Question: Cut Off For Damaging Mutation By Phylop, Lrtscore, Polyphen2, Mutationtaster
gravatar for Omid
8.6 years ago by
Omid570 wrote:

To predict damaging mutations by SIFT, I know the cut off is smaller than 0.05

I would be thankful to know the cut off for the other prediction programs which mentioned in below:

PhyloP LRTScore Polyphen2 MutationTaster

How can we decide about damaging or tolerated mutant by combination of these 5 programs?


ADD COMMENTlink modified 7.5 years ago by Biostar ♦♦ 20 • written 8.6 years ago by Omid570

Be aware that any cutoff is arbitrary and requires a subjective decision on the part of the user.

ADD REPLYlink written 8.6 years ago by Neilfws49k

There is also a program, Condel, that combines the output of several of these programs to produce a unified score.

ADD REPLYlink written 8.6 years ago by DG7.2k

Try VAAST it incorporates MAF data and the severity of amino acid substitutions. - disclaimer: I am a member of the Yandell lab.

ADD REPLYlink modified 8.6 years ago • written 8.6 years ago by Zev.Kronenberg11k
gravatar for DG
8.6 years ago by
DG7.2k wrote:

Generally these programs don't have hard and fast cut-offs. It is mostly subjective on the par tof the user in terms of a trade-off between false-positives and false-negatives. Typically I don't use actual cut-offs but try and combine the data (if using several programs) in a reasonable way to prioritize or rank variants based on the probability of the mutation being damaging. That way you don't miss something obvious to you, but perhaps not obvious to the programs being employed. Some of the programs report the probability of being harmless while others report the probability of being damaging while still others report p-values of significance. The obvious cut-off for p-values is of course 0.05 or 0.1 depending on what you want to allow for a false-discovery rate. For probabilities of being damaging it is far less clear, which is why I advocate using a ranking approach instead of hard filtering with a cut-off.

ADD COMMENTlink written 8.6 years ago by DG7.2k
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