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Table 1 Forty-one CpGs and their intraclass correlation coefficients (ICC) using 1) duplicated samples both measured using Qiagen targeted methyl panel, 2) replicated samples measured using Qiagen targeted methylated panel and Illumina HM450K assay

From: Repeatability of methylation measures using a QIAseq targeted methyl panel and comparison with the Illumina HumanMethylation450 assay

CpGs included on the QIAseq targeted methyl panel (and Illumina EPIC assay)

Repeatability (ICC, 95% CI), using duplicated samples both measured with Qiagen targeted methyl panel

Repeatability (ICC, 95% CI), using replicated samples measured with Qiagen targeted methyl panel and Illumina HM450K assay

CpG^

Chr

Position

WB samples

7 pairs

FFPE samples

3 pairs

Combined samples 10 pairs

WB samples

25 pairs

FFPE samples

7 pairs

Combined samples

32 pairs

cg18072778*

1

148,203,924

0.54 (0–0.90)

0.37 (0–0.94)

0.85 (0.54–0.96)

0 (0–0.39)

0.4 (0–0.88)

0.76 (0.56–0.88)

cg04546999*

1

152,956,430

0.19 (0–0.75)

0.80 (0–0.99)

0.92 (0.74–0.98)

0.09 (0–0.47)

0 (0–0.68)

0.8 (0.63–0.9)

cg17714793

1

153,538,431

0 (0–0.63)

0.99 (0.47–1)

0.72 (0.24–0.92)

   

cg01608070

1

157,853,274

0.98 (0.89–1)

0.46 (0–0.96)

0.96 (0.84–0.99)

   

cg21501207

1

162,383,000

0.89 (0.56–0.98)

0.28 (0–0.94)

0.80 (0.43–0.94)

   

cg26237810

1

200,669,215

0.52 (0–0.89)

0.96 (0–1)

0.78 (0.29–0.95)

   

cg26354017*

1

205,819,088

0.92 (0.64–0.98)

0.70 (0–0.97)

0.94 (0.78–0.98)

0.83 (0.67–0.92)

0.46 (0–0.86)

0.83 (0.69–0.92)

cg14159672*

1

205,819,179

0.95 (0.71–0.99)

0.96 (0.27–1)

0.98 (0.94–1.00)

0.79 (0.57–0.9)

0.76 (0.16–0.95)

0.82 (0.66–0.91)

cg14893161*

1

205,819,252

0.92 (0.63–0.98)

0.99 (0.59–1)

0.97 (0.89–0.99)

0.94 (0.86–0.97)

0.73 (0–0.94)

0.93 (0.86–0.96)

cg05841700

1

205,819,384

0.96 (0.80–0.99)

0.68 (0–0.98)

0.96 (0.88–0.99)

   

cg24503407*

1

205,819,493

0.92 (0.65–0.98)

0 (0–0.96)

0.95 (0.82–0.99)

0.87 (0.74–0.94)

0.8 (0.02–0.98)

0.88 (0.76–0.94)

cg16334093

1

205,819,601

0.87 (0.43–0.97)

0.64 (0–0.97)

0.87 (0.54–0.97)

   

cg07157834*

1

205,819,610

0.90 (0.47–0.98)

0 (0–0.89)

0.94 (0.75–0.98)

0.6 (0.29–0.81)

0.26 (0–0.82)

0.65 (0.39–0.81)

cg20004147

2

65,718,931

0.98 (0.92–1)

0.98 (0.47–1)

0.98 (0.94–1.00)

   

cg21824770

2

243,012,164

0.28 (0–0.78)

0 (0–0.95)

0.88 (0.58–0.97)

   

cg10123377

3

42,387,525

0.97 (0.87–0.99)

0.68 (0–0.97)

0.92 (0.72–0.98)

   

cg01760119

3

101,661,383

0.12 (0–0.7)

0.87 (0–0.99)

0.98 (0.93–1.00)

   

cg12012426

4

1,366,464

cg19704288*

4

1,582,182

0.24 (0–0.79)

0.76 (0–0.98)

0.81 (0.43–0.95)

0 (0–0.38)

0.81 (0.33–0.96)

0.82 (0.66–0.91)

cg02722613*, #

4

25,162,899

0.75 (0.18–0.94)

0 (0–0.89)

0.77 (0.38–0.93)

0.87 (0.71–0.94)

cg19182683

4

183,730,519

0.98 (0.91–1)

0.94 (0–1)

0.97 (0.89–0.99)

   

cg07158503*, #

5

135,415,693

0.63 (0–0.92)

0.96 (0.12–1)

0.79 (0.35–0.94)

0.55 (0.22–0.77)

cg11608150*

5

135,415,949

0.71 (0.02–0.93)

0.17 (0–0.97)

0.61 (0.03–0.89)

0.91 (0.81–0.96)

0.44 (0–0.94)

0.84 (0.7–0.92)

cg06478886*

5

135,416,030

0.79 (0.24–0.96)

0.98 (0.44–1)

0.85 (0.54–0.96)

0.94 (0.86–0.97)

0.31 (0–0.83)

0.9 (0.8–0.95)

cg04481923*

5

135,416,206

0.74 (0.05–0.95)

0 (0–0.89)

0.23 (0–0.71)

0.59 (0.28–0.78)

0.74 (0.04–0.95)

0.62 (0.34–0.79)

cg06536614*

5

135,416,381

0.81 (0.24–0.95)

0.47 (0–0.95)

0.63 (0.08–0.88)

0.71 (0.46–0.86)

0 (0–0.68)

0.7 (0.47–0.84)

cg25340688*

5

135,416,398

0.79 (0.21–0.96)

0.99 (0.66–1)

0.85 (0.47–0.95)

0.65 (0.36–0.83)

0.50 (0–0.88)

0.7 (0.47–0.84)

cg26896946*

5

135,416,405

0.82 (0.29–0.97)

0.55 (0–0.96)

0.76 (0.29–0.93)

0.68 (0.4–0.84)

0.31 (0–0.81)

0.72 (0.53–0.85)

cg00124993*

5

135,416,412

0.82 (0.21–0.96)

0.96 (0.13–1)

0.87 (0.55–0.97)

0.71 (0.45–0.86)

0.64 (0–0.92)

0.73 (0.52–0.86)

cg18797653*

5

135,416,613

0.89 (0.54–0.97)

0 (0–0.87)

0.89 (0.59–0.97)

0.50 (0.14–0.74)

0.76 (0.14–0.95)

0.56 (0.25–0.75)

cg09483595*

5

158,878,381

0.98 (0.91–1)

0.71 (0–0.98)

0.92 (0.68–0.98)

0 (0–0.4)

0.61 (0–0.91)

0.94 (0.88–0.97)

cg13373914

7

67,323,067

0.12 (0–0.74)

1.00 (0.94–1)

0.90 (0.63–0.98)

   

cg05141217

8

28,491,379

0.96 (0.80–0.99)

1.00 (0.9–1)

0.97 (0.87–0.99)

   

cg26708920

10

13,826,318

0.94 (0.72–0.99)

0.96 (0.01–1)

0.96 (0.86–0.99)

   

cg20054939*

12

133,614,314

0.66 (0–0.92)

0 (0–0)

0.08 (0–0.63)

0 (0–0.41)

0 (0–0.72)

0 (0–0.36)

cg20124410

13

107,333,224

0.58 (0–0.9)

0 (0–0.87)

0.32 (0–0.73)

   

cg10829391

14

101,069,717

0.95 (0.75–0.99)

0.59 (0–0.97)

0.87 (0.57–0.97)

   

cg26748794*

16

88,804,052

0.97 (0.84–0.99)

0.59 (0–0.97)

0.89 (0.63–0.97)

0.67 (0.41–0.83)

0.69 (0.01–0.92)

0.67 (0.41–0.83)

cg20443278*

17

77,962,099

0.62 (0–0.91)

0.78 (0–0.99)

0.96 (0.85–0.99)

0 (0–0.38)

0.24 (0–0.8)

0.83 (0.67–0.91)

cg14150973*

19

40,950,432

0 (0–0.67)

0 (0–0.88)

0 (0–0.54)

0 (0–0.39)

0 (0–0.65)

0 (0–0.35)

cg17884856*

20

44,334,913

0.93 (0.69–0.99)

0.84 (0–0.99)

0.88 (0.59–0.97)

0.89 (0.79–0.95)

0.05 (0–0.68)

0.59 (0.32–0.78)

  1. ^CpG names used Illumina nomenclature
  2. *CpGs included on the Infinium HM450K BeadChip. 24 and 22 CpGs were detected and passed QC on HM450K platform for WB and FFPE samples, respectively
  3. Genomic coordinates are based on human genome assembly hg19
  4. #CpGs that did not pass QC on HM450K platform for the FFPE DNA samples
  5. CpGs that did not pass QC on the QIAseq targeted methyl panel