Parallel profiling of DNA methylation and hydroxymethylation highlights neuropathology-associated epigenetic variation in Alzheimer’s disease

Table 1 Sample and demographic information for the three cohorts used

	Discovery cohort (450K array)		Validation cohort 1 (450K array)	Validation cohort 2 (pyrosequencing)
Treatment	BS	OxBS	BS	BS	OxBS
n passed QC	91	85	104	96	92
Gender [M/F]	51/40	48/37	42/62	54/42	52/40
Mean age (± SD)	81.2 (9.5)	81.3 (9.5)	84.9 (8.7)	85.0 (7.2)	84.8 (7.3)
Braak stage
0	8	7	5	5	5
I	3	3	11	6	6
II	11	10	8	37	35
III	6	6	13	0	0
IV	8	7	5	0	0
V	18	17	18	23	22
VI	37	35	44	25	24
Mean PMI [min] (± SD)	2539.5 (1288.1)	2490.7 (1288.5)	1997.6 (1227.0)	2960.6 (1943.8)	2958.9 (1958.7)

The discovery cohort consisted of 450K array BS and OxBS data generated in 96 individuals from the MRC London Brain Bank for Neurodegenerative Disease, with 91 BS arrays and 85 OxBS arrays passing quality control (QC). Validation cohort 1 consisted of previously published 450K array BS data generated in an independent cohort of 104 individuals also from the MRC London Brain Bank for Neurodegenerative Disease [7]. Validation cohort 2 consisted of pyrosequencing BS and OxBS data we generated in an independent cohort of 96 individuals from the Thomas Willis Oxford Brain Collection, with 96 BS and 92 OxBS samples passing QC. For each cohort, we analyzed the entorhinal cortex. Shown for each dataset are the number of samples (n) that passed QC, distribution of sex, mean age, Braak stage spread, and postmortem interval (PMI) (± standard deviation (SD))

ISSN: 1868-7083