Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi
The minfi package is widely used for analyzing Illumina DNA methylation array data. Here
we describe modifications to the minfi package required to support the …
we describe modifications to the minfi package required to support the …
Genome-wide study of DNA methylation shows alterations in metabolic, inflammatory, and cholesterol pathways in ALS
PJ Hop, RAJ Zwamborn, E Hannon… - Science translational …, 2022 - science.org
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with an estimated
heritability between 40 and 50%. DNA methylation patterns can serve as proxies of (past) …
heritability between 40 and 50%. DNA methylation patterns can serve as proxies of (past) …
DNA methylation as a mediator of the association between prenatal adversity and risk factors for metabolic disease in adulthood
Although it is assumed that epigenetic mechanisms, such as changes in DNA methylation
(DNAm), underlie the relationship between adverse intrauterine conditions and adult …
(DNAm), underlie the relationship between adverse intrauterine conditions and adult …
[HTML][HTML] Genetic and environmental influences interact with age and sex in shaping the human methylome
The methylome is subject to genetic and environmental effects. Their impact may depend on
sex and age, resulting in sex-and age-related physiological variation and disease …
sex and age, resulting in sex-and age-related physiological variation and disease …
[HTML][HTML] TET2 mutations are associated with hypermethylation at key regulatory enhancers in normal and malignant hematopoiesis
Mutations in the epigenetic modifier TET2 are frequent in myeloid malignancies and clonal
hematopoiesis of indeterminate potential (CHIP) and clonal cytopenia of undetermined …
hematopoiesis of indeterminate potential (CHIP) and clonal cytopenia of undetermined …
Meffil: efficient normalization and analysis of very large DNA methylation datasets
Motivation DNA methylation datasets are growing ever larger both in sample size and
genome coverage. Novel computational solutions are required to efficiently handle these …
genome coverage. Novel computational solutions are required to efficiently handle these …
[HTML][HTML] Controlling bias and inflation in epigenome-and transcriptome-wide association studies using the empirical null distribution
M van Iterson, EW van Zwet, Bios Consortium… - Genome biology, 2017 - Springer
We show that epigenome-and transcriptome-wide association studies (EWAS and TWAS)
are prone to significant inflation and bias of test statistics, an unrecognized phenomenon …
are prone to significant inflation and bias of test statistics, an unrecognized phenomenon …
Nicotinamide riboside improves muscle mitochondrial biogenesis, satellite cell differentiation, and gut microbiota in a twin study
HAK Lapatto, M Kuusela, A Heikkinen, M Muniandy… - Science …, 2023 - science.org
Nicotinamide adenine dinucleotide (NAD+) precursor nicotinamide riboside (NR) has
emerged as a promising compound to improve obesity-associated mitochondrial dysfunction …
emerged as a promising compound to improve obesity-associated mitochondrial dysfunction …
[HTML][HTML] Epigenomic analysis of Sézary syndrome defines patterns of aberrant DNA methylation and identifies diagnostic markers
R van Doorn, RC Slieker, SE Boonk… - Journal of Investigative …, 2016 - Elsevier
Sézary syndrome (Sz) is a malignancy of skin-homing CD4+ memory T cells that is clinically
characterized by erythroderma, lymphadenopathy, and blood involvement. Distinction of Sz …
characterized by erythroderma, lymphadenopathy, and blood involvement. Distinction of Sz …
[HTML][HTML] Age-related DNA methylation changes are tissue-specific with ELOVL2 promoter methylation as exception
Background The well-established association of chronological age with changes in DNA
methylation is primarily founded on the analysis of large sets of blood samples, while …
methylation is primarily founded on the analysis of large sets of blood samples, while …