ParaPheo Gene Analysis Deletion and Duplication


Sunquest Code:PPHEOG  
Epic Code:LAB6985Epic Name:ParaPheo Gene Analysis Del Dup
Synonyms:Familial; Hereditary; Paraganglioma; Genetic Testing; Pheochromcytoma, Neuroendocrine Neoplasm, Tumor of Adrenal Gland
Methodology:Next generation sequencing
CPT Code:81437, 81438, G0452
Turnaround Time:Performed Mon-Fri; results are reported in 28-42 days.
Special Instructions:Gene(s) or the name of the panel should be indicated in the comment section of EPIC order.
A signed informed consent in the patient's medical record is required; the consent should not be sent to the laboratory. The link to the Genetic Testing Consent Form is provided as a convenience for the providers and genetic counselors.
Bone Marrow Transplant Patients: If a patient is the recipient of an allogeneic transplant, this test must be done on a pre-transplant sample. Contact the Molecular Diagnostics lab to see if a pre-transplant sample is available.
Associated Links:

NGS Genetic Testing Consent Form



Collection Instructions

Specimen:Blood
Optimal Volume:10 mL
Minimum\Peds Volume:3 mL
Container:Yellow (ACD, Solution A) tube available from laboratory (Purple (EDTA))
Causes for Rejection:Frozen or clotted specimen, incorrect anticoagulant specimen more than 5 days old. Sample collected from bone marrow transplant recipient. Samples tested in hematology using automated instrumentation not accepted.


Processing and Shipping

Specimen Processing:Whole blood. Do not process. Store at room temperature.
Shipping Instructions:Ship at room temperature. Do not freeze.
Test Performed at or Referral Lab Molecular Diagnostics  (UMMC-East Bank)


Interpretive

Reference Range:By report
Use:The Paraganglioma cancer panel analyzes genes known to be associated with an increased lifetime risk of paraganglioma and other cancers. For many of the genes, published medical guidelines exist for detection, prevention risk reduction and/or treatment. This assay utilizes a next generation sequencing (NGS) platform. This platform allows simultaneous sequencing of a large number of genes using a single assay. Genomic DNA is extracted from the sample, and the sequencing libraries are prepared according to standard Illumina protocols using the TruSight One Sequencing Panel for enrichment of targeted genes. The enriched DNA libraries are sequenced on an Ilumina HiSeq 2500 instrument. Raw sequencing reads are mapped to the reference genome using BWA. Raw alignment files are realigned in the neighborhood of indels, and recalibrated for base quality accuracy using the Genome Analysis Tool Kit (GATK) Point mutation and indel calls in exons and adjoining intronic regions are made using the GATK Unified Genotyper. Variants are interpreted according to guidance issued by the American College of Medical Genetics.


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