Phenotypic, transcriptomic, and genomic features of clonal plasma cells in AL. (A) Immunophenotypic protein expression profiles of clonal plasma cells from patients with AL (red) and MGUS plus MM (blue). These latter patients were initially screened for bone marrow clonality using the same immunophenotypic approach because of suspected AL, but were finally diagnosed as having MGUS (n = 3) and MM (n = 3). In the principal component analysis (PCA) graphic view, every patient is represented by a single dot, and disease reference groups by 1 (dashed lines) and 2 (solid lines) standard deviation curves. (B) Unsupervised PCA shows differences in gene expression profiling between clonal PCs from patients with AL (red) and normal PCs from healthy donors (green). (C) Overview of CNAs and copy number neutral loss of heterozygosity (CNN-LOH) detected in clonal PCs from patients with newly diagnosed AL. Samples are distributed in the y-axis and chromosome location in the x-axis. Red shading indicates the presence of copy number gains, and blue indicates copy number losses. CNAs were reported when the 3 following criteria were met: ≥25 consecutive imbalanced markers per segment, ≥100 Kb minimum genomic size, and <50% overlap with paired control DNA and/or genomic variants of Toronto DB (DGV). Those cytogenetics alterations detected by FISH in each individual patient are detailed at the beginning of the corresponding row. CNN-LOH are represented by violet bars. Only CNN-LOH >5 Mb, with ≥25 consecutive imbalanced markers per segment, and <50% overlap with patient-paired CNAs were considered.