Fig. 2: Identification of cells harboring del(5q) deletion in MDS patients.

A Heatmap of the results of CopyKat showing the copy number alteration score given to each 200 kb bins in chromosome 5. In order to represent cells, a clustering has been performed within each sample (kmeans with k = 80), and a posterior clustering has been applied to detect the clusters containing the cells harboring the deletion. The control sample used by the algorithm is an MDS sample with normal karyotype, while the healthy sample with normal karyotype represents an additional negative control for the analysis. B Barplot representing the percentage of cells inferred by CaSpER that harbor an amplification, a deletion or a normal number of copy number variation in each branch of chromosome 5 per patient. The control corresponds to an MDS sample with normal karyotype, which is used as a reference by the algorithm. C Venn diagram representing the number and percentage of cells classified as del(5q) by both algorithms. D Pseudobulk normalized expression of the 6 CDR-genes with higher expression in our dataset (CD74, RPS14, BTF3, COX7C, HINT1 and RPS23) separated by genotype. N = 4 biologically independent samples were used. The number of del(5q) and non-del(5q) cells were used to generate the pseudobulks for each patient can be found in the Source Data. E Graph depicting the percentages of del(5q) cells inferred by karyotype, CaSpER and CopyKat for each patient. Selected cells correspond to the cells classified as del(5q) cells by both computational algorithms.