Fontanesi et al. BMC Genomics 2010, 11:639 http://www.biomedcentral.com/1471-2164/11/639 Page 3 of 15 Figure 1 Goat of different breeds used for CNVs discovery. A = Saanen; B = Camosciata delle Alpi; C = Girgentana; D = Murciano-Granadina. Chamois group. Girgentana is a Sicilian breed in an endangered status that is probably of Afghan and Hima- layan origin, well adapted to the dry Sicilian environ- ment and with very mild behavior. Girgentana goats have long corkscrew horns and cream/light-grey coat colour with, usually, a few small red spots around eyes and ears. Murciano-Granadina is a native Spanish breed with two colour types, solid black or solid brown (caoba). Specific criteria were used to call CNVs in this cross- species aCGH experiment. CNVs were reported using 10 different algorithms developed for data segmentation and averaging their results as implemented in the CGHweb server [77]. The averaged log2 ratio threshold used to call CNVs was empirically determined consider- ing the number of false positives called in the reference DNA self-self hybridization and the validation obtained by semiquantitative fluorescent multiplex PCR (SQF- PCR) (see Methods and data reported below for details). Applying these criteria, on the whole we identified 161 CNVs (Table 1 and Additional file 1). The largest num- ber of CNVs was identified in the Saanen breed and the lowest number was reported for the Camosciata delle Alpi analysed goat. About 74% of the identified CNVs were observed in only one breed. On average each sam- ple contained 17.9 CNVs. This result is comparable to what has been obtained in similar aCGH experiments that analysed the cattle [51], dog [45], and chicken [78] genomes, in which 11.6, 17.2 and 9.6 CNVs were evi- denced for each animal in the three species, respectively (Table 2). Two CNVs (not overlapped to any other CNV) were also called in the self-self hybridization pro- viding a rough estimation of the false discovery rate (FDR) among the set of identified CNVs (FDR = 11%). However, technical issues, like sequence divergence between the reference genome and the hybridized DNA and heterogeneity of DNA quality among different sam- ples, make it difficult to precisely estimate the experi- mental FDR. The estimated FDR using the self-self hybridization data in this cross-species experiment is a little bit larger than that obtained with homologous DNA hybridization in aCGH. Indeed, in an aCGH study in dog, FDR was about 3% due to only one CNV detected in the self-self hybridization [46]. However, in another experiment carried out in humans, FDR was estimated to be 8-24% [28].