Vitamin C boosts DNA demethylation in TET2 germline mutation carriers

We recently identified a family with lymphoma predisposition where a heterozygous truncating germline mutation in TET2 segregated with nodular lymphocyte predominant Hodgkin lymphoma. In a clinical trial of one year, we investigated the effects of oral 1 g/day vitamin C supplementation on DNA methylation by analyzing genome-wide DNA methylation and gene expression patterns from the family members.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

14 Datasets 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001010009	Fasq-files from 3 unaffected TET2 mutation carriers, 2 mutation carriers diagnosed with lymphoma and 3 family members without TET2 mutation. Time series data collected from 0, 6 and 12 months after daily dose of 1g vitamin C.	Illumina NovaSeq 6000	24
EGAD00010002410	Average methylation difference 12 months vs 0 months at Roadmap Epigenomics chromatin state annotations from different cell types using nanopolish. Data from 8 individuals.	Oxford Nanopore	1
EGAD00010002411	Average hypermethylation on transcription factor binding sites based on nanopolish calls; only positions showing higher methylation than sampleâ€™s average methylation at enhancers were included when defining the average methylation level. Data from 6 individuals at different time points.	Oxford Nanopore	1
EGAD00010002412	Average genome-wide methylation levels per sample at different time points using nanopolish calls. Data from 8 individuals.	Oxford Nanopore	1
EGAD00010002413	Average methylation levels based on nanopolish calls from Roadmap Epigenomics chromatin state annotations using different cell types. Data from 8 individuals at different time points.	Oxford Nanopore	1
EGAD00010002414	Average hydroxymethylation levels based on megalodon calls from Roadmap Epigenomics chromatin state annotations using different cell types. Data from 8 individuals at different time points.	Oxford Nanopore	1
EGAD00010002415	Average hydroxymethylation difference 12 months vs 0 months at Roadmap Epigenomics chromatin state annotations from different cell types. Data from 8 individuals.	Oxford Nanopore	1
EGAD00010002416	Proportion of hyper- and hypomethylated positions at Roadmap annotations. Data from 8 individuals.	Oxford Nanopore	1
EGAD00010002417	Average hydroxymethylation levels based on megalodon calls from Roadmap Epigenomics histone mark annotations using different cell types. Data from 8 individuals at different time points.	Oxford Nanopore	1
EGAD00010002418	CpG hydroxymethylation. Software: minimap2 v.2.16; Megalodon.	Oxford Nanopore	24
EGAD00010002419	Average genome-wide hydroxymethylation levels per sample at different time points using megalodon calls. Data from 8 individuals.	Oxford Nanopore	1
EGAD00010002420	CpG methylation. Software: minimap2 v2.16;Nanopolish.	Oxford Nanopore	24
EGAD00010002421	Average hydroxymethylation levels on transcription factor binding sites obtained from ENCODE (ChIP-sequencing of GM12878 lymphoblastoid cell line). Data from 6 individuals at different time points.	Oxford Nanopore	1
EGAD00010002422	Average methylation levels based on nanopolish calls from Roadmap Epigenomics histone mark annotations using different cell types. Data from 8 individuals at different time points.	Oxford Nanopore	1

Publications	Citations
Vitamin C boosts DNA demethylation in TET2 germline mutation carriers. Taira A, Palin K, Kuosmanen A, Välimäki N, Kuittinen O, Kuismin O, Kaasinen E, Rajamäki K, Aaltonen LA. Clin Epigenetics 15: 2023 7	3