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Table 1 Omics data description and technical variability management

From: Variability of multi-omics profiles in a population-based child cohort

Omics profile Matrix Sample size (omics available for both visits) Number of features Laboratory processing Batch correction Criteria for feature exclusion
DNA methylation Blood leukocytes 149 91601 Randomized by cohort and sex, and panel samples paired in plate and array Residuals of SVs protecting for cohort, sex and age. Cell type composition also corrected with SVs. < 98% call rate and < 62.5% ICC
Gene expression Whole blood 105 45438 Randomized by cohort and sex, and panel samples paired in plate. Residuals of SVs protecting for cohort, sex and age. Cell type composition also corrected with SVs. < 25% call rate
miRNA expression Whole blood 100 453 Randomized by cohort and sex, and panel samples paired in plate and array. Residuals of SVs protecting for cohort, sex and age. Cell type composition also corrected with SVs. < 25% call rate
Proteins Plasma 149 36 Randomized by cohort Overall protein average minus plate specific protein average subtracted for each individual and each protein < 30% measurements in the linear range (LIN)
Serum metabolites Serum 154 177 Fully randomized - > 30% CV and > 30% BLD + zeros
Urine metabolites Urine 154 44 Fully randomized - > 30% CV
  1. Definitions. Call rate (for DNA methylome): proportion of detection of a given CpG among samples; Call rate (for miRNA and gene expression): proportion of detection of gene or miRNA among samples. Abbreviations. SV surrogate variables, ICC interclass correlation coefficient [35], CV coefficient of variation, BLD below limit of detection