We now apply the HAS procedure to three statistics defined in Equations 21.1, 21.2 and 21.4. Figure 21.2 shows these statistics, the HAS fits, p-val-ues and locations with significant change in copy numbers between the two samples. It is obvious that the profile of the standard t-statistic is rougher than those of the other two statistics in the region between 100000 kb and 150000 kb. Standard t-test would miss some of the locations in this region. For all three statistics, the HAS procedure identified the whole trisomic region 6q15-6q25 which agrees with the results in Snijders et al. (13). Wang et al. (19) identified the same region by first building a hierarchical clustering tree and then selecting the 'interesting' clusters. It is interesting to note that, besides the documented trisomy in the 6q15-25 region, the HAS procedure also identified an isolated gain in the 6p region that is previously undocumented. It is likely that the gain, due to its apparently small size, may be too small to be detected by standard cytogenetic karyotyping methods.

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