Rare Diseases at the Omics era: current tools for frequent challenges

Sequencing methods mark a significant advancement in the study of rare diseases. Integrating data from various sources is becoming crucial for enhancing molecular analysis and diagnosis.

The goal of this CIVIS summer school is to offer high-quality, interdisciplinary courses that address these needs.

• Fundamental notions in medical genetics 
• Epigenetics
• iPSC to rare diseases
• Biomedical ethics
• R programming
• Bioinformatics workflows
• Sequencing technologies
• Variants analysis
• Splicing events
• Single Cell RNA-seq
• Spatial transcriptomics

The students will improve their knowledge and their skills in rare disease (fundamental notions medical genetics, epigenetics, iPSC to rare diseases, biomedical ethics, etc), cross-cutting skills (bioinformatics, sequencing technologies, variant analysis, scRNA-seq, spatial transcriptomics etc.) and soft skills (English, teamwork, critical thinking and synthesis skills, build a professional network etc).

The physical mobility part will be running between 28 June - 2 July 2027 in Marseille, France.

It will combine lectures with extensive hands-on training in genomics, epigenomics and bioinformatics. The programme will cover rare disease diagnostics, genome regulation, DNA repair, splicing, and iPSC applications, while practical sessions focused on DNA library construction, sample quality control, sequencing, Unix/ Linux, Slurm, reproducible workflows, and the analysis of epigenomic datasets. The course provided participants with practical experience using state-of-the-art experimental and computational approaches for rare disease research.

Team building and social events (Marseille calanques's hikes; pizza & quiz evenings, etc.) will be proposed during the physical mobility week.

The virtual part sessions will take place between 1 March - 28 May 2027, weekly.

It will provide participants with the theoretical foundations required for the hands-on training. It will cover an overview of next-generation sequencing technologies, the genetic and epigenetic basis of rare diseases, sequencing and programming applications in medical genetics. 

Participants will be introduced to single-cell, spatial transcriptomics technologies and multi-omics approaches. The sessions will also introduce participants with the analysis of omics datasets.

The assessment for this program will consist of:

• Virtual part: multiple-choice questions (MCQ) and/ or dataset analysis.
• Physical part: multiple-choice questions (MCQ).
• active participation in both parts (virtual and physical)

Motivation Letter

CV

Other

The evaluation will assess the applicant’s background and experience in molecular and cellular biology, including training courses and internships. It will also consider the alignment of the research project and/ or career goals with the summer school’s focus, as well as the applicant’s proficiency in English.

Aix-Marseille University, amU (France):

• Denis Puthier (coord.), researcher TAGC lab, full Professor at the Polytech school of engineering, co-head of the TGML Genomics platform, codeputy director for education of the Marseille Rare Disease’s institute)
• the TGML sequencing platform, Marseille: Anna Maria Alklaiany, Béatrice Loriod, Vincent Palomo, Hortense Vachon
• Diane Frankel, MCU-PH cellular biology, in MMG Lab and hospital AP-HM, codeputy director for education of the Marseille Rare Disease’s institute
  
• Frédérique Magdinier, researcher, MMG lab, director of the MMG lab and director of the Marseille Rare Diseases’ institute
• Aïtor Gonzalez, MCU, TAGC lab
• Svetlana Gorokhova, MCU-PH, MMG lab, AP-HM
• Mario Abaji, AHU, MMG laboratory, AP-HM
• Christophe Lachaud, researcher, CRCM lab
• AnaÏs Baudot, researcher, MMG lab
• Marc Bartoli, researcher, MMG lab
• the GBiM sequencing platform: Valérie Delague, MMG Lab
• Heather Etchevers, researcher, MMG lab
• Leslie Caron, researcher, MMG lab
• Christopher De Bono, researcher, MMG lab
• Sandrine Marquet, researcher, TAGC lab

Paris Lodron University of Salzburg (Austria):

• Angelika Lahnsteiner (coord.), assoc. Professor, Cancer (Epi-)genetics Lab, Depart. of Biosciences and Medical Biology
• Aarathy Geetha, senior scientist, Depart. of Biosciences and Medical Biology
• Peter Krenn, senior scientist, Depart. of Biosciences and Medical Biology

Université Libre de Bruxelles, ULB (Belgium):

• Isabelle Migeotte (coord.), clinical geneticist, ULB Genetics (Centre de Génétique Humaine) 
• Sebastian Neuens, clinical geneticist, ULB Genetics 
• Catheline Vilain, clinical geneticist, ULB Genetics