2452 Nucleic Acids Research, 2008, Vol. 36, No. 7 Figure 4. Graphical representation of SPIA results on 155 cell lines: pair-wise distances and probabilistic test using SNP panels of diﬀerent sizes. The number of possible combinations of pairs from a set of 155 samples is 11 935. Black dots represent distances were less than 90% of the genotype calls available. (A) The genotype distance was evaluated on the 5279 SNPs, which were ﬁltered starting from the 50K SNPs represented on the Xba Aﬀymentrix Array. The mean distance is 0.4736 and the standard deviation is 0.0358, accordingly to the conﬁnement of almost all the evaluations. Dots below the dotted gray line represent pairs of cell lines which are genotypically very similar to each other (they share more than 80% of the 5279 loci here considered), suggesting that they share the same ancestral. (B)–(E) Multi-panel distances using 80, 60, 40 and 20 SNPs randomly sampled from the top 100 SNPs selected through the multi-step selection process. The mean distances are signiﬁcantly higher respect to panel (A). The probability test was applied setting the match probability for the non-pair and for the matched pair population to 0.4 and 0.9 respectively and the parameter for the conﬁdence level to 3 and 2 respectively. Red, blue and green dots indicate ‘diﬀerent’, ‘uncertain’ and ‘similar’ test scores. the distance values increase between the ﬁrst collection of SNPs and the ﬁltered set of 5.3 K SNPs. Comparing the distances obtained for the smaller sets of SNPs (i.e. 80, 60, 40 and 20 SNPs) with the 5.3 K set, we see a signiﬁcant increment of percentage diﬀerences. This result holds on the independent validation set of cell lines, conﬁrming the ability of the selected SNPs to distunguish diﬀerent cell lines. When comparing the results obtained with 80, 60, 40 and 20 SNPs to each other, we observe that the mean pair- wise distances do not change signiﬁcantly. As expected, the standard deviations tend to increase when going from 80 to 20 SNPs (see Figure 4). We then added to the dataset the 9 cell lines identiﬁed as being very similar during the preprocessing step and therefore excluded from the SPN selection process and, by using the same sets (i.e. 80, 60, 40 and 20), we ran the distance and the statistical test, as described in the Materials and Methods section. Brieﬂy, this test scores each single pair as ‘diﬀerent’, ‘uncertain’ and ‘similar’, based on the total number of queried SNPs, on the number of matches and on a set of parameters adjusted on the required level of conﬁdence. The probability test was applied setting the match probability for the non-pair and for the matched pair population to 0.4 and 0.9, respectively, and the parameter for the conﬁdence level to 3 and 2, respectively. With 80 and 60 SNPs all the ‘real pairs’, eligible for the statistical test (10 out of 11), were scored as ‘similar’. No other cell line pair was scored as