Table 2

Results of internal controls of conversion of the three markers

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.

Tournier et al. BMC Cancer 2012 12:12   doi:10.1186/1471-2407-12-12

Open Data