Array-CGH and multipoint FISH to decode complex chromosomal rearrangements

BMC Genomics

Table 1 Chr3 rearrangements based array-CGH data and mpFISH counts

Nr	Cell Line	Ploidy C	Ploidy E	Region	Rearr FISH	Copy nr FISH	Copy nr E	ANILFR	sd	Abn CGH
1	U2020	2.4	2.2	R1		2	2.29	0.97	0.06	No
2				R2	tr tr	0	0.01	0.28	0.1	IL
3				R3		2	2.14	0.92	0.1	no
4				R4	tr	4	4.18	1.54	0.18	SC
5				R5	tr	6	6.32	2.19	0.23	TG
6	UOK125	2	1.8	R1		2	2.19	1.07	0.07	no
7				R2	tr	3	3.26	1.46	0.08	TG
8	CAKI1	3.2	3	R1	tr	2	2.06	0.74	0.05	TL
9				R2		3	3.10	0.98	0.05	no
10				R3	tr	4	4.21	1.23	0.05	TG
11	A498	3.2	3	R1		3	3.13	0.98	0.06	no
12				R2	tr tr	2	2.08	0.75	0.07	IL
13				R3		3	3.15	0.99	0.06	no
14	TK164	3.6	3	R1		3	3.50	0.98	0.05	no
15				R2	tr	4	4.97*	1.28	0.08	SC
16				R3	tr	5	6.03*	1.49	0.08	TG
17	UOK115	3.6	3.4	R1	tr	2	1.88	0.7	0.07	TL
18				R2	tr	4	3.71	1.12	0.06	TG
19	HONE1	3.8	3.8	R1		4	4.02	1.04	0.1	no
20				R2	tr	3	2.73	0.79	0.06	SC
21				R3	id id	1	0.34*	0.34	nc	IL
22				R4	tr	3	2.69	0.79	0.06	SC
23				R5	tr tr	2	1.72	0.6	0.06	IL
24				R6	tr	3	2.63*	0.78	0.08	SC
25				R7		4	4.37	1.11	0.1	no
26				R8	tr tr	5	5.15	1.26	0.11	IG
27				R9		4	3.80	1	0.05	no
28				R10	ampl	6	6.04	1.43	0.04	SC
29				R11	ampl	13	13.22	2.81	0.05	IG
30				R12	ampl	10	11.96*	2.57	nc	SC
31				R13	ampl	8	7.65	1.74	0.12	SC
32				R14	ampl	5	5.41	1.31	0.12	SC
33	UOK147	3.8	3.8	R1		4	4.14	1.07	0.06	no
34				R2	id	2	1.75	0.61	0.03	IL
35				R3		4	4.26	1.09	0.08	no
36				R4	du	5	5.04	1.24	nc	IG
37				R5		4	3.90	1.02	0.04	no
38				R6	tr tr	5	5.26	1.28	0.08	IG
39				R7	tr tr	3	3.02	0.85	0.08	IL
40				R8		4	4.03	1.04	0.07	no
41				R9	tr	5	4.96	1.22	0.07	SC
42				R10	tr	7	7.22	1.66	0.1	TG
43	CAKI2	4.8	5	R1	tr	4	3.58	0.81	0.06	TL
44				R2	ampl	6	5.83	1.16	0.08	SC
45				R3	ampl	10	9.67	1.74	0.02	SC
46				R4	ampl	14	14.98*	2.55	0.01	IG
47				R5	ampl	6	5.53	1.11	nc	no
48				R6	ampl	10	9.39*	1.7	0.1	IG
49				R7	ampl	6	5.57*	1.12	nc	SC
50				R8	ampl	10	8.78*	1.61	0.2	IG
51				R9	ampl	6	5.82	1.15	0.25	SC
52				R10	ampl	14	13.31*	2.29	nc	IG
53				R11	ampl	6	5.79	1.15	0.08	SC

"Ploidy C": ploidy determined from chromosome counting in relation to haploid number. "Ploidy E": expected ploidy calculated based on trend lines in Figure 6 (see details in the text). "Region": continuous chr3 parts containing a row of neighbouring clones (R1, R2...) of different copy number in the respective cell lines (see e.g. regions R1, R2... R10 in UOK 147 on Fig 4E). "Rearr FISH": chromosome rearrangements identified by metaphase mpFISH leading to copy number change (tr- translocation; id- interstitial deletion; du- duplication; ampl- amplification). "Copy nr FISH": copy number of the region identified in mpFISH experiments. "Copy nr E": expected copy number of the region counted by y = kx+B formula (*- exceptions, where the expected copy number was different from the real copy number due to heterogeneity or few data points). "ANILFR": average normalized inter-locus fluorescence ratio of the region; italics: lost regions and bold: regions of gain. "sd": standard deviation between NFR values within the region. "Abn CGH": chr3 abnormality detected by array-CGH. (no- normal; IL- interstitial loss; IG- interstitial gain; SC- step-wise change; TG- terminal gain; TL- terminal loss).

ISSN: 1471-2164