Genotyping and QC of DNA Samples

DNA samples of individuals (n = 241) were genotyped using the commercially available SNP chip, Illumina HumanOmniExpressExome‐8 v1.0. Opticall 0.7.0 with default settings was used for genotype calling [42 (link)]. Quality control steps and imputation of the genetic data were done similarly as for the 300BCG cohort. We identified and excluded seven samples as ethnic outliers based on (MDS) (Supporting Information Fig. S6B). We selected 4,296,378 SNPs with MAF 5% for follow‐up QTL mapping.

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Moorlag S.J., Matzaraki V., van Puffelen J.H., van der Heijden C., Keating S., Groh L., Röring R.J., Bakker O.B., Mourits V.P., Koeken V.A., de Bree L.C., Smeekens S.P., Oosting M., Gamboa R.A., Riksen N.P., Xavier R.J., Wijmenga C., Kumar V., van Crevel R., Novakovic B., Joosten L.A., Li Y, & Netea M.G. (2021). An integrative genomics approach identifies KDM4 as a modulator of trained immunity. European Journal of Immunology, 52(3), 431-446.

Publication 2021

HumanOmniExpressExome‐8 v1.0

Chip Genotype Snps

Corresponding Organization : University of Bonn

Other organizations : University Medical Center Groningen, University of Groningen, Statens Serum Institut, Odense University Hospital, University of Southern Denmark, Broad Institute, University of Oslo, Royal Children's Hospital, Murdoch Children's Research Institute

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