Is there any relationship exists in between scores which represents the functional significance of SNVs like SIFT, CADD, PolyPhan, MetaLR, MetaSVM and copy number variation present in the same sample. Is it possible to represent CNVs with some similar scores. I am also looking for related papers but none has found till now.
Hi Vivek,
to my knowledge, there is no functional prediction score (e.g. SIFT, MutPred, MutationTaster, PolyPhen2,...) for CNVs. Most of the dbNSFP data is only available for SNVs and small InDels (classical VCF format). There are some scores representing the intolerance of a gene for haploinsufficiency or duplication (e.g. ExAC CNV z-score, P-HI : https://doi.org/10.1371/journal.pgen.1001154 ) which are accessible via dbNSFP gene data. Additionally you can annotate your CNVs with common CNVs from DGV or ExAC (which is not quite easy).
Good luck with your research.
Hi Vivek,
One way we addressed the CNV scoring issue in the past, (esp. for non-exonic regions), was to get CADD scores for the entire locus and calculate an average. We validated this approach using the few CNVs actually annotated by CADD in the current database (1000 Genomes), and the correlation was pretty good.
HTH,
Kevin
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