Table 3

Validation of eight BW-MVPs and the PTPN7 CpG using DBS in the 17 discordant MZ twins

Infinium

DBS



CpG number

Gene

Meana ± SD

Range

Meanb ± SD

Range

Mean number of reads (range)

rPearson

P


cg14123607

APBA1

0.19 ± 0.08

0.06-0.43

0.09 ± 0.05

0.04-0.24

950 (440-1670)

0.61

0.0001

cg12170649

APPL2

0.83 ± 0.05

0.71-0.91

0.97 ± 0.02

0.93-0.99

1,120 (785-1,725)

-0.23

0.18

cg26404226

NA

0.52 ± 0.07

0.38-0.72

0.35 ± 0.08

0.21-0.54

1,201 (716-2,345)

0.73

<0.0001

cg15487251

IGF2BP2

0.57 ± 0.08

0.30-0.69

0.55 ± 0.10

0.24-0.68

1,156 (531-1,824)

0.80

<0.0001

cg10362113

PAPOLA

0.83 ± 0.12

0.41-0.98

0.84 ± 0.16

0.25-0.95

997 (188-1,689)

0.87

<0.0001

cg02409150

PHKG2

0.91 ± 0.05

0.80-0.98

0.93 ± 0.02

0.87-0.97

749 (294-1,301)

0.37

0.03

cg15049370

PPARGC1B

0.78 ± 0.07

0.62-0.98

0.96 ± 0.02

0.93-1.00

1,019 (522-1,792)

0.32

0.06

cg18384097c

PTPN7c

0.40 ± 0.17

0.16-0.89

0.28 ± 0.20

0.09-0.98

848 (383-1,334)

0.91

<0.0001

cg22768222

RUNX2

0.32 ± 0.09

0.05-0.55

0.20 ± 0.05

0.02-0.26

853 (302-1,347)

0.55

0.0008


Pearson's correlation coefficients (rPearson) between the (unadjusted) Infinium and the (unadjusted) DBS data are given as well as the overall mean methylation, standard deviation (SD) and the overall methylation range observed for the Infinium and the DBS data. aInfinium data (unadjusted) are expressed as mean β-value ± SD. bDBS data (unadjusted) are expressed as mean methylation level ± SD, where the methylation level is calculated by dividing the number of reads in which the particular CpG is methylated by the total number of sequenced reads. cBuccal marker. 'Mean number of reads (range)' is the average number of sequenced bisulfite reads per amplicon (minimum to maximum number of sequenced bisulfite reads per amplicon). P = P-value under H0: rPearson = 0. BW-MVP, birth weight-associated methylation variable position; DBS, deep bisulfite sequencing; MZ, monozygotic.

Souren et al. Genome Biology 2013 14:R44   doi:10.1186/gb-2013-14-5-r44

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