Fig. 2
Detecting somatic copy number alterations in neuroblastoma. A Schematic of the DNA allelic imbalance method for detecting somatic copy number alterations (SCNAs). B Difference in DNA allelic imbalance between normal and tumor tissues (δa) for 96 neuroblastoma patients across chromosome 1 (left panel). Results are compared to log2 fold-change in normalized read coverage between tumor and normal tissues estimated by CNVkit (right panel). C Occurrence matrix of the 10 most frequent SCNAs detected using the DNA-imbalance approach. SCNAs were filtered using SCNA score ≥ 0.09 and annotated based on their cytoband location. Neuroblastoma patients are grouped by MYCN z-score normalized gene expression. D Manhattan plot for Spearman’s correlation analysis between ASE (aRNA) and SCNA score for 945 NB-ASE genes. E Spearman’s rank correlation between allele-specific expression (aRNA) and SCNA score for KIF1B (left panel), a tumor suppressor in the chromosome 1p deletion region, and IP6K2 (right panel), a putative tumor suppressor within the 3p deletion region