Marcinkowska et al. BMC Genomics 2011, 12:183 http://www.biomedcentral.com/1471-2164/12/183 the exact boundaries of miRNA genes (including regula- tory elements) are difficult to determine, we used the genomic coordinates of all pre-miRNA loci deposited in miRBase (v 13.0; N = 715) as a proxy of miRNA gene sequences (three pre-miRNA loci located in the mito- chondrial genome were excluded from our analysis) [33,34]. We realize, however, that CNVs overlapping other functional regions of miRNA coding genes (e.g., promoters) can also affect miRNA biogenesis and func- tionality, and those CNVs will be missed in our analysis. The CNV-miRNAs identified in ‘DGV-deposited’ CNVs (N = 209) and in two sets of ‘polymorphic’ CNVs (N = 4 and N = 8) are shown in Additional file 2 and Table 1, respectively. Top-validated ‘DGV- deposited’ CNV-miRNAs are also shown in Table 2. Most miRNA loci identified in ‘polymorphic’ CNVs also overlapped with top-validated ‘DGV-deposited’ CNV regions (Table 1 and Table 2). All ‘polymorphic’ CNV-miRNAs were relatively frequent (combined minor genotype frequency >0.1 in at least one HapMap population). Among the identified miRNA-CNVs, we Table 1 miRNA loci localized in polymorphic CNV regions miRNAs localized in ‘polymorphic-SMC’ CNV regions Page 3 of 9 found deletions (e.g., hsa-mir-384 and hsa-mir-1324), duplications (e.g., hsa-mir-1972 and hsa-mir-1977), and multiple duplications (multiallelic polymorphisms; e.g., hsa-mir-1233 and hsa-mir-1268). The number of observed copies ranged from 0 (e.g., hsa-mir-384 and hsa-mir-650) to 6 (e.g., hsa-mir-1268). The sequences of miRNA deposited in miRBase are derived from discovery studies in which many strict miRNA verification criteria were applied (e.g. hairpin forming potential, evolutionary conservation, presence in multiple clones/sequence reads or homogeneity of the 5’end). The SNP frequency analysis presented in this study also confirmed global conservation of annotated pre-miRNA sequences. However, there is still a possibi- lity that some of the miRNAs in the miRBase represent experimental artifacts of false positive discoveries [35]. To provide additional data that can further validate miRNAs identified in CNVs we have conducted bioin- formatic analysis of their expression and conservation. Table 1 and Table 2 show that according to different miRNA expression resources summarized in mimiRNA dupl. genotypes CNV ID functional relevance expression (mimiRNA/[18]) conservation genotypes CNV ID functional relevance expression (mimiRNA/[18]) conservation miRNA ID mir- 1268 miRNA position chr15:20014593- 20014644 CNV region position chr15:19803370- 20089386 mir- chr15:32607783- chr15 chr15:32487975- 1233 32607864 32617680 mir- chr16:15011679- chr16 chr16:14897364- 1972 15011755 15016088 mir-384 chrX:76056092- chrX:76053855- 76056179 76057477 miRNAs localized in ‘polymorphic-DC’ CNV regions miRNA ID miRNA position dupl. CNV region position mir- chr1:556050- chrM chr1:554403- 1977 556128 560267 mir- chr3:75762604- chr3:75464498- 1324 75762699 75782745 mir- chr4:9166887- chr4:9117494- 548i-2 9167035 9354801 mir- chr6:34075727- chr6:34071086- 1275 34075806 34077139 mir- chr9:20144- chr1, chr9:485-38531 1302-2 20281 15,19 mir- chr15:32461562- chr15 chr15:32450046- 1233 32461643 32662643 mir- chr15:32607783- chr15 chr15:32450046- 1233 32607864 32662643 mir-650 chr22:21495270- chr22:20711019- 21495365 21578950 2,3,4,5,6 0,1,2,3 2,3,4 0,1,2 2057 2082 2141 2648 2,3,4 1,2 1,2 1,2 2,3 2,3,4,5 2,3,4,5 0,1,2 3.1 1432.2 1815.3 2853.1 4134_full 6351.3 6351.3 8103_full dupl. - localization of duplicated copies; mimiRNA/[18] - miRNA expression according to database mimiRNA/and according to resent result of expression analysis in primary fibroblast cells (high - high expression, absent - low or undetectable expression in fibroblast cells, - not analyzed). 1) recurrently deleted in classical Hodgkin’s lymphoma [47] 1) 2) upregulated in blood cells of MS patients [41] 1) 1) 1) not reported/NA not reported/NA not reported/NA in several tissues/NA not reported/NA not reported/NA not reported/NA not reported/NA not reported/NA not reported/NA not reported/NA in several tissues (mostly ovary and ovary-derived cancers)/ high primates primates primates mammals primates primates primates primates primates primates primates primates