Summary of array CGH results on individuals with microdeletions and microduplications of 3q29. (A) Ideogram of chromosome 3 showing the location of the 3q29 cytogenetic band. (B) Representative SignatureChipWG result plot for an individual with a single copy loss of 11 BAC clones spanning the entire 1.6 Mb common microdeletion region. Each clone represented on the array is arranged along the x-axis according to its location on chromosome 3 with the most distal/telomeric p-arm clones on the left and the most distal/telomeric q-arm clones on the right. The blue line represents the ratios for each clone from the first experiment (control/patient), and the pink line represents the ratios for each clone obtained from the second experiment in which the dyes have been reversed (patient/control). (C) Representative SignatureChipWG result plot for an individual with a single copy gain of 11 BAC clones spanning the entire 1.6 Mb common microdeletion region. (D) Diagram showing the deletion sizes of 13 individuals with microdeletions of 3q29 as refined using the high-density, custom 3q29 oligonucleotide microarray. Vertical dashed lines in D and E indicate the location of the low-copy repeats (LCRs) in the 3q29 interval for which oligonucleotides were not included on the microarray. Blue bars shown at the bottom of the diagram indicate the location of paired LCRs within 3q29; their precise orientation is illustrated by arrows. Orange bars indicate the location of other segmental duplications that share no homology with any other regions on chromosome 3. LCRs A, B, and C are ~40 kb, ~20 kb, and ~20 kb long, respectively, with > 90% identity to their paired counterparts and are simplified for illustrative purposes (based on the Segmental Duplications Database, May 2004 (hg17) draft). (E) Diagram showing the duplication sizes of 17 individuals with microduplications of 3q29 as refined using the high-density, custom 3q29 oligonucleotide microarray. Blue arrows show the location of the LCRs that mediate the common 1.6 Mb microdeletion/microduplication and are not drawn to scale. (F-J) Photographs of five of the 11 individuals with common-sized microdeletions of 3q29. Individuals shown in F and G are siblings.