miRNA mapping to CNAs. (A) Schematic representation of the approach to identify miRNAs within CNAs. Each of the 6 cell lines were simultaneously analyzed for CNAs by aCGH and small RNA expression by massively parallel sequencing on the Illumina platform. The CNAs for the 6 cell lines were annotated (Table 1) and subsequently merged. Similarly, miRNA expression data from all 6 cell lines were used to identify expressed miRNAs that map to the CNAs (Table 2). By this approach, we were able to identify miRNAs that map to a homozygous deletion in one cell line by using miRNA expression values from the pooled data. (B) Distribution summary of miRNAs mapping to leukemia-associated genomic alterations found in 6 human leukemia cell lines. According to the current miRNA database (miRBase v13.0), there are 702 human miRNAs. Of these, 542 miRNAs map to CNAs identified in the 6 leukemia cell lines. After small RNA sequencing, 99 miRNAs (of 542) are expressed above background and map to CNAs. (C-D) Proportion (in percent) of the 99 expressed miRNAs within each cell line mapping to genomic regions of amplifications or deletions.