NMD Escape NMDetective score question

[Carly van der Heide]

Hello,

I am using the NMDetective-A and B subtracks within the new NMD Escape Track. It looks like the scoring mechanism for these subtracks is different than what is described in the Linderboom et al. 2016 paper. In the paper, the NMDetective score has a range from zero to one, but in the subtracks the score is described as "Scores range from approximately −1 to +1. Positive values indicate that a PTC at that position is predicted to trigger NMD (the mRNA is degraded). Negative values indicate that the PTC is predicted to escape NMD (the truncated mRNA may be translated into an aberrant protein). Values near zero indicate intermediate or uncertain NMD efficiency."

I am specifically looking at nonsense variants in the SCN2A gene, and I don't see any negative score values at all in any of the data I downloaded. 

Is the score range truly -1 to +1 or is this a mistake in the description? 

[Gerardo Perez]

Hello,

Thank you for writing in about the NMDetective-A and B score range.

You found a real discrepancy, not an error on your end. The score range for NMDetective-A and B really is 0 to 1, matching the Lindeboom et al. 2016 paper, which is why you were not seeing any negative values in SCN2A. The "approximately -1 to +1" text on the description page didn't match the paper. We have updated the description pages:

https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=nmdDetectiveA
https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=nmdDetectiveB

Thank you again for bringing this to our attention.

I hope this helps. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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