Figure 2

Array-CGH profiles of chromosome 22 in tumors displaying complex aberrations. The chromosome 22 array-CGH plots consist of 480 chromosome 22 clones ordered from centromere to telomere and 9 chromosome X controls between the vertical lines, as well as 31 non-chromosome 22 controls plotted on the right hand side. The y-axis displays the raw fluorescent intensity ratios for each clone on the genomic array. The position of the NF2 gene is highlighted with the vertical grey bar. A) Array-CGH profile of case M64 displaying a single copy loss of the majority of the chromosome with a biallelic deletion encompassing a single measurement point (clone ID 151) [GenBank:AC005529], specifically targeting the NF2 gene (highlighted by a grey circle). Encircled clones centromeric of NF2 display fluorescent ratio consistent with two copies; clone IDs 61–63 [GenBank:D87000–D87003] (previously reported Copy Number Polymorphism, CNP) and clone IDs 99–100 [GenBank:AL049759–AL050312]. Clone ID 400 [GenBank:Z84478] positioned towards the telomere, also exhibit two gene copies (highlighted by a circle). Control clone derived from chromosome 10 encompassing SUFU1B gene presents with one copy loss (highlighted by a circle). B) Array-CGH profile of case M32 displaying an interstitial deletion encompassing the NF2 gene and a terminal deletion. Clones spanning the DAL-1 gene on chromosome 18 and clones spanning the PTCH1B locus on chromosome 9 display a fluorescent ratio consistent with a one copy loss are highlighted by a circle. C) Case M109 displaying a gain spanning clone IDs 5–48 [Genbank:AC006548–AC007957] followed by a large terminal deletion covering clones 49–480 [Genbank:AC009516–AC002055]. Two CNPs are positioned at clone IDs 13–15 and 63 [Genbank: AC008079–AC008132 and D87003] and are indicated by circles. D) Meningioma M101 displaying a large one copy loss for the majority of the chromosome apart from a region encompassing clone IDs 348–366 [GenBank:AL080242–Z82176] and a CNP spanning clone IDs 60–61 [GenBank:D88269–D87000]. E) Detection of multiple interstitial deletions outside the NF2 region, spanning clone IDs 85–89 (R1, highlighted by a circle), 181–262 and 311–360 [GenBank: U07000–AP000348, AC005004–Z69907 and AL022311–Z83851] and a terminal deletion covering clone IDs 390–480 [GenBank:Z93244–AC002055] in case M11. A CNP spanning clone IDs 14–15 [GenBank:AC008132–AC008103] is highlighted by a circle.