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Test Code WESPP Whole Exome Sequencing Plus Pharmacogenomics


Advisory Information


This test is only available for trios (proband, biological mother, and biological father).

 

Clients must provide all 3 samples for this test to be performed.

 

If you have different whole exome sequencing needs, contact Customer Service at 800-533-1710. To order pharmacogenomics-focused testing only, see PGXFP / Focused Pharmacogenomics Panel.



Additional Testing Requirements


 



Shipping Instructions


Specimen preferred to arrive within 96 hours of collection.



Necessary Information


1. Complete the Patient Information and Informed Consent forms within the Whole Exome Sequencing: Ordering Checklist, Patient Information, and Informed Consent forms, available in Special Instructions.

2. In addition, submit relevant clinic notes and a pedigree. Send all paperwork with the specimens to the laboratory. The paperwork may also be faxed directly to the whole exome sequencing genetic counselors at 507-284-0670.



Specimen Required


Samples from both biological parents are required. Order WESPP on the patient and both parents.

 

Specimen Type: Whole blood

Container/Tube:

Preferred: Lavender top (EDTA) or yellow top (ACD)

Acceptable: Any anticoagulant

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send specimen in original tube.

3. Label the parental samples with full name and date of birth. Do not label the parental samples with the child's name.

Additional Information: To ensure minimum volume and concentration of DNA is met, the preferred volume of blood must be submitted. Testing may be canceled if DNA requirements are inadequate.


Useful For

Identifying a molecular diagnosis in patients with a known or suspected genetic disorder, which can allow for:

-Better understanding of the natural history/prognosis

-Targeted management (anticipatory guidance, management changes, specific therapies)

-Predictive testing of at-risk family members

-Testing and exclusion of disease in siblings or other relatives

-Recurrence risk assessment

-Reproductive decision-making

 

Serving as a second-tier test for patients in whom previous genetic testing for specific syndromes was negative

 

Providing a potentially cost-effective alternative to establishing a molecular diagnosis compared to multiple independent molecular assays

 

Identifying patients who may be at risk for altered metabolism of drugs modified or metabolized by the genes included in the Pharmacogenomic Associations Table in Special Instructions

Additional Tests

Test ID Reporting Name Available Separately Always Performed
PWEST PGx Panel, Whole Exome Sequencing No Yes

Testing Algorithm

Whole blood samples must be collected from the patient's biological parents and are required for the analysis of the patient's results. Analysis of these samples is included in the list price for the patient's test and additional charges will not be applied to the parental samples.

 

In addition to analysis of variants associated with the patient's reported phenotype, analysis for reportable secondary findings in genes included in the American College of Medical Genetics and Genomics' (ACMG) recommendations will be included.(1) Patients may opt-out of receiving these test results.

 

Complete the Patient Information and Informed Consent forms and send to the laboratory along with the specimen. The forms are located within the Whole Exome Sequencing Plus Pharmacogenomics: Ordering Checklist, Patient Information, and Informed Consent forms in Special Instructions. The completed forms may also be faxed directly to the whole exome sequencing genetic counselors at 507-284-0670.

 

When this test is ordered, analysis for a select number of clinically significant pharmacogenomic variants will always be performed on the proband sample and reported separately under PWEST / Pharmacogenomic Panel, Whole Exome Sequencing (see Pharmacogenomic Variant Table in Special Instructions). This analysis will always include CYP2D6 genotype testing via Luminex, and may include additional reflex assays at an additional charge, see CYP2D6 Comprehensive Cascade Testing Algorithm in Special Instructions.

 

See Whole Exome Sequencing Plus Pharmacogenomics (WESPP): Questions and Answers for Providers in Special Instructions for additional information.

 

Sanger sequencing may be performed for verification of results.

Method Name

WESPP: Next-Generation Sequencing followed by Polymerase Chain Reaction (PCR) and Sanger Sequencing

CYP2D6 pharmacogenomic testing on the proband: Polymerase Chain Reaction (PCR) with Allele-Specific Primer Extension (ASPE)

Reporting Name

Whole Exome Plus Pharmacogenomics

Specimen Type

Varies

Specimen Minimum Volume

1 mL

Specimen Stability Information

Specimen Type Temperature Time
Varies Ambient (preferred)
  Frozen 
  Refrigerated 

Reject Due To

No specimen should be rejected.

Reference Values

An interpretive report will be provided that includes variants likely causative of the patient’s reported clinical features, variants possibly relevant to the patient’s reported clinical features, variants in genes of uncertain significance, and medically actionable secondary findings (unless the patient opts out).

 

For pharmacogenomic results, an interpretative report will be provided that gives a phenotype based upon the detected genotype and an interpretation for predicted drug response.

Day(s) and Time(s) Performed

Performed weekly, Varies

Analytic Time

12 weeks

Performing Laboratory

Mayo Medical Laboratories in Rochester

Test Classification

This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the U.S. Food and Drug Administration.

CPT Code Information

Codes Always Applied to Proband Sample:

81415-Exome (unexplained constitutional or heritable disorder/syndrome); sequence analysis

81416 x 2-Exome (eg, unexplained constitutional or heritable disorder or syndrome); sequence analysis, each comparator exome (eg, parents, siblings)

81226-CYP2D6 (cytochrome P450, family 2, subfamily D, polypeptide 6) (eg, drug metabolism), gene analysis, common variants (e.g., *2, *3, *4, *5, *6, *9, *10, *17, *19, *29, *35, *41, *1XN, *2XN, *4XN)

 

Codes only applied if additional testing is needed to clarify CYP2D6 results:

81479-Unlisted Molecular Pathology procedure

LOINC Code Information

Test ID Test Order Name Order LOINC Value
WESPP Whole Exome Plus Pharmacogenomics In Process

 

Result ID Test Result Name Result LOINC Value
113159 Interpretation In Process