The paper introduces a two-step normalization strategy for DNA methylation microarray data to reduce sex bias by separately normalizing autosomal and sex chromosome CpGs.

Bioinformatics · Jun 30, 2022Peer-reviewedBioinformatics

Uncertainty quantification of reference based cellular deconvolution algorithms

Dorothea Seiler Vellame, Gemma L. Shireby, Ailsa MacCalman, Emma Louise Dempster, Joe Burrage, T.J. Gorrie-Stone, Leonard C. Schalkwyk, Jonathan S. Mill, Eilis J. Hannon

This paper introduces and validates a metric to assess the accuracy of cellular deconvolution in DNA methylation studies, showing it identifies biases in different demographic groups.

bioRxiv · Jun 15, 2022 · PreprintBioinformatics

Genomic and phenomic insights from an atlas of genetic effects on DNA methylation

Josine L. Min, Gibran Hemani, Eilis J. Hannon, Koen F. Dekkers, Juan Castillo Fernandez, René Luijk, Elena Carnero‐Montoro, Daniel John Lawson, Kimberley Burrows, Matthew J Suderman, Andrew D. Bretherick, Tom G. Richardson, Johanna Klughammer, Valentina Iotchkova, Gemma C. Sharp, , Marinus H. van IJzendoorn

The paper identifies genetic variants influencing DNA methylation in blood and shows their associations with complex traits and diseases, but finds limited direct causality.

Nature Genetics · Sep 1, 2021Peer-reviewedGenetic & Genomic Medicine

DNA methylation-based sex classifier to predict sex and identify sex chromosome aneuploidy

Yucheng Wang, Eilis J. Hannon, Olivia A. Grant, T.J. Gorrie-Stone, Meena Kumari B, Jonathan S. Mill, Xiaojun Zhai, Klaus Dieter McDonald-Maier, Leonard C. Schalkwyk

The paper presents a DNA methylation-based sex classifier that predicts sex and identifies sex chromosome aneuploidy using CpG sites from whole blood samples.

BMC Genomics · Jun 28, 2021Peer-reviewedBioinformatics

DNA methylation covariation in human whole blood and sperm: implications for studies of intergenerational epigenetic effects

Fredrika Åsenius, T.J. Gorrie-Stone, Ama Brew, Yasmin Panchbhaya, Elizabeth Williamson, Leonard C. Schalkwyk, Vardhman K. Rakyan, Michelle L. Holland, Sarah J. Marzi, David J. Williams

The paper examines DNA methylation differences between human blood and sperm, finding limited correlation and no significant obesity-related changes in sperm methylation.

PLoS Genetics · Oct 13, 2020Peer-reviewedGenomics

Leveraging DNA methylation quantitative trait loci to characterize the relationship between methylomic variation, gene expression and complex traits.

Eilis J. Hannon, T.J. Gorrie-Stone, Melissa Smart, Joe Burrage, Amanda Hughes, Yanchun Bao, Meena Kumari B, Leonard C. Schalkwyk, Jonathan S. Mill

The paper identifies mQTLs and pleiotropic associations between DNAm, gene expression, and complex traits using SMR and a large UK cohort.

The American Journal of Human Genetics · Oct 25, 2018Peer-reviewedGenetics

Properties of the epigenetic clock and age acceleration

Louis Y. El Khoury, T.J. Gorrie-Stone, Melissa Smart, Amanda Hughes, Yanchun Bao, Alexandria Andrayas, Joe Burrage, Eilis J. Hannon, Meena Kumari B, Jonathan S. Mill, Leonard C. Schalkwyk

The paper examines the properties of the Horvath epigenetic clock in older individuals and finds age acceleration measures are age-dependent and may lead to misleading associations with diseases like Alzheimer's.

bioRxiv · Jul 6, 2018 · PreprintGenomics