CARTaGENE flagship paper

This repository includes the source code required to process data and create tables and figures featured in the flagship paper of the CARTaGENE study in Quebec, Canada.

Citation

McClelland P, Femerling G, Laflamme R, Mejia-Garcia A, Dehkordi MS, Xiao H, Diaz-Papkovich A, Pelletier J, Grenier JC, Lo KS, Anderson-Trocmé L, Bellavance J, Chapdelaine V, Gagnon G, Mori A, Martinez G, Mohler K, de Malliard T, Labbé C, Labrecque M, Montpetit A, Spiegelman D, Rouleau GA, Théroux JF, Zhou H, Girard SL, Hussin JG, Laberge AM, Bhérer C, Tetreault M, Gagliano Taliun SA, Taliun D, Gravel S, Lettre G. A multi-ancestry genetic reference for the Quebec population. medRxiv [Preprint]. 2025 May 16:2025.05.14.25327536. doi: 10.1101/2025.05.14.25327536

Browsers

These interactive web-based tools enable users to query and browse analysis results from the CARTaGENE flagship manuscript:

• CARTaGENE Variant Browser
• CARTaGENE PheWeb
• CARTaGENE eQTL Browser

Contents

1. PCA_UMAP_clustering - contains source code used for the Principal Component Analyses (PCA) and Uniform Manifold Approximation and Projection (UMAP) in the "Genetic structure in CaG" section of the manuscript.

2. IBD - contains source code used for the identity-by-descent (IBD) analyses and generating tables and figures in the "Genetic structure in CaG" section of the manuscript.

3. ARG-based_imputation_and_regional_frequency - contains source code used to identify likely carriers in genotyping array data in the "Variants of clinical interest (VCI): using CaG to go beyond founder variants" section of the manuscript.

4. Genotype_processing - contains source code used for the genotyping array data pre-processing before genotype imputation and GWASs.

5. HLA - contains source code used for the HLA data generation, analysis and generating tables and figures in the "Human Leukocyte Antigen (HLA) genotyping" section of the manuscript.

6. Phasing - contains source code used for statistical phasing and benchmarking phasing quality in the "Haplotype reference panel and genotype imputation" section of the manuscript.

7. Imputation - contains source code used for preparing and benchmarking the genotype imputation reference panel in the "Haplotype reference panel and genotype imputation " section of the manuscript.

8. GWAS - contains source code used for genome-wide association scans, fine-mapping, and generating tables and figures in the "Genome-wide association studies (GWAS)" section of the manuscript.