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Table 1 Nominated intragenic copy number aberration candidates

From: The prognostic role of intragenic copy number breakpoints and identification of novel fusion genes in paediatric high grade glioma

Candidate.ID Gene Chromosome Sample Copy number change Comments
1 FAF1 1 HGG091 Deletion  
  FAF1 1 HGG140 Deletion  
2 CD84 1 HGG088 Amplification  
3 LGALS8 1 HGG070 Deletion  
4 KIDINS220 2 HGG077 Amplification  
5 DHX57 2 HGG063 Amplification Fusion candidate
6 TMEM178 2 HGG063 Amplification Fusion candidate
7 WDR49 3 HGG010 Amplification  
8 PDCD10 3 HGG157 Deletion  
9 CHIC2 4 HGG077 Amplification  
10 ITGA1 5 HGG029 Deletion  
11 EPHA7 6 HGG139 Deletion  
12 LANCL2 7 HGG060 Amplification  
13 ECOP 7 HGG060 Amplification  
14 KCND2 7 HGG152 Amplification  
  KCND2 7 HGG162 Amplification  
14 SND1 7 HGG090 Deletion  
15 CSMD3 8 HGG054 Deletion  
  CSMD3 8 HGG140 Deletion  
  CSMD3 8 HGG153 Deletion  
16 SLC24A2 9 HGG151 Deletion  
  SLC24A2 9 HGG011 Deletion  
17 MTAP 9 HGG022 Deletion  
  MTAP 9 HGG007 Deletion  
18 ANKRD26 10 HGG068 Deletion  
19 RET 10 HGG139 Amplification Fusion candidate
20 CSGALNACT2 10 HGG139 Amplification Fusion candidate
21 PTPRE 10 HGG086 Deletion  
  PTPRE 10 HGG145 Deletion  
22 RAB6IP1 11 HGG092 Amplification  
23 PSMA1 11 HGG092 Amplification  
24 TMTC1 12 HGG010 Amplification  
  TMTC1 12 HGG068 Amplification  
25 LRRK2 12 HGG068 Amplification  
26 MYO1A 12 HGG029 Amplification  
27 XRCC6BP1 12 HGG029 Amplification  
28 OSBPL8 12 HGG065 Amplification  
  OSBPL8 12 HGG162 Amplification  
29 RB1 13 HGG154 Deletion  
30 PCDH17 13 HGG059 Deletion  
31 CD276 15 HGG006 Deletion  
32 MEF2A 15 HGG011 Deletion  
33 DNAH2 17 HGG143 Amplification  
34 NF1 17 HGG154 Deletion  
  NF1 17 HGG140 Deletion  
35 BRIP1 17 HGG077 Deletion  
36 KCNB1 20 HGG139 Amplification  
37 SYN3 22 HGG017 Deletion  
  SYN3 22 HGG146 Deletion  
38 TIMP3 22 HGG146 Deletion  
39 PHF21B 22 HGG072 Deletion  
  1. 39 unique intragenic breakpoints found within 51 cases of paediatric high grade glioma. Direction of copy number shift (gain/loss) is reported, as well as candidate fusion events.