Fig. 1

Microarray analysis, partial karyotype, and FISH comparison for case K4 [46,X,der(X)t(X;Y)(p22.33;p11.2)]. Two hybridizations were performed simultaneously with dye reversal using female reference DNA (A). Entire set of 381 clones (only 362 were analyzed) was arrayed in quadruplicate blocks, resulting in four determinations for each clone, two on the forward and two on the reverse hybridizations. Representative section is enlarged. Panel B is a partial karyotype from two metaphase spreads depicting the additional chromatin material on one of the X chromosomes (arrows). Panel C presents the data analysis for the array. In the column marked “raw” for raw data, the mean values of the T/R ratios and error bars are shown for one hybridization in blue and for the dye reversal in red. Effect of normalization is shown by comparing the middle set of data marked “normalized” with the “raw” data. There are several clones from the Y chromosome that show displacement to the left in blue and to the right in the dye reversal, both indicating a gain of Y material in the patient versus the female reference DNA. In the “combined” column, the sign of one of the two reversed hybridizations is changed and the data are averaged with gains to the right and losses to the left. For the combined data, there is a strong indication of a gain of four clones (identification printed in blue) corresponding to the Yp11.3 region as shown in the circle. In D, FISH analysis with an SRY probe confirmed the presence of Y DNA on the short arm of one X chromosome.