Copy number alterations and loss of heterozigocity were inferred by a Hidden Markov Model-based algorithm implemented in the GTC software program, using parameter settings recommended by Affymetrix for tumoral/ normal paired samples and a minimum physical length of at least 5 consecutive SNPs for putative genetic alterations. ����Genetic gains���� and ����losses���� were defined according to GTC working criteria. In turn, ����high CN gains���� and ����homozygous losses���� were considered to be present when CN values were found, respectively. At every locus, LOH was assumed to be present when a single allele was detected in tumor DNA from heterozygous individuals at a greater percentage than the other allele; it was further subclassified as either true LOH, when loci at which one of the parental copies of a chromosome was deleted, or as copy neutral LOH , when tumoral DNA displayed two copies of a chromosomal region from one parent in the absence of the allele derived from the other parent. Analysis of LOH was restricted to DNA sequences from autosomal chromosomes. In all cases, iFISH studies were performed on an aliquot of the single cell suspension prepared from the tumor Adriamycin sample. A set of 12 locus-specific FISH probes directed against DNA sequences localized in 11 different human chromosomes and specific for those chromosomal regions more frequently gained or deleted in PDAC, were systematically used to validate the results obtained with the SNP-arrays . The methods and procedures used for the iFISH studies have been previously described in detail . For all continuous variables, mean values and their standard deviation and range were calculated using the SPSS software package ; for dichotomic variables, frequencies were reported. In order to evaluate the statistical significance of differences observed between groups, the Mann-Whitney U and X2 tests were used for continuous and categorical variables, respectively . A multivariate stepwise regression analysis was performed to examine the correlation between the chromosomal abnormalities found by iFISH versus SNP-array techniques. Hierarchical clustering analysis was performed to classify cases according to their CN genetic profile by using the Cluster 3.0 software . Clustering was run using an Euclidean distance metric and the average linkage method. For visualization of dendograms the TreeView software 1.0.4 was used. P-values,.01 were considered to be associated with statistical significance. PDAC are heterogeneous tumors that frequently display complex genetic profiles as confirmed in the present study where multiple CNV and LOH regions were identified in every case analyzed. Overall, our findings indicate that the genetic profile of primary PDAC is defined by imbalanced losses of chromosomes together with gains of the chromosomal regions. These results confirm previous analyses using chromosome banding techniques , CGH , aCGH , low-resolution 100K SNP-arrays and gene sequencing MLN4924 in vivo combined or not with SNParray technology . Despite a high correlation was also found between the SNP-array results and iFISH analyses performed on the same series of primary tumors samples – as regards the most commonly deleted and gained chromosomal regions, a higher frequency of deletions at chromosomes 1p and 17q, and gains at chromosomes 7q and 20q were found by SNP- arrays vs. iFISH technique .