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Test ID LBOR0230  Pharmacogenetics Panel (14-Gene)

Additional Codes

AKA

Capecitabine, Fluorouracil, Azathioprine, Mercaptopurine, Thioguanine, Clopidogrel, Pitavastatin, Pravastatin, Rosuvastatin, Dexlansoprazole, Lansoprazole, Omeprazole, Pantoprazole, Efavirenz, Voriconazole, , Abacavir, Celecoxib, Flurbiprofen, Ibuprofen, Meloxicam, Piroxicam, Codeine, Tramadol, Amitriptyline, Clomipramine, Doxepin, Imipramine, Sertraline, Trimipramine, Atomoxetine, Desipramine, Nortriptyline, Paroxetine, Tacrolimus, Warfarin, Ondansetron, Simvastatin, Fosphenytoin, Phenytoin, Escitalopram, Citalopram, Fluvoxamine, Venlafaxine, Voritoxetine,  Fluvastatin,  Lovastatin, Atorvastatin, Clobazam, Siponimod, Valbenazine, Tetrabenazine, Deutetrabenazine, Pitolisant, Eliglustat, Pimozide, Iloperiodone, Brexpiprazole, Metoclopramide, Aripiprazole, ABCG2, CYP2B6, CYP2C Cluster, CYP2C9, CYP2C19, CYP2D6, CYP3A5, CYP4F2, DPYD, HLA-B*5701, NUDT15, SLCO1B1, TPMT, , VKORC1, PharmGx, Pharmacogenetic, Pharmacogenomics, PGx

Specimen Type/Requirements

Whole blood in Lavender top (EDTA) tube

 

Samples will not be accepted for patients that have undergone an allogenic transplant (e.g., bone marrow or peripheral stem cell from a donor) or have undergone a liver transplant.

 

Chemotherapy patients:  DNA quality may be affected if patient has received chemotherapy within the last 120 days.  Clients will be contacted to provide additional specimen if DNA quality is insufficient.

 

All specimens should be sent in the original container and should not be aliquoted to another tube. In addition, the specimen submitted should ONLY be used for this testing and should not be shared with any other testing that would also utilize this specimen type.

 

Testing is not affected by hemolysis or lipemia of whole blood samples.  

Specimen Volume

Specimen Volume

Specimen Type

Preferred Volume

Minimum Volume

 Whole Blood, Lavender top (EDTA) tube

 2.0 - 4.0 mL  

1.0 mL

 

Stability/Transport

Stability/Transport

 Room Temperature  

 72 hours  

 

 Refrigerated  

 7 days  

 Preferred for transport  

 Frozen  

 Not Acceptable   

 

Performing Lab

Sanford Medical Genetics Laboratory, Sioux Falls

Report Available

7 -10 days

The report includes a comprehensive medication report based on the genotypes detected.

Performed Test Frequency

Monday through Friday

Methodology

Targeted next-generation sequencing (tNGS) is performed for the genes listed above. Data is processed and analyzed using the Sanford GeneART pipeline. When CYP2D6 is reported, copy number variants are assessed by droplet digital PCR (ddPCR) using CYP2D6-specific probes for intron 2 and exon 9. When the copy number call is one and two at the sites tested, due to the detection of a CYP2D6-hybrid gene, comprehensive Sanger sequencing is used to resolve discrepancies identified when correlating the genotype to the final copy number one call. Sequences are aligned to the GRCh37/hg19 reference genome. Annotation and interpretation of results are performed using Sanford's GeneART software.

CPT

81418

Additional Information

Useful For

  • Identifying genetic changes known to have an effect on drug metabolism.
  • Interrogating the cause of personal or family history of an adverse drug reaction or therapeutic failure for a large group of drugs and thereby guide drug and dose selection.

 

Pharmacogenetics (PGx) is the study of these gene variants related to a body’s response to and interaction with many common prescription and over-the-counter medications. These gene variants are associated with a predicted drug response or drug disposition which may predispose a patient to risk of drug-related toxicity or lack of therapeutic benefit.

 

The following 14 genes are included in this panel:

 

Gene

Alleles Detected

ABCG2 (NM_004827.3)

c.421C (p.GLN141)

CYP2B6

*5, *6, *7, *18, *22

CYP2C cluster

g.96405502G

CYP2C19

*2, *3, *4, *5, *6, *7, *8, *9, *10, *16, *17, *22, *24, *25, *26, *35

CYP2C9

*2, *3, *4, *5, *6, *8, *11, *12, *13, *15, *16

CYP2D6

*2, *3, *4, *5, *6, *7, *8, *9, *10, *12, *14, *15, *17, *21, *29, *39, *41, *42, *49, *56, *59, *114, allele duplication

CYP3A5

*3, *6, *7

CYP4F2

*3

DPYD (NM_000110.4)

c.299_302del

c.557A>G (p.Y186C)

c.703C>T (p.R235W)

c.1129-5923C>G, c.1236G>A

c.1156G>T (p.E386*)

c.1679T>G (p.I560S)

c.1898del (p.P633Qfs)

c.1905+1G>A

c.2846A>T (p.D949V)

c.2983G>T (p.V995F)

HLA-B*57:01 screen

positive

NUDT15

*2, *3, *4, *5, *6, *7, *8, *9

SLCO1B1

*5, *14, *15, *37

TPMT

*2, *3A, *3B, *3C, *4, *11, *14, *15, *23, *29, *41

VKORC1 (NM_024006.5)

c.-1639G>A

 

Limitations

This analysis does not detect all variants with known impact on enzyme expression and activities. Non-genetic factors, variations in the other genes involving drug metabolism, or drug-drug interactions are not measured by this assay.  The interpretation of nucleotide changes is based on our current understanding of each gene. This interpretation may change over time as more information about a gene becomes available.

The minimum depth of coverage is 16 reads. If the minimum depth of coverage is not met for alleles classified as Tier 1 and Tier 2 by the Association for Molecular Pathology and for some alleles with increased prevalence, based on population frequencies, additional testing may be performed to ensure accurate target assessment and reporting.

Phasing for alleles is not performed. Thus, diplotype reporting is based on which is predicted to be most prevalent in the general population per the clinical pharmacogenomics testing and reporting guidelines from the American College of Medical Genetics and Genomics (PMID: 35177334). Usually, ambiguities between possible diplotypes do not change the final phenotype. When it is known that the phenotype may change, due the possible reportable diplotypes, a comment will be included in the report describing the alternate diplotype considered and the corresponding phenotype.

As with all genetic testing, patients with a history of chronic lymphocytic leukemia (CLL) or active leukemia are at increased risk for sequencing errors due to misattribution of somatic variants to constitutional genetic results due to a high leukemic cell burden in the blood sample. Genetic results can also be confounded if an individual had certain types of blood transfusions within 30 days of sample collection, has ever had a liver transplant, or had an allogeneic (from another individual) bone marrow or stem cell transplant. This test is not meant to diagnose or treat any disease. All clinical information should be interpreted and used by an experienced clinician or pharmacist along with genetic information to decide a specific drug dosing.