Table of contents

1.     The International economic environment

2.     Introduction to genomics

3.     Introduction to health economics

4.    Analyse the aspects of demand in health economics

5.    The notion of supply in health economics

6.    Stakeholders and decision-making in the healthcare

7.     Price and Reimbursement

8.    Assessing cost-effectiveness of Personalised Medicine

9.    Cost-effectiveness analysis: Determining the cost items

10.  Cost-effectiveness analysis: Measuring the effectiveness

11.  Conclusion and future perspective

Economic Evaluation in Genomic Medicine

Economic evaluation in Genomic Medicine

Instructor: Vasilis Fragoulakis, PhD; Christina Mitropoulou, MBA; The Golden Helix Foundation, London, UK

Course overview 

The first section provides the definition of economic evaluation in health services and its relation to the economic science. It also discusses whether or not personalized medicine can coexist with the economic evaluation, what are the points that they intersect and why it is necessary to make economic assessments. At the same time, the methodology of the economic evaluation is outlined combined with examples of application in medical practice. In particular, the methodology includes an introduction to the method of economic evaluation, the various aspects of cost-effectiveness analysis with regard to alternative approaches, accompanied by specific examples in medical practice, the appropriate measure of cost-effectiveness analysis and the evaluation criteria that are used in health.

The second section discusses the decision criteria based on the cost-effectiveness analysis, from which the final decision to adopt or reject new technology, new therapy, or innovative drug, is derived. In addition, there are various ways of assessing the quality of life in cost-utility analysis and utility estimation methods. This section ends with the summary of the disadvantages and the assumptions of the cost-utility analysis.

In the third section, the most important technical issues related to the economic evaluation are summarized. In particular, the definition of the willingness to pay (λ) and how it is calculated in different countries is presented, along with the different types of economic models and their use as practical tools for making and implementing political decisions.

In the fourth and final section, the principles of economic analysis in personalized medicine are thoroughly analyzed. In particular, the various economic models used in personalized medicine are presented, both in prospective and in retrospective studies. Also, reference is made to the concept of measurable efficacy in personalized medicine, while detailed examples and standard economic assessment studies in pharmacogenomics and personalized medicine are discussed. Finally, the challenges of the economic assessment in the field of personalized medicine and the future perspectives of this discipline are summarized.

Duration: 3 months

Table of contents

Chapter 1 – Introduction to health economics (Economic science, the framework for the application of economic assessment in healthcare services.) 

Chapter 2 – Introduction to Precision Medicine (Introduction to human genetics and genomics. The concept of precision medicine, applications of Pharmacogenomics and genomics into health economics.)

Chapter 3 – Introduction to economic evaluation. (Genomics into health economics, systematic Review for economic evaluations in Genomic Medicine)

Chapter 4 – Decision criteria based on cost-effectiveness analysis. The final decision to adopt or reject a new technology, new therapy or innovative drug.

Chapter 5 – Assessing the quality of life in cost-utility analysis and utility estimation methods. Issues in cost-utility analysis.

Chapter 6 – Important technical issues in the economic evaluation. The value of λ in different countries. How much does it cost a year of life?

Chapter 7 – Cost estimation in economic studies. Sensitivity analysis.

Chapter 8 – Economic analysis and economic models in personalized medicine.

Chapter 9 – Measurable effectiveness in personalized medicine. Examples of economic evaluation in personalized medicine.

Chapter 10 – Price and reimbursement.

Chapter 11 – Challenges of economic evaluation in the field of personalized medicine. Conclusions and future prospects. 

Evaluation

The overall evaluation of the students will be based on the assessment of a task that will be related to the topics discussed in this course.  

Pharmacogenomics in Clinical Care and Drug Discovery

Pharmacogenomics in clinical care and drug discovery

Instructor: Prof. Dr. George P. Patrinos; University of Patras, Department of Pharmacy, Patras, Greece

Course overview

Pharmacogenomics is the cornerstone of Genomic and Precision Medicine, aiming to redefine disease management and patient stratification. As such, pharmacogenomic testing becomes fundamental to the development and clinical use of several molecular diagnostics as well as targeted therapies. Notwithstanding, there are still barriers (scientific, economic, educational, ethical, legal) that need to be overcome prior to the application of pharmacogenomic technologies towards innovative clinical strategies and optimized therapeutic outcomes. For this to be achieved, continued research as well as the participation of all involved stakeholders becomes critical. This course aims to summarize the current knowledge on how the discipline of genetics and genomics can influence drug discovery and development, and more broadly to the practice of health care.

The first part of the course includes an introduction to the discipline of Pharmacogenomics, accompanied by an historical perspective. This part also refers to the analytical methods used in pharmacogenomic testing.

The second part of the course includes examples from the clinical applications of pharmacogenomics. In particular, examples of use cases in oncology, cardiology, psychiatry, infectious diseases, transplantation, etc are discussed, focusing in particular on the corresponding drug-gene-pharmacogenomic biomarker combinations, focusing in particular on the required dose adjustements.

The third part of the course discusses the impact of population differences in the prevalence of pharmacogenomic biomarkers and their role in population pharmacogenomics. It also alludes to the complex phenotypes and rare drug outcomes resulting from rare pharmacogenomic variants. Lastly, this part summarizes the various regulatory aspects of pharmacogenomics and their role in drug development.

The fourth part of this course provides an outline of databases and other useful resources for Pharmacogenomics, such as the PharmGKB knowledgebase, etc. It also discusses the various new trends in the pharmacogenomics field, such as pharmacometabolomics-aided pharmacogenomics and the application of whole genome sequencing in pharmacogenomics.

The fifth and final part of the course is dedicated to the various ethical aspects of pharmacogenomics and the implications of the accompanying pharmacogenomics-related legislation. Lastly, this part discusses the role and impact of Pharmacogenomics on public health.

Duration: 3 months

Table of contents 

1. Introduction and history of Pharmacogenomics

2. Analytical methods in Pharmacogenomics

3. Pharmacogenomics in clinical settings – Oncology

4. Pharmacogenomics in clinical settings – Cardiology

5. Pharmacogenomics in clinical settings – Psychiatry and Infectious diseases

6. Population differences and complex phenotypes in pharmacogenomics

7. Regulatory aspects of pharmacogenomics and its role in drug development

8. Useful resources for Pharmacogenomics

9. New trends in Pharmacogenomics

9.1. Pharmacometabolomics-aided pharmacogenomics

9.2. Pharmacogenomics and whole genome sequencing

10. Ethical aspects of pharmacogenomics and implications

10.1. Pharmacogenomics legislation

10.2. Secondary information

11. Public Health Pharmacogenomics

12. Conclusions and future perspectives

Evaluation

The overall evaluation of the students will be based on the assessment of a task that will be related to the topics discussed in this course. 

Nutrigenomics

Nutrigenomics

Instructor: Dr. Cristiana Pavlidis

Duration: 3 months

Table of contents

1. Basic knowledge of nutrition 

2. History and the role of heredity in nutrition 

3. Nutrient-Related pathologies

4. Nutrigenomics: Genes and nutrition

5. The role of genomics in dietary intake  

6. Genomic Medicine: Implication in individualising nutritional choices 

7.  Companion methodological approaches in nutrigenomics: Proteomics and Metabolomics 

8. Nutrigenomics and obesity

9. Role of gut microbiote in nutrition

10. Economic aspects of nutrition

11. Ethics of the individualization of nutrition through genomics 

Evaluation

The overall evaluation of the students will be based on the assessment of a task that will be related to the topics discussed in this course. 

On-site training courses

On-site training courses in Human Genome Informatics are provided on a regular basis in London and aim to provide hands-on experience in basic aspects of human genome informatics. The next available on-site training course is scheduled for March 2nd, 2018 (please see below).  

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On-site Course: Bioinformatics and Clinical Genomics

On-site Course: Bioinformatics and Clinical Genomics

Next available on-site courses:

- March 2nd, 2018, London, UK

- May 4th, 2018, San Gwann, Malta

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Instructors: Dr. Darrol J. Baker; The Golden Helix Foundation, London, UK; Prof. Dr. George P. Patrinos; University of Patras, Department of Pharmacy, Patras, Greece 

What will this course be delivering?

We will spend two days on your site, delivering a fun, yet intensive, course in clinical genomic and bioinformatics. The course is designed to bridge knowledge gaps between genomics and high-end computing. The course will provide insight into the past, present and future of precision bioinformatics, with particular emphasis on clinical finding of variants. The simple aim being for users to turn up to the class with, in effect, an empty laptop and by the end of class having the basic knowledge and know how to deliver clinical called variants on a set of whole genome data.

Schedule

Day 1 - Understanding the Software, Hardware needs and Designing Pipelines.

On Day 1, we will cover the fundamentals of what you need to run a successful pipeline of genome data: On both the plant and animal side: Installation of software, tools and scaling your IT to cope with genome demand. We will focus on building your genome pipeline and run your first pipeline of data.

Day 2 - Implementation of data: Finding meaning in the data.

On Day 2, we will provide insight into your data and learn about the very good, very bad and very ugly practices used within clinical diagnostics, nutrigenomics and personalised medicine industry. How to spot bad quality data and corrective actions you can make to your data and suppliers.

Post Course

We, if you wish, follow up with you on a quarterly basis to help you with your understanding completely free. We can also consult or offer further in-house training for your groups (see in-house training below)

Objectives

·       - Work on your issues and use your data, where ever possible within three days.

·       - Get to grips with the fundamentals of whole genome analysis and clinically calling variants.

·       - Creating a sustainable and scalable genomics pipelines.

·       - Learn about the main aspects of the industry, including key terminology and concepts

·       - Understand today’s global landscape of genomic interpretation.

·       - Gain insight into public and private initiatives across Americas, Europe and Asia

·       - Discover the role of genomic data in the business of clinical diagnostics.

·       - Explore business models and options for exploitation of genome-based technologies.

·       - Identify commercial opportunities in diagnostics arising from genome data aggregation

·       - Understand human factors for market penetration of DNA testing

·       - Understand the future of advanced stratified diagnostics in the clinic

·       - Analyse leverage your data, datasets and their value

·       - Discover the emerging industry of pharmacogenomics and stratified medicine.

·       - Learn to translate and commercialise clinical outcomes derived from genome data

·       - Identify opportunities in the genomics landscape as part of individual health planning

·       - Learn how innovative companies are investing in this new multi-trillion dollar industry

·       - Understand how to implement genomic and precision medicine into practice

·       - Appreciate the challenges and opportunities in transitioning to precision based care

·       - Get to grips with artificial intelligence, machine learning and big data in precision medicine

·       - Understand the evolving world of ‘-omics’ and how software is enabling the analysis of vast sums of health data

·       - Learn about precision medicine opportunities beyond tumour genome sequencing, cancer therapeutics and metabolic conditions.

Target Audience

These courses are ideally suited to those already working in, and those who would like to enter the Genomic and Precision Medicine disciplines and related technologies, Biopharma, Healthcare and Clinical Research Industries. These include life science industry representatives from pharmaceutical, medical devices and diagnostic industries, clinical innovators, hospital executives, payers, policy makers, multidisciplinary researchers, patient advocates, angel, venture capital investors and academia. However, this industry is evolving and you may not fit the normal target audience, but feel you have something to offer. We have had people from automotive, space sciences, oil exploration and indeed deep-sea discovery taking this course, since programme design and algorithms usages are very similar and can offer ‘a fresh pair of eyes’ to a given issue.

On demand on-site training

On demand on-site training. Apart from the above means of training, the Golden Helix Academy offers the option of on-site training on demand, where experienced instructors provide training of academic or corporate staff on demand at your premises, namely your institution or company in your own country. On demand on-site training course are tailor-made to meet your needs and time schedule. The themes of the on demand onsite training revolve around pharmacogenomics, cancer genomics, economics and Health Technology Assessment, and genome informatics.

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Webinar Bioinformatics

Friday 12th of June 2020

This webinar is designed to introduce undergraduate and graduate-level students in health sciences or related fields to the field of bioinformatics and health informatics, as well as demonstrate the opportunities that come with the available big data for research and industry. The final section of the webinar provides an overview of next-generation sequencing technologies and their application in personalised medicine, whilst also allowing interaction with the participants in the form of Q&A.

The webinar will be delivered in Greek.

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