Genome position and gene amplification

Table 1 Thirteen *DHFR** insertion site clones and their response to methotrexate

Name	Chr.	Chr. band	Sequence¹ (bp)	Exp.²	IC-50³ (nM)	MTX⁴ (nM)	Expression⁵ (%)	No. of colonies⁶	Colonies screened⁷	DHFR* amplicon⁸	DHFR* gain⁹
1M-34	9	q34.3	137,580,684	→	43	120	4,172	26.5 (8.50)	10	4	0
1M-39	13	q32.1	96,707,451	←	22	65	3,835	0.5 (1.00)	0	0	0
1M-42	8	q22.3	102,162,871	←	21	75	2,660	5.5 (3.25)	15	13	2
1M-43	11	q13.1	65,526,684	→	22	65	1,828	13 (10.50)	9	0	3
1M-45	11	q23.3	118,293,388	←	70	200	5,329	2.5 (3.00)	8	1	6
1M-57	3	q27.1	185,207,363	→	15	75	2,047	3.5 (3.75)	12	3	8
1M-67	1	p34.3	39,533,783	→	31	90	2,306	0.5 (1.00)	3	1	0
1M-72	2	q35	217,190,120	←	16	65	5,077	1.0 (2.00)	2	1	1
1M-73	12	p13.2	12,767,229	←	20	65	3,116	0.5 (1.00)	1	0	0
1M-75	22	q12.2	28,977,607	→	32	90	3,307	25.5 (12.75)	3	1	1
1M-83	19	q13.2	45,618,743	→	14	65	756	1.0 (1.75)	6	0	1
1M-84	17	q12	34,161,068	→	23	75	3,934	11.0 (11.00)	4	0	0
1M-89	19	q13.33	53,682,371	→	25	75	4,288	2.0 (1.00)	9	3	0

¹Position in the human genome sequence (UCSC Genome Browser, May 2004 freeze). ²Exp., Direction of DHFR* integration in the genome; arrow to the right indicates that the DHFR* coding sequence is integrated in the direction from the p-arm to the q-arm of the chromosome. ³Methotrexate concentration that causes 50% inhibition of the cell growth after 6 days. ⁴Methotrexate (MTX) concentration used for selection of resistant colonies. ⁵Expression of DHFR* measured indirectly by quantitative RT-PCR (EGFP expression normalized to GUSB expression, 2^-(dCt) × 100). ⁶Median number (and interquartile range in parentheses) of resistant colonies per 10 cm plate after 28 days of methotrexate treatment. ⁷Number of independent resistant colonies screened by array CGH. ⁸Resistant colonies with amplification of the DHFR* integration region. ⁹Resistant colonies with low level copy number gain of the DHFR* integration region. Chr., chromosome.

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