Why do results conflict regarding the prognostic value of the methylation status in colon cancers? the role of the preservation method

Tournier, Benjamin; Chapusot, Caroline; Courcet, Emilie; Martin, Laurent; Lepage, Côme; Faivre, Jean; Piard, Françoise

doi:10.1186/1471-2407-12-12

Table 2 Results of internal controls of conversion of the three markers

From: Why do results conflict regarding the prognostic value of the methylation status in colon cancers? the role of the preservation method

Identity	FFPE DNA 1		FFPE DNA 2		FFPE DNA 2		FFPE DNA 2		Cryo. DNA		Cryo. DNA		Cryo. DNA
	LINE-1		LINE-1		MLH1		MGMT		LINE-1		MLH1		MGMT
	PCR 1	PCR 2	PCR 1	PCR 2	PCR 1	PCR 2	PCR 1	PCR 2	PCR 1	PCR 2	PCR 1	PCR 2	PCR 1	PCR 2
1	check	failed	passed	passed	passed		passed		passed	passed	passed		passed
2	failed	passed	check	passed	⁄		passed		passed	passed	passed		passed
3	passed	passed	check	check	⁄		failed	failed	passed	passed	passed		passed
4	failed	failed	passed	check	⁄		failed	passed	passed	passed	passed		passed
5	failed	passed	failed	check	⁄	passed	passed	passed	passed	passed	passed		passed
6	check	passed	passed	passed	passed		passed		passed	passed	passed		passed
7	failed	failed	failed	check	passed	passed	failed	passed	passed	passed	passed		check	check
8	passed	failed	passed	passed	passed		passed		passed	passed	passed		passed
9	check	passed	passed	passed	passed		passed		passed	passed	passed		passed
10	failed	failed	passed	passed	passed		passed		passed	passed	passed		passed
11	failed	failed	check	passed	⁄	passed	check	check	passed	passed	passed		passed
12	failed	failed	failed	check	passed	⁄	passed	check	passed	passed	passed		passed
13	check	check	passed	passed	passed		passed		passed	passed	passed		passed
14	check	passed	passed	passed	⁄	passed	passed		passed	passed	passed		passed
15	check	check	passed	passed	passed		passed		passed	passed	passed		passed
16	passed	passed	check	check	⁄	passed	passed	passed	passed	passed	passed		passed
17	failed	failed	passed	passed	passed		check	passed	passed	passed	passed		passed
18	passed	failed	passed	passed	⁄		passed		passed	passed	passed		passed
19	check	failed	failed	passed	⁄		check	passed	check	passed	passed		failed	check
20	passed	check	passed	passed	passed		failed	passed	passed	passed	passed		passed
21	check	check	failed	check	⁄		failed	failed	passed	passed	check	failed	passed
22	passed	check	check	check	passed		failed	passed	passed	passed	passed		passed
23	passed	check	passed	passed	passed		passed		passed	passed	passed		passed
24	passed	passed	passed	passed	passed		passed		passed	passed	passed		passed
25	passed	failed	passed	passed	⁄		passed	passed	passed	passed	passed		passed
26	check	check	passed	passed	passed		check	passed	passed	passed	passed		check	check
27	check	passed	passed	passed	passed		passed		failed	⁄	⁄		⁄
28	passed	passed	passed	passed	passed		failed	failed	passed	passed	passed		passed
29	check	check	passed	passed	passed		passed		passed	passed	passed		passed
30	passed	passed	passed	passed	failed	check	check	passed	passed	passed	passed		passed
31	failed	failed	passed	passed	⁄		passed		passed	passed	passed		passed
32	passed	passed	passed	passed	passed		passed		passed	passed	passed		passed
33	passed	passed	check	check	passed	⁄	check	passed	passed	passed	passed		passed
34	check	check	passed	passed	⁄		failed	passed	passed	passed	passed		passed
35	check	failed	passed	passed	⁄		failed	passed	passed	passed	passed		passed
36	passed	passed	passed	passed	failed	failed	passed		passed	passed	passed		passed
37	check	passed	check	failed	passed	passed	failed	failed	passed	passed	passed		check	check
38	passed	passed	check	check	passed	passed	passed		passed	passed	passed		failed	failed
39	check	check	passed	check	passed		check	passed	passed	passed	passed		passed
40	check	check	passed	passed	⁄		failed	passed	passed	passed	passed		passed

From left to right the table gives results for DNA from FFPE tissues extracted with the classical method (FFPE DNA 1), extracted with the dedicated method (FFPE DNA 2) and DNA from cryo-preserved tissues (Cryo. DNA). "Passed" indicates a good conversion (0.0 to 5.0% of unconverted cytosines). "Check" indicates an uncertain conversion (5.0 to 7.0% of unconverted cytosines). "Failed" indicates a poor conversion (more than 7.0% of unconverted cytosines). Slash bar indicates there was no amplification. Results in bold emphasize controls of conversion giving "check" or "failed" results.

Back to article page

ISSN: 1471-2407

Contact us

Submission enquiries: bmccancer@biomedcentral.com
General enquiries: ORSupport@springernature.com

BMC Cancer

Contact us