DNA methylation-based predictors of health: applications and statistical considerations

PD Yousefi, M Suderman, R Langdon… - Nature Reviews …, 2022 - nature.com
DNA methylation data have become a valuable source of information for biomarker
development, because, unlike static genetic risk estimates, DNA methylation varies …

DNA methylation-based biomarkers and the epigenetic clock theory of ageing

S Horvath, K Raj - Nature reviews genetics, 2018 - nature.com
Identifying and validating molecular targets of interventions that extend the human health
span and lifespan has been difficult, as most clinical biomarkers are not sufficiently …

Pathway enrichment analysis and visualization of omics data using g: Profiler, GSEA, Cytoscape and EnrichmentMap

J Reimand, R Isserlin, V Voisin, M Kucera… - Nature protocols, 2019 - nature.com
Pathway enrichment analysis helps researchers gain mechanistic insight into gene lists
generated from genome-scale (omics) experiments. This method identifies biological …

Inflammation and cancer

M Murata - Environmental health and preventive medicine, 2018 - Springer
Infection and inflammation account for approximately 25% of cancer-causing factors.
Inflammation-related cancers are characterized by mutagenic DNA lesions, such as 8-oxo-7 …

Clinical epigenetics: seizing opportunities for translation

M Berdasco, M Esteller - Nature Reviews Genetics, 2019 - nature.com
Biomarker discovery and validation are necessary for improving the prediction of clinical
outcomes and patient monitoring. Despite considerable interest in biomarker discovery and …

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

A Colaprico, TC Silva, C Olsen, L Garofano… - Nucleic acids …, 2016 - academic.oup.com
Abstract The Cancer Genome Atlas (TCGA) research network has made public a large
collection of clinical and molecular phenotypes of more than 10 000 tumor patients across …

Droplet Cas12a assay enables DNA quantification from unamplified samples at the single-molecule level

H Yue, B Shu, T Tian, E Xiong, M Huang, D Zhu… - Nano Letters, 2021 - ACS Publications
DNA quantification is important for biomedical research, but the routinely used techniques
rely on nucleic acid amplification which have inherent issues like cross-contamination risk …

SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions

W Zhou, TJ Triche Jr, PW Laird… - Nucleic acids research, 2018 - academic.oup.com
We report a new class of artifacts in DNA methylation measurements from Illumina
HumanMethylation450 and MethylationEPIC arrays. These artifacts reflect failed …

Review The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge

K Tomczak, P Czerwińska… - Contemporary Oncology …, 2015 - termedia.pl
The Cancer Genome Atlas (TCGA) is a public funded project that aims to catalogue and
discover major cancer-causing genomic alterations to create a comprehensive “atlas” of …

DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning

C Angermueller, HJ Lee, W Reik, O Stegle - Genome biology, 2017 - Springer
Recent technological advances have enabled DNA methylation to be assayed at single-cell
resolution. However, current protocols are limited by incomplete CpG coverage and hence …