[ensembl-dev] PolyPhen2 prediction discrepancies between VEP 88 and dbNSFP v3.0

[Crone, Bradley]

Hello,


I'm working with PolyPhen2 scores and predictions in VEP 88 and comparing these back to scores reported in dbNSFP v3.0.

I find a large number of discrepancies between HumDiv scores from VEP and dbNSFP. I've looked at a small subset of 10 mismatches.

Directly comparing scores/predictions with PolyPhen2's website, all PolyPhen2 scores match with a dbNSFP score, and not a VEP score:


CHROM    POS    REF    ALT    GENE    VEP-FEATURE    VEP-IMPACT    VEP_CSQ    VEP_POLYPHEN_SCORE    VEP_POLYPHEN_PRED    DBNSFP_POLYPHEN2_HDIV_SCORE    DBNSFP_POLYPHEN2_HDIV_PRED    pph2_prob      pph2_FPR      pph2_TPR
2    73679572    C    A    ALMS1    NM_015120.4    MODERATE    missense_variant    0.952    P    0.987,0.972,0.026    D,D,B    0.026         0.188         0.949
1    216011417    A    T    USH2A    NM_206933.2    MODERATE    missense_variant    0.155    B    0.933    P    0.933        0.0573         0.804
12    48398104    T    C    COL2A1    NM_001844.4    HIGH    start_lost    0    U    0.219,0.14    B    0.14         0.136         0.923
1    103427757    C    G    COL11A1    NM_080629.2    MODERATE    missense_variant    0    U    0.999    D    0.999       0.00574         0.136
12    48377197    G    T    COL2A1    NM_001844.4    MODERATE    missense_variant    0.784    P    0.001,0.0    B    0             1             1
6    70981396    C    A    COL9A1    NM_001851.4    MODERATE    missense_variant    0.555    P    0.31,0.0    B    0.31         0.112         0.904
10    73377145    G    A    CDH23    NM_001171930.1    MODERATE    missense_variant    1    P    1.0,1.0,0.998    D    1       0.00026       0.00018
1    216496954    T    C    USH2A    NM_206933.2    MODERATE    missense_variant    1    P    0.971,0.413    D,B    0.413         0.103         0.893
17    18064707    C    A    MYO15A    NM_016239.3    MODERATE    missense_variant    0    U    0.941,0.761,0.165,0.523,0.981,0.953    P,P,B,P,D,P    0.523        0.0959         0.882
1    103462662    C    T    COL11A1    NM_001190709.1    MODERATE    missense_variant    1    P    1.0    D    1       0.00026       0.00018


Any idea for this discrepancy?


Thanks,

Brad


________________________________
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20170612/32a6e229/attachment.html>