PharmCAT Genes & Drugs

Genes

The following tables list genes used by PharmCAT to find drug recommendation, along with the sources that use the gene.

Genes PharmCAT will attempt to match

The Named Allele Matcher will search the given sample file for locations associated with these genes and attempt to match them to known allele definitions.

Gene CPIC PharmGKB-DPWG
ABCG2 :heavy_check_mark: :heavy_check_mark:
CACNA1S :heavy_check_mark:  
CFTR :heavy_check_mark:  
CYP2B6 :heavy_check_mark: :heavy_check_mark:
CYP2C19 :heavy_check_mark: :heavy_check_mark:
CYP2C9 :heavy_check_mark: :heavy_check_mark:
CYP3A4   :heavy_check_mark:
CYP3A5 :heavy_check_mark: :heavy_check_mark:
CYP4F2 :heavy_check_mark:  
DPYD :heavy_check_mark: :heavy_check_mark:
G6PD :heavy_check_mark:  
IFNL3 :heavy_check_mark:  
NUDT15 :heavy_check_mark: :heavy_check_mark:
RYR1 :heavy_check_mark:  
SLCO1B1 :heavy_check_mark: :heavy_check_mark:
TPMT :heavy_check_mark: :heavy_check_mark:
UGT1A1 :heavy_check_mark: :heavy_check_mark:
VKORC1 :heavy_check_mark: :heavy_check_mark:

Genes handled by outside callers

These genes will not get allele matches from PharmCAT*. However, you can use an outside caller like Stargazer or StellarPGx to get CYP2D6 diplotype calls, or Optitype to get HLA calls, and then supply that to PharmCAT for use in matching recommendation data.

See Outside Call Format for formatting details and Calling-CYP2D6.md or Calling-HLA.md for how to obtain CYP2D6 or HLA calls, respectively, using sequencing data.

Gene CPIC PharmGKB-DPWG
CYP2D6 :heavy_check_mark: :heavy_check_mark:
F5   :heavy_check_mark:
HLA-A :heavy_check_mark: :heavy_check_mark:
HLA-B :heavy_check_mark: :heavy_check_mark:
MT-RNR1 :heavy_check_mark:  

* Except for CYP2D6 if the requisite research mode is enabled.

Drugs

The following table lists drugs for which PharmCAT has recommendations for, along with their sources.

Drug CPIC PharmGKB-DPWG
abacavir :heavy_check_mark: :heavy_check_mark:
acenocoumarol   :heavy_check_mark:
allopurinol :heavy_check_mark: :heavy_check_mark:
amikacin :heavy_check_mark:  
amitriptyline :heavy_check_mark: :heavy_check_mark:
aripiprazole   :heavy_check_mark:
atazanavir :heavy_check_mark:  
atomoxetine :heavy_check_mark: :heavy_check_mark:
atorvastatin :heavy_check_mark: :heavy_check_mark:
azathioprine :heavy_check_mark: :heavy_check_mark:
brexpiprazole   :heavy_check_mark:
capecitabine :heavy_check_mark: :heavy_check_mark:
carbamazepine :heavy_check_mark: :heavy_check_mark:
celecoxib :heavy_check_mark:  
citalopram :heavy_check_mark: :heavy_check_mark:
clomipramine :heavy_check_mark: :heavy_check_mark:
clopidogrel :heavy_check_mark: :heavy_check_mark:
codeine :heavy_check_mark: :heavy_check_mark:
dapsone :heavy_check_mark:  
desflurane :heavy_check_mark:  
desipramine :heavy_check_mark:  
dexlansoprazole :heavy_check_mark:  
doxepin :heavy_check_mark: :heavy_check_mark:
efavirenz :heavy_check_mark: :heavy_check_mark:
eliglustat   :heavy_check_mark:
enflurane :heavy_check_mark:  
escitalopram :heavy_check_mark: :heavy_check_mark:
flecainide   :heavy_check_mark:
flucloxacillin   :heavy_check_mark:
flucytosine   :heavy_check_mark:
fluorouracil :heavy_check_mark: :heavy_check_mark:
flurbiprofen :heavy_check_mark:  
fluvastatin :heavy_check_mark:  
fluvoxamine :heavy_check_mark:  
fosphenytoin :heavy_check_mark:  
gentamicin :heavy_check_mark:  
haloperidol   :heavy_check_mark:
halothane :heavy_check_mark:  
hormonal contraceptives for systemic use   :heavy_check_mark:
hydrocodone :heavy_check_mark:  
ibuprofen :heavy_check_mark:  
imipramine :heavy_check_mark: :heavy_check_mark:
irinotecan   :heavy_check_mark:
isoflurane :heavy_check_mark:  
ivacaftor :heavy_check_mark:  
kanamycin :heavy_check_mark:  
lamotrigine   :heavy_check_mark:
lansoprazole :heavy_check_mark: :heavy_check_mark:
lornoxicam :heavy_check_mark:  
lovastatin :heavy_check_mark:  
meloxicam :heavy_check_mark:  
mercaptopurine :heavy_check_mark: :heavy_check_mark:
methoxyflurane :heavy_check_mark:  
methylene blue :heavy_check_mark:  
metoprolol   :heavy_check_mark:
nitrofurantoin :heavy_check_mark:  
nortriptyline :heavy_check_mark: :heavy_check_mark:
omeprazole :heavy_check_mark: :heavy_check_mark:
ondansetron :heavy_check_mark:  
oxcarbazepine :heavy_check_mark: :heavy_check_mark:
pantoprazole :heavy_check_mark: :heavy_check_mark:
paromomycin :heavy_check_mark:  
paroxetine :heavy_check_mark: :heavy_check_mark:
peginterferon alfa-2a :heavy_check_mark:  
peginterferon alfa-2b :heavy_check_mark:  
pegloticase :heavy_check_mark:  
phenprocoumon   :heavy_check_mark:
phenytoin :heavy_check_mark: :heavy_check_mark:
pimozide   :heavy_check_mark:
piroxicam :heavy_check_mark:  
pitavastatin :heavy_check_mark:  
plazomicin :heavy_check_mark:  
pravastatin :heavy_check_mark:  
primaquine :heavy_check_mark:  
propafenone   :heavy_check_mark:
quetiapine   :heavy_check_mark:
rasburicase :heavy_check_mark:  
ribavirin :heavy_check_mark:  
risperidone   :heavy_check_mark:
rosuvastatin :heavy_check_mark:  
sertraline :heavy_check_mark: :heavy_check_mark:
sevoflurane :heavy_check_mark:  
simvastatin :heavy_check_mark: :heavy_check_mark:
siponimod   :heavy_check_mark:
streptomycin :heavy_check_mark:  
succinylcholine :heavy_check_mark:  
tacrolimus :heavy_check_mark: :heavy_check_mark:
tafenoquine :heavy_check_mark:  
tamoxifen :heavy_check_mark: :heavy_check_mark:
tegafur   :heavy_check_mark:
tenoxicam :heavy_check_mark:  
thioguanine :heavy_check_mark: :heavy_check_mark:
tobramycin :heavy_check_mark:  
toluidine blue :heavy_check_mark:  
tramadol :heavy_check_mark: :heavy_check_mark:
trimipramine :heavy_check_mark:  
tropisetron :heavy_check_mark:  
venlafaxine :heavy_check_mark: :heavy_check_mark:
voriconazole :heavy_check_mark: :heavy_check_mark:
vortioxetine :heavy_check_mark:  
warfarin :heavy_check_mark: :heavy_check_mark:
zuclopenthixol   :heavy_check_mark:
PharmCAT is managed at Stanford University & University of Pennsylvania (NHGRI U24HG010862).