1. Suppl. Fig. 1: Microarray image of case 36, displaying a 0.57-Mb triplication of 7q21.13, along with the copy number and allele segregation patterns indicative of cases in group 1. Solid arrows indicate the exclusive AAAB (top) and ABBB (bottom) heterozygotes. Open arrows show the AAAA (top) and BBBB (bottom) homozygotes. The allele running dosage, which is an average of 5 contiguous markers, is depicted by the smooth signal in the center of the figure. The bar at the bottom of the figure is indicative of a region of gain.

2. ab Suppl. Fig. 2: a, b Dual-color FISH images of case 52 (14q11.2), displaying the single homologue triplication. The green-red, red-green, green-red pattern illustrates the inverted orientation of the middle copy in the interphase image. The yellow color is due to a partial overlap of the red and green signals.

3. Suppl. Fig. 3: Microarray image of case 120, a 2.59-Mb triplication of 22q11.21, displaying the copy number and allele segregation pattern indicative of cases in group 2. In addition to the 3:1 heterozygotes, there are 2:2 ratio heterozygotes that segregate to the midline, similar to the 3:1 heterozygotes in the normal flanking regions. This case represents a VCF/DiGeorge-related triplication. There are 3 regions of segmental repeats, two of which are delineated by the vertical lines, with the third in the marker gap inside the interval.

4. ab Suppl. Fig. 4: a, b Dual-color FISH images of case 80, displaying an 8.62-Mb triplication of 5q12.1q13.2. Again, the inverted orientation of the middle copy is apparent in the interphase image.

5. Suppl. Fig. 5: Composite of microarray images for cases 116 (top), 117 (middle), and 118 (bottom) of group 2. These images show the identical triplicated interval at 18q22, in addition to the 3:1 and 2:2 HTZ allele patterns of group 2. The most common non-random triplication interval was at 8p22 (cases 85-98).

6. Suppl. Fig. 6: Composite microarray images of cases 80 (blue) and 81 (green) from group 2. These display the triplicated interval from 5q12.1 to 5q13.2 and the 3:1 and 2:2 HTZ allele patterns of group 2 terminating with repeats.

7. Suppl. Fig. 7: This microarray image of case 127 in group 3 shows a 14.7-Mb triplication of 3p25.1p24.1. The image also shows terminal homozygosity (shown by 2 tracts and solid blue box beneath) adjacent to the triplicated segment, which displays the 2:2 HTZ allele pattern, characteristic of cases in group 3.

8. ab Suppl. Fig. 8: a, b FISH images of case 130, a 15.5-Mb triplication of 9p22.3p21.3, displaying the single homologue triplication and the inverted orientation of the middle segment.

9. Suppl. Fig. 9: Microsatellite assay result within the 13.6-Mb HMZ region adjacent to the 14.7-Mb triplication of 3p25p24.1 of case 127. The test confirms a maternal exclusion consistent with paternal UPD. M = Mother; C = child; F = father.

10. Suppl. Fig. 10: Follow-up array testing of case 132 within the 2.23-Mb HMZ region adjacent to the 3.07-Mb triplication of 17q25.3. The HMZ allele results confirm maternal UPD through multiple paternal exclusions of alleles present in the proband (arrows).

11. Suppl. Fig. 11: Microarray image of case 135, displaying the 1.59-Mb triplication of 3q11.2. The lack of heterozygosity is indicative of the allele segregation pattern seen in group 4 cases.

12. ab Suppl. Fig. 12: a, b FISH images of case 135, displaying single homologue rearrangement of triplicated segment in both interphase and metaphase images.

13. Suppl. Fig. 13: Microarray image of case 145 displaying the 4-copy region within a HMZ stretch (indicated by solid blue section in the middle), indicative of cases in group 5. This 1.25-Mb alteration is consistent with a duplication of 6q15 on each homologue, typically related to consanguinity.

14. ab Suppl. Fig. 14: a, b FISH images of case 149, showing the 586-kb duplication of 16p11.2 on each homologue both interphase and metaphase images.