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Open AccessArticle

Ultra-Low DNA Input into Whole Genome Methylation Assays and Detection of Oncogenic Methylation and Copy Number Variants in Circulating Tumour DNA

1
Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
2
Department of Oncology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
3
Pathology and Data Analytics, Leeds Institute of Medical Research, St James University Hospital, Leeds LS2 9JT, UK
*
Author to whom correspondence should be addressed.
The S-CORT Consortium members are listed in the Acknowledgments.
These authors contributed equally to this work.
Academic Editor: Ernesto Guccione
Received: 30 December 2020 / Revised: 6 February 2021 / Accepted: 12 February 2021 / Published: 19 February 2021
Background: Abnormal CpG methylation in cancer is ubiquitous and generally detected in tumour specimens using a variety of techniques at a resolution encompassing single CpG loci to genome wide coverage. Analysis of samples with very low DNA inputs, such as formalin fixed (FFPE) biopsy specimens from clinical trials or circulating tumour DNA is challenging at the genome-wide level because of lack of available input. We present the results of low input experiments into the Illumina Infinium HD methylation assay on FFPE specimens and ctDNA samples. Methods: For all experiments, the Infinium HD assay for methylation was used. In total, forty-eight FFPE specimens were used at varying concentrations (lowest input 50 ng); eighteen blood derived specimens (lowest input 10 ng) and six matched ctDNA input (lowest input 10 ng)/fresh tumour specimens (lowest input 250 ng) were processed. Downstream analysis was performed in R/Bioconductor for quality control metrics and differential methylation analysis as well as copy number calls. Results: Correlation coefficients for CpG methylation were high at the probe level averaged R2 = 0.99 for blood derived samples and R2 > 0.96 for the FFPE samples. When matched ctDNA/fresh tumour samples were compared, R2 > 0.91 between the two. Results of differential methylation analysis did not vary significantly by DNA input in either the blood or FFPE groups. There were differences seen in the ctDNA group as compared to their paired tumour sample, possibly because of enrichment for tumour material without contaminating normal. Copy number variants observed in the tumour were generally also seen in the paired ctDNA sample with good concordance via DQ plot. Conclusions: The Illumina Infinium HD methylation assay can robustly detect methylation across a range of sample types, including ctDNA, down to an input of 10 ng. It can also reliably detect oncogenic methylation changes and copy number variants in ctDNA. These findings demonstrate that these samples can now be accessed by methylation array technology, allowing analysis of these important sample types. View Full-Text
Keywords: circulating tumour DNA; formalin fixed paraffin embedded; epigenome circulating tumour DNA; formalin fixed paraffin embedded; epigenome
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MDPI and ACS Style

Whalley, C.; Payne, K.; Domingo, E.; Blake, A.; Richman, S.; Brooks, J.; Batis, N.; Spruce, R.; S-CORT Consortium; Mehanna, H.; Nankivell, P.; Beggs, A.D. Ultra-Low DNA Input into Whole Genome Methylation Assays and Detection of Oncogenic Methylation and Copy Number Variants in Circulating Tumour DNA. Epigenomes 2021, 5, 6. https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes5010006

AMA Style

Whalley C, Payne K, Domingo E, Blake A, Richman S, Brooks J, Batis N, Spruce R, S-CORT Consortium, Mehanna H, Nankivell P, Beggs AD. Ultra-Low DNA Input into Whole Genome Methylation Assays and Detection of Oncogenic Methylation and Copy Number Variants in Circulating Tumour DNA. Epigenomes. 2021; 5(1):6. https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes5010006

Chicago/Turabian Style

Whalley, Celina; Payne, Karl; Domingo, Enric; Blake, Andrew; Richman, Susan; Brooks, Jill; Batis, Nikolaos; Spruce, Rachel; S-CORT Consortium; Mehanna, Hisham; Nankivell, Paul; Beggs, Andrew D. 2021. "Ultra-Low DNA Input into Whole Genome Methylation Assays and Detection of Oncogenic Methylation and Copy Number Variants in Circulating Tumour DNA" Epigenomes 5, no. 1: 6. https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes5010006

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