Drug Response; Therapeutic management

Guidance for selecting a drug therapy and/or dose

Individuals needing preemptive or reactive genotyping for pharmacogenomic purposes.

Is research allowed on the sample after clinical testing is complete? Help
Research testing is only performed under IRB approved protocol with an opt-out policy in place.

Genomic DNA is extracted from whole blood or saliva. Genotype Assay (Tier 1): Genotyping is performed using a PCR-based 5'-nuclease assay. Fluorescently labeled detection probes anneal to the target DNA. PCR is used to amplify the section of DNA that contains the variant. If the detection probe is an exact … Genomic DNA is extracted from whole blood or saliva. Genotype Assay (Tier 1): Genotyping is performed using a PCR-based 5'-nuclease assay. Fluorescently labeled detection probes anneal to the target DNA. PCR is used to amplify the section of DNA that contains the variant. If the detection probe is an exact match to the target DNA, the 5'-nuclease polymerase degrades the probe, the reporter dye is released from the effects of the quencher dye, and a fluorescent signal is detected. Genotypes are assigned based on the allele-specific fluorescent signals that are detected.(User Guide: TaqMan SNP Genotyping Assay, Applied Biosystems, Revision A.0 January 2014) Copy Number Assay (Tier 1): This assay utilizes a duplex real-time PCR, which includes 1 copy number probe and a reference assay per reaction. Each copy number probe detects the genomic sequence of interest and the reference assay detects a sequence that is known to be present in 2 copies in a diploid genome. Relative quantitation is used to determine the relative copy number of the target of interest in a genomic DNA (gDNA) sample normalized to 10 ng/mcL for each probe. Each probe is normalized to the known copy number of the reference sequence, and compared to a calibrator sample with known copies of the target sequence included with each run.(Package insert: Taqman Copy Number Assays Revision D, Applied Biosystems, Carlsbad, CA) Sequencing Assays (Tier 2): The CYP2D6 allele of interest is amplified by PCR. The PCR product is then purified and sequenced in both directions using fluorescent dye-terminator chemistry. Sequencing products are separated on an automated sequencer and trace files analyzed for variations in the exons and intron/exon boundaries of all 9 exons using mutation detection software and visual inspection. (Unpublished Mayo method) View more

Other

Positive results are confirmed when appropriate.

Tests performed
Entire test performed in-house

Accuracy and analytical sensitivity for targeted simple variant(s) (SNVs and INDELs): (>99%). Accuracy and specificity for del/dup detection: (>99%).

Rare variants may be present that could lead to false-negative or false-positive results. If results obtained do not match the clinical findings (phenotype), additional testing should be considered. Samples may contain donor DNA if obtained from patients who received non-leukoreduced blood transfusions or allogeneic hematopoietic stem cell transplantation. Results from … Rare variants may be present that could lead to false-negative or false-positive results. If results obtained do not match the clinical findings (phenotype), additional testing should be considered. Samples may contain donor DNA if obtained from patients who received non-leukoreduced blood transfusions or allogeneic hematopoietic stem cell transplantation. Results from samples obtained under these circumstances may not accurately reflect the recipient's genotype. For individuals who have received blood transfusions, the genotype usually reverts to that of the recipient within 6 weeks. For individuals who have received allogeneic hematopoietic stem cell transplantation, a pretransplant DNA specimen is recommended for testing. CYP2D6 genetic test results in patients who have undergone liver transplantation may not accurately reflect the patient's CYP2D6 status. This method may not detect all CYP2D6 variants that result in altered CYP2D6 activity. Therefore, absence of a detectable variant does not rule out the possibility that a patient has altered CYP2D6 metabolism due to other CYP2D6 variants that cannot be detected with this method. Furthermore, when 2 or more variants are identified, the cis-/trans- status (whether the variants are on the same or opposite chromosomes) is not always known. A complicating factor in correlating CYP2D6 genotype with phenotype is that many drugs or their metabolites are inhibitors of CYP2D6 catalytic activity. Selective-serotonin reuptake inhibitors (SSRIs), as well as some tricyclic antidepressants (TCAs) and other drugs, may reduce CYP2D6 catalytic activity. Patients in all metabolizer categories, except poor metabolizer, may have CYP2D6 enzyme activity inhibited by a variety of medications or their metabolites. Consequently, an individual may require a lower medication dose than predicted by genotyping alone. It is important to interpret the results of testing in the context of other coadministered drugs. CYP2D6 alleles with decreased function may metabolize different drugs at different rates, ranging from normal to poor, but the literature on this is incomplete at this time. This test is not designed to provide specific dosing or drug selection recommendations and is to be used as an aid to clinical decision making only. Drug-label guidance should be used when dosing patients with medications regardless of the predicted phenotype. View more

Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Formal PT program

PT Provider: Help
American College of Medical Genetics / College of American Pathologists, ACMG/CAP

Software used to interpret novel variations Help
Variants may be analyzed using any combination of the following: Alamut, REVEL, Polyphen-2, SIFT, AGVGD, MutationTaster, SpliceSiteFinder-like, MaxEntScan, NNSPLICE, GeneSplicer, SpliceAI, gene-specific online databases, ISCA, UCSC Genome Browser

Laboratory's policy on reporting novel variations Help
All novel alterations and copy number variants are evaluated for potential pathogenicity and included in the written report, accordingly.