HGNC gene mapping in hg38

When using hg38 cases in Scout we have noticed that some genes aren’t mapped to the gene symbol. Like this:

It seems it is using the hg19 data to do the ID<->symbol mapping, as it is the default of hgnc_genes(), hgnc_gene() and hgnc_id() functions. And in most places where these functions are used, no build version is given.

My naive solution to this would be to, in all places these functions are used, change for example:

hgnc_gene = store.hgnc_gene(xxx)

to

genome_build = case_obj.get('genome_build', '37')
hgnc_gene = store.hgnc_gene(xxx, build=genome_build)

But I’m not confident this is the right solution. Any input appreciated!

[bjhall]

Thanks @northwestwitch for looking at this! I started digging in it last week but was slightly overwhelmed by many places that needed to be fixed, and I didn’t really understand what some of them were doing. And some of them were not in the context of a case (mainly panel stuff), so I wasn’t sure how to treat those either.

In addition to hgnc_gene(), the following functions also take an optional “build” parameter, which as far as I can tell appear to have been left out in a few places throughout the code. I’m not sure if they are relevant, but it’s an observation I made…

hgnc_id()
all_genes()
hgncid_to_gene()
gene_by_alias()
genes_by_alias()

[northwestwitch]

Thanks, I’ll look into these functions as well! It is a bit overwhelming, I agree! The easiest would be to modify in the code the default params from “37” to “38”. The problem is that we can’t since our pipeline is still using build 37. But fixing here and there should work, eventually!