Fontanesi et al. BMC Genomics 2010, 11:639 http://www.biomedcentral.com/1471-2164/11/639 Table 1 Summary of CNVs identified in the analysed goat breeds Breed (no. of animals) Saanen (3) Camosciata delle Alpi (1) Girgentana (3) Murciano-Granadina (2) Total (9) Number of CNVs Total 62 8 54 37 161 Gain 24 4 20 11 59 Loss 38 4 34 26 102 CNV average size (kb) 73.1 122.4 118.4 107.3 98.6 Unique 50 5 37 27 119 161 1,041 - - 51,997 355 214 155 80 33 96 17.9 11.6 - - 1300 17.8 21.4 17.2 2-385 11 9.6 10,681 26.4-48.35 127 177 304 913 - - 123 60 - - 3,359 33 90.3 158.6 72.0 228.0 2.96 - 101.2 309.5 271.5 64.0 256.0 166.7 Page 4 of 15 References This study [51] [52] [28] [34] [35] [37] [45] [39] [54] [43] [78] Species Goat Cattle Cattle Human Human Dog Mouse Mouse Rat Chicken Chimpanzee 20 Macaque 9 9 90 20 270 40 9 211 201 3 10 385 k oligo aCGH 385 k oligo aCGH 6.3 million oligo aCGH BAC aCGH2 42 million oligo aCGH BAC aCGH2 385 k oligo aCGH 385 k oligo aCGH 385 k oligo aCGH 2.1 million oligo aCGH 385 k oligo aCGH 385 k oligo aCGH 6.3 ~6 0.4 - 0.06 - 6.5 4.73 ~5 1 ~54 2.6 CNV regions (CNVRs) were determined by aggregating overlapping CNVs identified in different animals as pre- viously reported [28,51] and considering a conservative approach due to the specificity of our experiment (see Methods for details). On the whole, we detected 126 CNVRs covering about 11.39 Mb of the virtual goat genome referred to the bovine genome, version Btau_4.0 (Figure 2 and Additional file 2). This fraction corre- sponds to 0.432% of the latter genome, considered add- ing bases in the 29 autosomes and the X chromosome assembled in the Btau_4.0 version (11.39 Mb/2634 Mb). The chrUnAll (unassembled scaffolds) of the Btau_4.0 version was not included in the tiling array due to diffi- culties in interpreting the results that might have been derived by the short assembled fragments and mapping uncertainty [51]. In addition, the tiling arrays included 4,673 oligonucleotides designed on a portion of BTA13 (from nucleotide position 48 Mb to nucleotide position 78 Mb) derived from the UMD Bos taurus v. 2.0 assem- bly [75]. This additional BTA13 portion was included in the tiling arrays because the agouti signaling protein (ASIP) gene was not correctly assembled in the Btau_4.0 version of BTA13 and was reported in unassembled scaffolds only. This UMD 2.0 BTA13 region was added as an internal control because we previously demon- strated that the ASIP gene and the close S-adenosylho- mocysteine hydrolase (AHCY) gene are included in a goat CNVR [22]. This CNVR may represent a recurrent interspecies CNVR since the same two genes are involved in a large duplicated region in sheep [61]. Table 2 Comparison between this and other similar CNV studies using aCGH in mammalian and avian species No. of aCGH individuals platforms Mean probe spacing (kb) Total no. of Mean no. of CNVs CNVs per individual Total no. of CNVR mean CNVRs size (kb) 1 No. of strains (2-6 individuals per strain). 2 Whole Genome TilePath array comprising 26,574 large insert clones. 3 Median probe spacing. 4 Considering nonrepetitive parts of the genome. 5 Depending on the strain. 6 Median size.