Fig. 3 | Nature Communications

Fig. 3

From: Flexible and scalable diagnostic filtering of genomic variants using G2P with Ensembl VEP

Fig. 3

Sensitivity and precision of VEP-G2P Analysis GQ genotype quality, MAF minor allele frequency, alt:ref the ratio of alternate to reference alleles. TP true positive, FP false positive, TN true negative, FN false negative. Sensitivity = TP/(TP + FN). Precision = TP / (TP + FP). a Evaluation of G2P accuracy for likely causative variants in 94 genes achieving genome-wide significance (GWS) for de novo mutations in the DDD study. b G2P accuracy against the set of variants previously identified by DDD in the first 1133 samples, excluding de novo mutations. c ROC curves for VEP-G2PDD performance on 1700 DDD probands with de novo mutations (DNM) identified in the 484 monoallelic genes. The points on the curves represent varying MAF cut-offs: not seen in any control databases (bottom left), MAF < 1:100000, MAF < 1:50000, MAF < 1:25000, MAF < 1:10000 (top right). The region in the top left corner of the ROC space graph has been expanded to scale using the regions bounded by the dashed line rectangles. d The effect of consequence type and MAF on precision and recall (PR curves) of VEP-G2PDD using the same data analysed for the ROC space in c. The highest precision [0.812, 0.863] is achieved for LOF variants but with the lowest recall [0.425, 0.437]. The highest recall is achieved for variants of all consequence types [0.897, 0.942] at the cost of decreased precision [0.334, 0.476]. Analysing only missense variants with CADD≥ 30 or CADD ≥  20 leads to improvements in precision at the cost of decreasing recall

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