FIGURES AND TABLES

Figure 1.

(a) Case 6 chromosome 6: Giemsa-stained chromosomes, (no abnormalities were found). CGH profile of DNA sample labeled by ULS^® analyzed with the Quips software. Both the 14.7 Mb duplication at 6p and the 3.5 deletion at 6q were detected using a threshold of 0.85–1.15. CGH profile of DNA sample labeled by nick translation, analyzed on the Cytovision^® using HR-CGH software. The 14.7 Mb duplication was clearly visible, but the deletion at 6q was not detected. The black lines represent the dynamic reference interval (CI 99.5%), while the brown lines represent the slide average ratio of the patient. At 6q the brown lines do not exceed the ratios of the dynamic reference interval and no deletion is detected. CGH profile of DNA sample labeled by nick translation analyzed with the Quips software (slide exchange test). The duplication on 6p was clearly visible, but the deletion on 6q is not, since the slide average ratio (blue lines) had a value close to 1.0 (normal). (b) Case 8 chromosome 6: Giemsa-stained chromosomes, (no abnormalities were found). CGH profile of DNA sample labeled by ULS^® analyzed with the Quips software. A 1.8 Mb deletion at 6p was visible using a threshold of 1.10–0.9. No false-positive results on other chromosome regions were observed. CGH profile of DNA sample labeled by nick translation, analyzed on the Cytovision^® using HR-CGH software. The 1.8 Mb deletion on 6p was not detectable. CGH profile of DNA sample labeled by nick translation analyzed with the Quips software (slide exchange test). The 1.8 Mb deletion on 6p was not detectable using a threshold of 1.15–1.85. Narrowing down the threshold to 0.90–1.10 resulted in false-positive duplication of 6q and no deletion of 6p could be detected.

Figure 2.

(a) Case 16 chromosome 13: Giemsa-stained chromosomes (no abnormalities were found). CGH profile of DNA sample labeled by ULS^® analyzed with the Quips software. A 3.9 Mb deletion on 13q was visible using a threshold of 1.15–0.85. CGH profile of DNA sample labeled by nick translation, analyzed on the Cytovision^® using HR-CGH software. The 3.9 Mb deletion at 13q was not visible probably due to the dynamic reference interval (CI 95%) at 13q (black lines). CGH profile of DNA sample labeled by nick translation analyzed with the Quips software (slide exchange test). The 3.9 Mb deletion on 13q was detected using a threshold of 1.15–1.85. CGH profile of DNA sample labeled by ULS^® analyzed on the Cytovision^® using HR-CGH software (slide exchange test). The 3.9 Mb deletion on 13q was not detected using CI 95%. (b) Case 14 chromosome 9: Quinacrine-stained chromosomes, original chromosome analysis (no abnormalities were found). Giemsa-stained chromosomes (no abnormalities were found). CGH profile of DNA sample labeled by ULS^® analyzed with the Quips software. A 4.1 Mb deletion on 9q was visible using a threshold of 1.15–0.85. The repetitive sequences are not completely suppressed in the heterochromatin region of chromosome 9. CGH profile of DNA sample labeled by nick translation, analyzed on the Cytovision^® using HR-CGH software. The 4.1 Mb deletion on 9q was not visible since the ratio of dynamic reference interval deviated as much from normal (ratio 1.0) as the ratio of the patient sample. CGH profile of DNA sample labeled by nick translation analyzed with the Quips software (slide exchange test). The 4.1 Mb deletion on 9q was detected using a threshold of 1.15–1.85. The repetitive sequences were not completely suppressed in the heterochromatic region of chromosome 9. CGH profile of DNA sample labeled by ULS^®, analyzed on the Cytovision^® using HR-CGH software (slide exchange test). The 4.1 Mb deletion on 9q was not detected, incomplete suppression of the repetitive sequences was not fully corrected by the dynamic reference interval (CI 95%).

Figure 3.

Case 13 chromosome 15. Giemsa-stained chromosomes (no abnormalities were found). CGH profile of first hybridization of DNA sample labeled by ULS^® analyzed with the Quips software. The deletion on 15q11–q13 was not detected due to the insufficient suppression of the repetitive sequences, closely located to the deletion. Incomplete suppression of repetitive sequence was also observed on many other chromosomes in this hybridization and this made the analysis uninterpretable. CGH profile of DNA sample labeled by nick translation analyzed on the Cytovision^® using HR-CGH software. The deletion on chromosome 15 was easily detected, as the software uses a standard reference interval (CI 99.5%) that is excluding the region containing repetitive sequences (black lines) from analysis. Second hybridization with DNA sample labeled by ULS^® and analyzed with the Quips software CGH. The deletion was easily detected when the repetitive sequences were completely suppressed by Cot-1-DNA.

Figure 4.

CGH profile of case 8, DNA sample labeled by ULS^® and analyzed with the Quips software CGH. A 1.8 Mb deletion on 6p is visible using a threshold of 1.10–0.90. No false-positive results were observed on other chromosome regions. Repetitive sequences were incompletely blocked by Cot-1 DNA on chromosome 1, 9, 13 and 15.

Table 1 - CGH analysis performed blinded and semiblinded.