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Table 1 Age of tumour material, performance at QC checkpoints and number of failed HM450K probes in failed and a subset of successful samples on HM450K platform

From: Tools for translational epigenetic studies involving formalin-fixed paraffin-embedded human tissue: applying the Infinium HumanMethyation450 Beadchip assay to large population-based studies

Sample

Age of tumour material (years)

QC 1 (total ng)

QC 2 (∆Cq ≤ 6)

QC 3 (∆Cq ≥ 4)

Number of failed probes

2657a

20

209

1.43

5.45

125,491

3282a

20

483

0.68

8.09

196,914

25098a

11

334

3.25

5.94

28,751

27042a

7

671

1.83

9.84

22,334

1537

15

47

0.86

5.56

502

2245

12

256

1.04

8.16

272

6075

19

27.3

1.00

4.28

788

6112

20

159.8

1.61

6.72

534

8613

18

51.5

1.87

4.64

794

10350

13

1078

2.7

4.83

9995

10780

14

749

4.1

4.24

6678

15291

14

114.6

1.24

6.96

485

17940

17

583

4.13

4.83

5436

21200

10

71.2

1.17

4.17

694

21635

13

172.4

2.73

4.62

1083

35915

9

305

2.78

7.28

512

35995

8

270

4.28

4.00

3379

37246

12

180.5

3.74

4.14

2714

40593

12

63.9

1.64

6.04

1079

41223

11

1579

2.95

6.42

1489

  1. aDenotes failed samples on the HM450K assay (according to study criteria)