IMPACT 505 gene panel coding

[whit...@mskcc.org]

Hello,

 

I noticed the way the IMPACT panels are coded in cbioportal.org differ from the way they are coded in cbioportal.mskcc.org. The example below is comparing IMPACT505 panel (pulled from each using the API):

 

> setdiff(msk_505$hugoGeneSymbol, pub_505$hugoGeneSymbol)

[1] "H3F3A"     "H3F3B"     "H3F3C"     "HIST1H1C"  "HIST1H2BD"

[6] "HIST1H3A"  "HIST1H3B"  "HIST1H3C"  "HIST1H3D"  "HIST1H3E"

[11] "HIST1H3F"  "HIST1H3G"  "HIST1H3H"  "HIST1H3I"  "HIST1H3J"

[16] "HIST2H3C"  "HIST2H3D"  "HIST3H3" 

 

 

> setdiff(pub_505$hugoGeneSymbol, msk_505$hugoGeneSymbol)

[1] "H1-2"  "H2BC5" "H3-3A" "H3-3B" "H3-4"  "H3-5"  "H3C1"  "H3C10"

[9] "H3C11" "H3C12" "H3C13" "H3C14" "H3C2"  "H3C3"  "H3C4"  "H3C6"

[17] "H3C7"  "H3C8"

 

Is this intentional?

 

Thanks!

Karissa

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[whit...@mskcc.org]

Related to this, it also appears the alias resolving is different between public/MSK dbs as well:

 

Public (https://www.cbioportal.org/)

get_alias("H3-4")

[1] "H3.4"    "H3/g"    "H3FT"    "H3t"     "HIST3H3"

 

MSK (https://cbioportal.mskcc.org/)

get_alias("H3-4")

Error – no aliases returned

 

> get_alias("HIST3H3")

[1] "H3.4" "H3/g" "H3FT" "H3t" : H3-4 Does not come up as an alias option.

 

Thanks!

Karissa

[debr...@mskcc.org]

Hi Karissa,

 

Thanks for reaching out! That’s odd indeed

 

I’m CC’ing the curation team on this to see if know why these differ

 

Thanks!

Ino

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