BiG - Introduction to BioInformatics and Genomic Medicine

Description

The MOOC BiG "Introduction to BioInformatics and Genomic Medicine" aims to address all the bioinformatics aspects necessary for the production and interpretation of High-Throughput Sequencing (HTS) or Next Generation Sequencing (NGS) data within a clinical genetics laboratory with examples of rare diseases and oncogenetics.

This introductory course is primarily intended for health professionals using genomics. Its objective is to provide specific and adapted contents to enable them to understand the different steps from phenotyping to molecular diagnosis and to have a critical eye on the analyses while taking into account the pitfalls and limits of NGS. Designed by a French team, it will also present the functioning of the genomic pathway in France.

For the general public or the curious, the objective is to make them aware of a technique that plays an increasingly important role in the diagnosis of genetic diseases.

Format

The MOOC will be self paced. Learners will have access to all the contents from the beginning. Each teaching unit will explore a step of NGS processing by focusing on different themes with videos in french subtitled in English, texts and self-correction exercises. Interactive content, such as python-based jupyter notebooks will permit us to go further in genome interpretation and programming.

The pedagogical content consists of a description of genomics issues, the technological and technical challenges of high-throughput sequencing, the interpretation of variants, analysis and the bioinformatic methods used. You will therefore follow a bioinformatics pipeline of reverse analysis in stages, i.e. starting from the interpretation of the result of an NGS analysis to go back to the raw files.

As genomic medicine and NGS require a wide range of skills, we suggest you make your own path through the MOOC according to your profile and learning objectives.

- For the beginners, the introductive unit “Back to Basics” will guide you through the basics of genetics, bioinformatics and genomic medicine.
- Unit 1 sets the context and will be of interest to all learners, with the example of the French model.
- Unit 2 is at the crossroads between clinical, biological, bioanalytical and bioinformatics. It will be of interest to all those who will be prescribing or interpreting genetic results as well as bioinformatics pipeline designers.
- Units 3, 4 and 5 are increasingly focused on bioinformatics. Bioinformaticians will be in familiar territory, it may be more difficult for those who do not handle these tools on a daily basis.

In short, pick what you find most useful or follow the guide!

A forum is dedicated to online exchanges between learners and pedagogical team !

Prerequisites

This MOOC is particularly aimed at health professionals, students or practicing physicians, for whom genetics is part of their daily work. This includes geneticists, genetic counsellors, engineer bioinformaticians as well as non-geneticists physicians or other health professions who wish to broaden their skills.

In addition, it is also intended for the general public wishing to understand the bases of applied bioinformatics to genomic medicine and the medical interpretation of genetic variations.

It is recommended to have prior knowledge of human genetics to better benefit from the content of this course. To refresh your knowledge, a "back to basics" content will be available at the beginning of the MOOC!

Assessment and certification

Successful completion (70%) of the exam at the end of each unit will result in a certificate of achievement. This MOOC does not provide academic certification at this time.

Course plan

- Introduction to Genomic Medicine
  Genetics basics
  Discover Bioinformatics in genetics
- Genomics and Rare Diseases
  Genomics and Oncogenetics
  Genomics and Technologies
  Genomics and Bioinformatics
- Introduction
  Population frequency databases
  Phenotype-genotype databases
  Functional data aggregation tools
  Interpretation in oncogenetics
  Conclusion
- Principles of detection
  File formats: VCF
  Detection of variations in oncogenetics
- Alignment methods and algorithms
  File formats: BAM, SAM and CRAM
  Quality criteria of alignment
  Reads visualisation
- Principles
  File Formats: FASTA, FASTq
  Quality criteria of a somatic variation

Course team

JULIEN THEVENON

MD, PhD Medical geneticist - University Hospital of Grenoble Alpes (France) Head of the Genetics, Genomics and Procreation department. Coordinator of a centre of excellence for rare diseases with developmental abnormalities and malformative syndromes, within the AnDDI-Rare (French rare diseases network). Co-head of the AURAGEN genomic laboratory.

KÉVIN YAUY

MD, PhD student in Bioinformatics. Medical geneticist Universities of Montpellier and Grenoble Alpes, SeqOne Genomics With a particular interest in clinical genetics and bioinformatics, Kevin co-lead of French national courses on bioinformatics for genomic medicine. His main research interest aims to build software and data science tools to explore the human genome in order to overcome diagnostic odyssey in rare disease.

EVAN GOUY

MD, M Ed Sc Junior Doctor in medical genetics Instructional designer Reims and Lyon University Hospitals Since the beginning of his medical studies, he has been interested in medical education and teaching with a particular interest for ICTEs (Information and Communication Technologies for Education) and clinical supervision. This led him to do a Master degree in learning sciences which made it possible to launch the first version of this MOOC.The next step is the end of the residency and maybe a thesis in educational sciences applied in medical genomics?

Gael Guillou

Instructional designer - Digital University for Health studies in France - UNESS A full-time instructional designer in the healthcare sector. Has as a broad professional background working across the globe in various branches : language tutoring; pharmaceutical; accounting; cold chain; nuclear and vacuum technologies; IT, real estate and agriculture. Today designs online learning courses and develops digital educational tools for the medical community of University teachers and students in 40 universities in France.

Organizations

Université de Paris

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License

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