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

Table 1 Nominated intragenic copy number aberration candidates

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

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.

ISSN: 2051-5960