Table 1.
Overview of sample numbers with “omics” datasets across the 3 Rotterdam Study (RS) cohorts with the number and type of measurement for each omic method
| Genomics data type | Total | Datapoints/sample | RS Ia | RS IIa | RS IIIa | |
|---|---|---|---|---|---|---|
| Number | Type | |||||
| GWAS SNP data | 11,502 | 40,000,000 | SNPs | 6291 | 2157 | 3054 |
| Exome array | 3183 | 250,000 | SNPs | 3183 | – | – |
| Whole exome sequencing (WES) | 3778 | 693,000 | Variants | 3778 | – | – |
| Whole genome sequencing (WGS) | 96 | 3,000,000 | Variants | 96 | – | – |
| Genome wide expression (array) | 881 | 25,000 | Genes | – | – | 881 |
| Genome wide expression (RNA Seq) | 829 | 18,000,000 | Reads | – | 500 | 329 |
| Genome wide DNA methylation | 1600 | 450,000 | CpG’s | 100 | 500 | 1000 |
| Telomere length (PCR) | 1800 | 1 | – | 1800 | – | – |
| Mitochondrial DNA (PCR) | 500 | 1 | – | 500 | – | – |
| Microbiome 16S rRNA (faeces) | 2000 | 500 | OTU’s | – | – | 2000 |
| Metabolomics (NMR/UPLC MS) | 1826 | 4000 | Metabolites | 1826 | – | – |
| Metabolomics (NMR “Nightingale”) | 5381 | 228 | Metabolites | 2880 | 663 | 1838 |
| Serum protein profileb | 9820 | 35 | Proteins | 3812 | 2542 | 3466 |
| Total ‘omic’ datapoints in RS: | 43,196 × 62,422,765 = 2,696,413,756,940 | |||||
SNP single nucleotide polymorphism, CpG a two-nucleotide position (C next to G on the same strand) of which the C can be methylated; OTU operational taxonomic unit
aRS1, First cohort of the Rotterdam Study; RS2, Second cohort of the Rotterdam Study; RS3, Third cohort of the Rotterdam Study
bTotal estradiol, total testosterone, sex hormone-binding globulin, dehydroepiandrosterone, dehydroepiandrosterone sulfate, androstenedione, 17-hydroxyprogesterone, cortisol, corticosterone, 11-desoxycortisol, vitamin D, thyroid stimulating hormone, free T4, interleukins, C-reactive protein, Insulin-like growth factor 1, insulin, iron, ferritin, transferrin, fibrinogen, homocysteine, folic acid, riboflavine, pyridoxine, SAM/SAH ratio, cobalamine, Lp-PLA2, Fas/Fas-L, abeta42/40