Description

Objectives in terms of knowledge (course content) :

• Basic concepts and methodologies used in comparative genomics (orthology, paralogy, synteny, evolutionary rates…)
• Evolution of prokaryotic and eukaryotic genomes (mechanisms and evolutionary trends)
• Applied Comparative Genomics: phylogenetic footprinting, phylogenetic profiles, prediction of functional links, identification of targets by genotype/phenotype correlations…
• Population genomics
• Personal and medical genomics: variations and polymorphism, types of personal genomic data, detection and prioritization of variants, examples of large-scale projects

Compétences visées

Objectives in terms of acquired skills :

• Mastery of main internet resources dedicated to comparative genomics
• Ability to mobilize multidisciplinary knowledge
• Ability to develop an integrative strategy to answer a complex biological problem
• Ability to analyse personal NGS data to identify variants (quality, mapping, variant calling)
• Ability to prioritize candidates to identify disease–causing variants
• Capacity for a critical analysis of high-throughput data
• Awareness of ethical issues raised by patient data

Bibliographie

• 1000 Genomes Project Consortium, Auton, A., Brooks, L.D., Durbin, R.M., Garrison, E.P., Kang, H.M., Korbel, J.O., Marchini, J.L., McCarthy, S., McVean, G.A., et al. (2015). A global reference for human genetic variation. Nature 526, 68–74.
• Biagini, S.A., Ramos-Luis, E., Comas, D., and Calafell, F. (2020). The place of metropolitan France in the European genomic landscape. Hum Genet 139, 1091–1105.
• Eilbeck, K., Quinlan, A., and Yandell, M. (2017). Settling the score: variant prioritization and Mendelian disease. Nat Rev Genet 18, 599–612.
• Hug, L.A., Baker, B.J., Anantharaman, K., Brown, C.T., Probst, A.J., Castelle, C.J., Butterfield, C.N., Hernsdorf, A.W., Amano, Y., and Ise, K. (2016). A new view of the tree of life. Nature Microbiology 1, 16048.
• Karczewski, K.J., and Snyder, M.P. (2018). Integrative omics for health and disease. Nat Rev Genet 19, 299–310.
• Nevers, Y., Defosset, A., and Lecompte, O. (2020). Orthology: Promises and Challenges. In Evolutionary Biology—A Transdisciplinary Approach, P. Pontarotti, ed. (Cham: Springer International Publishing), pp. 203–228.
• Rehm, H.L. (2017). Evolving health care through personal genomics. Nat Rev Genet 18, 259–267.
• Spang, A., Saw, J.H., Jørgensen, S.L., Zaremba-Niedzwiedzka, K., Martijn, J., Lind, A.E., Eijk, R., Schleper, C., Guy, L., and Ettema, T.J.G. (2015). Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173–179.
• Tam, V., Patel, N., Turcotte, M., Bossé, Y., Paré, G., and Meyre, D. (2019). Benefits and limitations of genome-wide association studies. Nat Rev Genet 20, 467–484.

Contacts

Responsable(s) de l'enseignement

• Odile Lecompte

MCC

Les épreuves indiquées respectent et appliquent le règlement de votre formation, disponible dans l'onglet Documents de la description de la formation.

Régime d'évaluation

CT (Contrôle terminal, mêlé de contrôle continu)

Coefficient

1.0

Évaluation initiale / Session principale - Épreuves

Seconde chance / Session de rattrapage - Épreuves