What does mapping_rank mean in grch37/civic/civic.biomarkers.tsv ？

[sunsong95]

Thanks for your research！

I'm very interested in how pcgr integrates the scattered annotation resources into the final results. I observed that the files in the civic directory of grch37 data bundle are created by files in https://civicdb.org/releases, but I don't quite understand how to get the column named "mapping_rank" which in the civic.biomarkers.tsv, and what does it mean?

In addition, column named "alterationtype" is modified based on the civic source infomation? For example, I noticed "missense variant,transcript_ Fusion" was changed to "TRANSLOCATION_FUSION_MUT"

Thanks!

[sigven]

Hi @sunsong95,

Very good observation! The mapping_rank variable is created during consolidation of CIViC data, it's essentially a numeric indicator for how precise a given biomarker is reported in the literature (and accordingly by CIViC). I believe this matter is frequently ignored by many, but it's an important aspect for variant interpretation, and for how a given variant in a given tumor can be mapped towards biomarkers. Essentially, a mapping_rank of 1 means that the biomarker (variant) was mapped exactly to the genome (with ref and alt alleles, en example being BRAF V600E), a mapping_rankof 2 means that the biomarker was mapped to a codon (e.g. BRAF V600), a mapping_rank of 3 is for the exon (e.g. EGFR exon 19), 4 is at the gene level (mutations), and 5 is also at the gene level (non-mutations, i.e. expression biomarkers etc).

Yes, the alteration_type is modified internally in PCGR, basically for convenience and slight simplificiation, but essentially using the CIViC data to set this variable.

Hopefully this may clarify somewhat.

kind regards, Sigve

[sunsong95]

Hi @sigven

Thank you for your reply.

I also want to know if I can update the annotation resources files (e.g. CIViC or cancerhotspots) by myself so that the clinical annotation notes are always up-to-date. If I only update the annotation file in the corresponding folder (e.g. ~/grch37/civic/), can I get the correct result/report?

For example, I noticed that the data package of civic (https://civicdb.org/releases) is updated almost every month. So if I can update the resource pack in time, it would be great.

Thanks!

[sigven]

Hi @sunsong95,

I am afraid it will not work just yet, although I surely realize that this will be the optimal situation, to ensure that all databases are up-to-date. PCGR relies on a fairly large number of resources, and I have established multiple update scripts for these, but as now not yet streamlined so that users can update whenever they like. I hope to support such a strategy in the future, meanwhile I will try to update the bundle more frequently than what i have done recently. Sorry for this slight inconvenience, but it requires a fair amount of work to ensure that it works without errors for the users.

kind regards, Sigve