MutationTaster2: mutation prediction for the deep-sequencing age

JM Schwarz, DN Cooper, M Schuelke, D Seelow - Nature methods, 2014 - nature.com
Nature methods, 2014nature.com
We compared the predictions of the web versions of MutationTaster2, SIFT (http://sift. jcvi.
org/), PolyPhen-2 (http://genetics. bwh. harvard. edu/pph2/) and PROVEAN (http://provean.
jcvi. org/index. php) on 1,100 polymorphisms and 1,100 disease mutations with variants
causing single amino acid exchanges. MutationTaster2 had the highest accuracy (88%) of
the tools tested (Table 1). The actual performance of MutationTaster2 is even better because
the program automatically detects and categorizes confirmed polymorphisms and known …
We compared the predictions of the web versions of MutationTaster2, SIFT (http://sift. jcvi. org/), PolyPhen-2 (http://genetics. bwh. harvard. edu/pph2/) and PROVEAN (http://provean. jcvi. org/index. php) on 1,100 polymorphisms and 1,100 disease mutations with variants causing single amino acid exchanges. MutationTaster2 had the highest accuracy (88%) of the tools tested (Table 1). The actual performance of MutationTaster2 is even better because the program automatically detects and categorizes confirmed polymorphisms and known disease mutations. In a realworld example using exome data, MutationTaster2 yielded a false positive rate of 1% for homozygous alterations (Supplementary
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