Journal Article

An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BeadArray

Koestler, Devin C., Hansen, Helen M., Kelsey, Karl T., Christensen, Brock C., Butler, Rondi A., Salas, Lucas A., Wiencke, John K.

2018

Overview

Genome-wide methylation arrays are powerful tools for assessing cell composition of complex mixtures. We compare three approaches to select reference libraries for deconvoluting neutrophil, monocyte, B-lymphocyte, natural killer, and CD4+ and CD8+ T-cell fractions based on blood-derived DNA methylation signatures assayed using the Illumina HumanMethylationEPIC array. The IDOL algorithm identifies a library of 450 CpGs, resulting in an average R 2  = 99.2 across cell types when applied to EPIC methylation data collected on artificial mixtures constructed from the above cell types. Of the 450 CpGs, 69% are unique to EPIC. This library has the potential to reduce unintended technical differences across array platforms.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Accuracy / Algorithms / Animal Genetics and Genomics / B-cells / B-lymphocytes / Bioinformatics / Biomedical and Life Sciences / Blood / Blood Cells - metabolism / CD4 antigen / CD8 antigen / CD8-positive T-lymphocytes / CpG Islands / Datasets / Deoxyribonucleic acid / DNA / DNA Methylation / Epigenetics / Ethnicity / Evolutionary Biology / Gene expression / Gene Library / Genetic testing / genome / Genomes / Human Genetics / Humans / Life Sciences / Lymphocytes / Lymphocytes B / Lymphocytes T / Male / Method / Microbial Genetics and Genomics / Monocytes / Natural killer cells / Neutrophils / Oligonucleotide Array Sequence Analysis / Plant Genetics and Genomics