ArticleEpigenetics & chromatin2019
Accurate ethnicity prediction from placental DNA methylation data.
Article in Epigenetics & chromatin, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Development and Validation of a Novel Placental DNA Methylation Biomarker of Maternal Smoking during Pregnancy in the ECHO Program.Environmental health perspectives · 2024Trial
- Sex-linked placental DNA methylation associated with early-onset preeclampsia.Research square · 2026Article
- Population epigenetics: deciphering DNA methylation diversity and its implications for health, disease, and evolution.Molecular biology and evolution · 2026Review
- DNA methylation in the placenta and household socioeconomic status: the SPAH study.Clinical epigenetics · 2026Article
- Characterizing placental dysfunction with DNA methylation profiling and placental histopathology.Placenta · 2026Article
- Sex-influenced DNA methylation differs by placental cell type.Biology of sex differences · 2026Article
- Article
- Distinct Co-methylation Patterns in African and European Populations and Their Genetic Associations.Genomics, proteomics & bioinformatics · 2025Article
- Placental epigenetic clocks derived from crowdsourcing: Implications for the study of accelerated aging in obstetrics.iScience · 2025Article
- Epigenomic signatures of accelerated epigenetic aging are associated with congenital heart disease in newborns.BMC medical genomics · 2025Article
- Breaking rules: the complex relationship between DNA methylation and X-chromosome inactivation in the human placenta.Biology of sex differences · 2025Article
- Immediate and durable effects of maternal tobacco consumption on placental DNA methylation: a replication and discovery study.Environmental epigenetics · 2025Article
- Technical considerations for placental tissue processing and the subsequent impact on genome-wide DNA methylation analysis.Clinical epigenetics · 2024Article
- MethylGenotyper: Accurate Estimation of SNP Genotypes and Genetic Relatedness from DNA Methylation Data.Genomics, proteomics & bioinformatics · 2024Article
- Genetic control of DNA methylation is largely shared across European and East Asian populations.Nature communications · 2024Article
- Associations between placental hydroxymethylation and birthweight.Epigenetics reports · 2024Article
- Genome-wide neonatal epigenetic changes associated with maternal exposure to the COVID-19 pandemic.BMC medical genomics · 2023Observational
- The application of epiphenotyping approaches to DNA methylation array studies of the human placenta.Epigenetics & chromatin · 2023Article
- Evaluation of pediatric epigenetic clocks across multiple tissues.Clinical epigenetics · 2023Article
- Sexually dimorphic methylation patterns characterize the placenta and blood from extremely preterm newborns.BMC biology · 2023Article
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Authors and funding
9 authors.
Funding
Abstract
backgroundThe influence of genetics on variation in DNA methylation (DNAme) is well documented. Yet confounding from population stratification is often unaccounted for in DNAme association studies. Existing approaches to address confounding by population stratification using DNAme data may not generalize to populations or tissues outside those in which they were developed. To aid future placental DNAme studies in assessing population stratification, we developed an ethnicity classifier, PlaNET (Placental DNAme Elastic Net Ethnicity Tool), using five cohorts with Infinium Human Methylation 450k BeadChip array (HM450k) data from placental samples that is also compatible with the newer EPIC platform.
resultsData from 509 placental samples were used to develop PlaNET and show that it accurately predicts (accuracy = 0.938, kappa = 0.823) major classes of self-reported ethnicity/race (African: n = 58, Asian: n = 53, Caucasian: n = 389), and produces ethnicity probabilities that are highly correlated with genetic ancestry inferred from genome-wide SNP arrays (> 2.5 million SNP) and ancestry informative markers (n = 50 SNPs). PlaNET's ethnicity classification relies on 1860 HM450K microarray sites, and over half of these were linked to nearby genetic polymorphisms (n = 955). Our placental-optimized method outperforms existing approaches in assessing population stratification in placental samples from individuals of Asian, African, and Caucasian ethnicities.
conclusionPlaNET provides an improved approach to address population stratification in placental DNAme association studies. The method can be applied to predict ethnicity as a discrete or continuous variable and will be especially useful when self-reported ethnicity information is missing and genotyping markers are unavailable.
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