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Table 2 Methylation levels of the samples as estimated by MS-HRM and SMART-MSP.

From: Quality assessment of DNA derived from up to 30 years old formalin fixed paraffin embedded (FFPE) tissue for PCR-based methylation analysis using SMART-MSP and MS-HRM

   Methylation levels estimated for CDKN2A Methylation levels estimated for RARB
Sample Immunohistochemistry for p16 MS-HRM SMART-MSP MS-HRM SMART-MSP
    Lowest estimate Average estimate Highest estimate   Lowest estimate Average estimate Highest estimate
1 (1978) Negative 0.1%-1% 1.7% 2.7% 3.4% Failed ampl 0% 0% 0%
2 (1978) Negative 0% 0% 0% 0% 0.1%-1% 0% 0% 0%
3 (1978) Positive 0% 0% 0% 0% Het met 0% 0% 0%
4 (1978) Negative 0% 0% 0% 0% 1%-10% 2.4% 9.5% 30.8%
5 (1978) Positive 0% 0% 0% 0% 10%-100% 14.4% 20.3% 28.7%
6 (1978) Negative 0% 0% 0% 0% 0.1%-1% 0.1% 0.3% 0.4%
7 (1978) Negative 0% 0% 0% 0% 0% 0% 0% 0%
8 (1978) No data 10%-100% 20.3% 25.0% 28.7% 10%-100% 57.4% 61.6% 75.8%
9 (1983) Negative 1%-10% 0.7% 1.9% 5.4% Failed ampl 4.1% 5.8% 7.2%
10 (1983) Positive 0% 0% 0% 0% 10%-100% 21.8% 26.8% 33.0%
11 (1983) Negative 0.1%-1% 1.7% 2.4% 3.3% Het met 0% 0% 0%
12 (1983) Positive 0% 0% 0% 0% 1%-10% 18.9% 33.0% 53.6%
13 (1983) Negative 1%-10% 19.0% 27.0% 30.8% 0% 0% 0% 0%
14 (1983) Negative 0.1%-1% 0.8% 2.5% 6.3% Het met 0.2% 0.4% 1.4%
15 (1983) Negative 0% 0% 0% 0% 0.1%-1% 0.3% 0.9% 5.1%
16 (1988) Negative 0% 0% 0% 0% Het met 0.4% 0.8% 1.3%
17 (1988) Negative 0% 0% 0% 0% 10%-100% 93.3% 114.9% 186.6%
18 (1988) Negative 0% 0% 0% 0% Failed ampl 0% 0% 0%
19 (1988) Negative 1%-10% 3.4% 5.8% 10.9% Het met 0.2% 0.8% 3.8%
20 (1988) Negative 10%-100% 12.5% 14.4% 21.8% 0% 0% 0% 0%
21 (1988) Positive 0% 0% 0% 0% Het met 0.1% 0.5% 2.4%
22 (1988) Positive 0% 0% 0% 0% Het met 2.2% 2.7% 3.8%
23 (1988) Negative 10%-100% 18.9% 20.3% 21.7% 0% 0% 0% 0%
24 (1988) Negative 10%-100% 9.5% 14.4% 15.4% Het met 0.1% 0.2% 0.7%
25 (1988) Negative 10%-100% 6.3% 7.7% 10.9% 0% 0% 0% 0%
26 (1988) Negative 0% 0% 0% 0% Het met 0.2% 0.3% 0.6%
27 (1988) Negative 10%-100% 12.5% 14.4% 15.4% Failed ampl 0% 0% 0%
28 (1988) Positive 0% 0% 0% 0% 0% 0% 0% 0%
29 (1993) Negative 1%-10% 3.6% 5.8% 7.7% 0% 0% 0% 0%
30 (1993) Positive 0% 0% 0% 0% 1%-10% 2.9% 8.8% 14.4%
31 (1993) Negative 0% 0% 0% 0% Het met 0.3% 0.7% 1.4%
32 (1993) Negative 10%-100% 21.8% 26.8% 30.8% 0.1%-1% 0.1% 0.3% 0.7%
33 (1993) Negative 0% 0% 0% 0% 0% 0% 0% 0%
34 (1993) Negative 10%-100% 25.0% 40.6% 61.6% 1%-10% 2.9% 5.4% 8.8%
35 (1993) Positive 0% 0% 0% 0% Het met 0.3% 0.6% 0.8%
36 (1993) Negative 10%-100% 5.1% 10.9% 17.7% 0.1%-1% 0.2% 0.6% 1.4%
37 (1993) Positive 0% 0% 0% 0% 1%-10% 23.3% 25.0% 28.7%
38 (1993) Positive 0% 0% 0% 0% 0% 0% 0% 0%
39 (1998) Negative 0.1%-1% 0% 0% 0% 0% 2.5% 2.9% 3.4%
40 (1998) Negative 0.1%-1% 0.1% 0.1% 0.2% Het met 0.6% 1.5% 3.1%
41 (1998) Negative 10%-100% 19.0% 23.3% 28.7% 0% 0% 0% 0%
42 (1998) Positive 0% 0.1% 0.3% 0.7% Het met 0.2% 0.4% 1.4%
43 (1998) Positive 0% 0% 0% 0% 0% 0% 0% 0%
44 (1998) Positive 0.1%-1% 0.1% 0.2% 0.4% Het met 2.9% 3.6% 5.4%
45 (1998) Positive 0% 0% 0% 0% 0.1%-1% 0.2% 0.7% 2.9%
46 (1998) Positive 0% 0% 0% 0% 0.1%-1% 0% 0% 0%
47 (1998) Positive 0% 0% 0% 0% 10-100% 21.8% 30.8% 50.0%
48 (1998) Positive 0% 0% 0% 0% Failed ampl 0% 0% 0%
49 (2003) Positive 0% 0% 0% 0% 0% 0% 0% 0%
50 (2003) Positive 0% 0% 0% 0% Het met 0.5% 1% 2.1%
51 (2003) No data 0% 0% 0% 0% 0% 0% 0% 0%
52 (2003) Positive 0.1%-1% 0.4% 0.6% 1.0% 1%-10% 2.7% 3.9% 5.1%
53 (2003) Negative 10%-100% 2.7% 6.3% 16.5% 1%-10% 4.1% 10.2% 26.8%
54 (2003) Negative 0% 0% 0% 0% 0% 0% 0% 0%
  1. An average methylation estimate as well as the highest and lowest possible methylation estimates calculated from the Ct-values of the triplicates for the gene and the control is given for SMART-MSP.
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BMC Cancer

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