Genome-wide DNA Methylation Analysis

Genome-wide DNA methylation was measured using the HumanMethylation450K (HM450K) BeadChip array (Illumina). For each sample, a total of 300–500 ng of tumour DNA was bisulfite-converted using Zymo Gold EZ-DNA kit (Irvine, CA) and restored using the DNA Restoration Kit as per the manufacturer’s instructions (Illumina, CA, United States). Sample DNA quantity was assessed using an in-house modified quality control protocol [80 (link)]. Samples that passed the final quality check were run on the HM450K array (Illumina) according to manufacturer’s instructions.

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Suman M., Dugué P.A., Wong E.M., Joo J.E., Hopper J.L., Nguyen-Dumont T., Giles G.G., Milne R.L., McLean C, & Southey M.C. (2021). Association of variably methylated tumour DNA regions with overall survival for invasive lobular breast cancer. Clinical Epigenetics, 13, 11.

Publication 2021

HM450K array

A 300 Bisulfite Dna methylation Genome Gold Tumour dna

Corresponding Organization :

Other organizations : University of Melbourne, Monash University, Monash Health, Cancer Council Victoria, The Alfred Hospital, Alfred Health

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Variable analysis

independent variables

Genome-wide DNA methylation

dependent variables

Measured outcomes

control variables

Sample DNA quantity assessment using an in-house modified quality control protocol
Samples that passed the final quality check

controls

Positive control: Not specified
Negative control: Not specified

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