Table 1.
Performance of UK Biobank SNP chips versus sequencing for protein coding variants in UK Biobank
| SNP chip and dataset | Sensitivity, % (95% CI) | Specificity, % (95% CI) | Positive predictive value, % (95% CI) | Negative predictive value, % (95% CI) |
|---|---|---|---|---|
| UK Biobank Axiom (n=45 871): | ||||
| All exome variants | 96.3 (96.2 to 96.4) | 99.9 (99.9 to 99.9) | 85.9 (85.7 to 86.1) | 99.9 (99.9 to 99.9) |
| MAF>1% | 99.8 (99.8 to 99.8) | 99.7 (99.7 to 99.8) | 99.0 (98.9 to 99.1) | 99.9 (99.9 to 99.9) |
| MAF<0.001% | 29.5 (27.4 to 31.5) | 99.9 (99.9 to 99.9) | 16.1 (14.9 to 17.3) | 99.8 (99.8 to 99.8) |
| UK Biobank BiLEVE (n=4037): | ||||
| All exome variants | 96.9 (96.8 to 97.0) | 99.9 (99.9 to 99.9) | 91.1 (91 to 91.2) | 99.9 (99.9 to 99.9) |
| MAF>1% | 99.7 (99.7 to 99.8) | 99.7 (99.7 to 99.8) | 98.7 (98.6 to 98.8) | 99.9 (99.9 to 99.9) |
| MAF<0.001% | 4.4 (3.1 to 5.8) | 99.9 (99.9 to 99.9) | 9.4 (6.8 to 12.0) | 99.7 (99.7 to 99.8) |
Results are split by SNP chip and variant group: all exome variants, common variants (MAF >1%) and very rare variants (MAF <0.001%). Results are based on simple mean and standard error of each metric across all relevant single nucleotide variants; insertions and deletions are excluded.
MAF=minor allele frequency.