Differences in how patients experience disease can be explained in great part by their genomic differences. Enabling precision medicine hence requires identifying genomic features associated with disease risk, prognosis or response to treatment. This is often achieved using genome-wide association studies (GWAS), which look for associations between single nucleotide polymorphisms (SNPs) and a phenotype. However, for many complex traits, the SNPs they uncovered account for little of the known heritable variation.

SCAPHE builds on the hypothesis that this is due to the effect of non-additive interactions between SNPs, together with a lack of robustness stemming from the relatively small sample sizes. This last issue can be alleviated by integrating biological networks to GWAS. Hence SCAPHE proposes to develop novel machine learning algorithms for GWAS, integrating biological networks and modeling non-additive SNP effects, to robustly detect SNP combinations associated with a phenotype.

SCAPHE is funded by ANR JCJC 2018, a program by the French National Research Agency to fund Young Researchers. You can find the full text of the proposal here.

logo « financé par l'ANR »

People

People taking part in SCAPHE include

Publications, preprints, posters

  • Héctor Climente-González, Christine Lonjou, Fabienne Lesueur, GENESIS Study collaborators, Dominique Stoppa-Lyonnet, Nadine Andrieu, Chloé-Agathe Azencott. Boosting GWAS using biological networks: A study on susceptibility to familial breast cancer, PLoS Computational Biology (2021).
  • Héctor Climente-González, Chloé-Agathe Azencott. martini: an R package for genome-wide association studies using SNP networks BioRxiv (2021).
  • Diane Duroux, Héctor Climente-González, Chloé-Agathe Azencott, Kristel Van Steen, Interpretable network-guided epistasis detection BioRxiv (2020).
  • Lotfi Slim, Hélène de Foucauld, Clément Chatelain, Chloé-Agathe Azencott, A systematic analysis of gene-gene interaction in multiple sclerosis BioRxiv (2020).
  • Asma Nouira, Chloé-Agathe Azencott, Multitask group lasso for genome-wide association studies, poster at SMPGD 2020.

Code

Events

SCAPHE allowed us to attend ISMB/ECCB 2019 and ProbGen 2019.