Supplementary Figure 6: True positive and true negative prediction rates of variant-level methods and MSC, estimated by a set of 4,152 recently acquired HGMD disease-associated deleterious alleles of 1,119 missense mutations. | Nature Methods

Supplementary Figure 6: True positive and true negative prediction rates of variant-level methods and MSC, estimated by a set of 4,152 recently acquired HGMD disease-associated deleterious alleles of 1,119 missense mutations.

From: The mutation significance cutoff: gene-level thresholds for variant predictions

Supplementary Figure 6

(A) True positive and true negative (private non-disease-causing variants of patients) prediction rates by CADD, PolyPhen-2 and SIFT, using fixed cutoffs, hot zone approach (combining RVIS and PolyPhen-2), and MSC estimates with 90%, 95% and 99% CIs generated by the HGMD mutation database. (B) True positive (new deleterious mutations that were not used to generate the ClinVar-based MSC scores) and true negative (private nondisease-causing variants of patients) prediction rates by CADD, PolyPhen-2 and SIFT, using fixed cutoffs, hot zone approach (combining RVIS and PolyPhen-2), and MSC estimates with 90%, 95% and 99% CIs generated by the ClinVar mutation database.

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