ICARUS

Study of U3-1402 and DS-1062a Antibody Drug Conjugates in Advanced Breast and Lung Cancer Patients

ICARUS BREAST01 NCT04965766 and ICARUS LUNG01 NCT04940325 are two multicentric phase II French clinical trials resulting from the collaboration between Gustave Roussy and Daiichi Sankyo. The BREAST01 trial aims at assessing the activity of patritumab deruxtecan (U3-1402; targets HER3) in advanced breast cancers, while the LUNG01 trials investigates datopotamab deruxtecan (DS-1062a; targets TROP2) in advanced or non-resectable non-small cell lung cancers (NSCLC).

Principal investigators

• Dr. Barbara PISTILLI
• Pr. David PLANCHARD
• Dr. Guillaume MONTAGNAC

Repository organisation

data

• cln all patient- and sample-related raw and curated tables
• histopathology the raw slides, annotations, and tables necessary for the histopathological analysis
• resources various resources files such as the capture BED for the WES, lists of genes of interests, list of oncogenic pathways etc.
• rna all analysis-ready tables generated by the RNAseq pipeline
• wes all analysis-ready tables generated by the WES pipeline and excel summary tables of QC per each batch executed.

See data/README.md to learn about data access.

code

Folder hosting the bioinformatic pipelines employed on the sequencing files and the analysis scripts developed for the project.

• common folder with code for external tools added as git sub modules and with scripts for defining utils
• histopathological_analysis a set of scripts to perform all the analysis related to the histopathological data. See code/histopathological_analysis/README.md for more details.
• pipeline_rna a Snakemake pipeline performing a comprehensive analysis of bulk RNA-seq data in order to quantify gene expression using SALMON+Tximport before proceeding to DEA (DESeq2), GSEA, and immune deconvolution.
• pipeline_wes a Snakemake pipeline performing a comprehensive analysis of WES data in order to identify, filter, and annotate somatic mutations, copy-number alterations, purity and ploidy in each pair of tumor/normal. It may also run in tumor-only mode for most all analyses. See pipelines/wes/README.md for more details.
• stats_paper folder with a single script which computes various statistics presented in the main text or the methods.
• tables_paper folder with scripts for generating tables supporting the paper (supplementary tables) or supporting data releases (EGA, cbioportal, etc).
• wes_analysis folder with scripts for drawing various types of oncoplots.

Contributors

• Bastien JOB https://github.com/aoumess; [email protected]
• Marc DELOGER https://github.com/mdeloger; [email protected]
• Yoann PRADAT https://github.com/ypradat; [email protected]
• Loïc Le Bescond https://github.com/loic-lb; [email protected]