Cancer Gene Mutation Panel [CANPNL]

Cancer Gene Mutation Panel [CANPNL]
WSLH Department: Cytogenetics
WSLH Test Code:840C40
Includes:Test Component: This test is validated to concurrently identify >2,800 genetic variants in 50 targeted genes using multiplex PCR followed by next generation sequencing (see table below). These genetic alterations can be important diagnostic, prognostic, and predictive biologic markers associated with cancer and as a result may provide important individualized information regarding both tumor development and progression, along with prediction to cancer therapies. *** ABL1, AKT1, ALK, APC, ATM, BRAF, CDH1, CDKN2A, CSF1R, CTNNB1, EGFR, ERBB2, ERBB4, EZH2, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, GNA11, GNAQ, GNAS, HNF1A, HRAS, IDH1, ISH2, JAK2, JAK3, KDR, KIT, KRAS, MET, MLH1, MPL, NOTCH1, NPM1, NRAS, PDGFRA, PIK3CA, PTEN, PTPN11, RB1, RET, SMAD4, SMARCB1, SMO, SRC, STK11, TP53, VHL *** Next generation sequencing of amplification products are performed on the Ion Torrent Personal Genome Machine and analyzed with the Torrent Suite Software. Reference DNA sequences used for these genes can be found at hhtp://www.ncbi.nlm.nih.gov/refseq/rsg/. This mutation panel is designed to detect targeted mutations only. Confirmation of these mutations is performed by traditional or real time PCR followed by Sanger sequencing, fluorescent melting curve analysis and/or pyrosequencing.
Methodology:**(CPT Code: 81445)** Next Generation Sequencing
Availability:Once a week.
Turn-around Time:2 weeks.
Recommended Uses:Formalin-fixed, paraffin embedded tissue, whole blood or bone marrow aspirate
Contraindications: 
Specimen Requirements:1 mL Whole blood or Bone Marrow in EDTA (Lavender Top), FFPE: Three slides each containing 5 microns (uM) of FFPE tissue. Second slide should be H&E stained with the tumor circled.
Collection Kit/Container: 
Patient Preparation: 
Collection Instructions: 
Specimen Handling and Transport:Three slides each containing 5 microns (uM) of FFPE tissue should be sent. Second slide should be H&E stained with the tumor circled. Please indicate percent tumor on Intra-Lab Send-Out Form. Blood/Bone Marrow Aspirate - Whole Blood. Do not centrifuge. Many insurers require a prior authorization (PA) for this test. Please check patient coverage and send copy of PA to lab with the test request. Transport at room temperature. Outreach: Transport with a cold pack. Avoid excessive heat.
Unacceptable Conditions: 
Requisition Form:Cytogenetics Lab Neoplasia Diagnosis Form #132
Required Information:Batched runs begin on Monday or first working day of each week. Ordering source must fill out Referral Screening Flow Sheet prior to specimen collection. Contact UWHC Test Referral office at (608)262-6388 prior to collection.
Results include:A written interpretive report is provided by the laboratory detailing all genetic variants detected and genes in the panel. The significance of genetic variants to pathogenicity and therapeutic response will be indicated whenever possible.
Limitations:A "Not Detected" result may be due to either insufficient tissue or tumor present in the sample, tumor heterogeneity, to the presence of inhibitors or to bias or inefficiencies in PCR amplification. The 50 genes covered are not all sequenced in their entirety. Mutations outside the 207 amplicons will not be detected. The limit of detection of this assay is estimated to be 5% at 500X coverage and 10% at 200X coverage and mutations below 100X coverage cannot reliably be detected. This technology cannot detect large insertions, deletions, duplications or genomic copy number variants. Rare or complex polymorphisms may be present that could lead to false negative or positive results. This test cannot differentiate between somatic or germline genetic variants. Additional testing may be necessary to clarify the significance of results if there is a potential for hereditary risk. It is recommended that patients receive genetic consultation where appropriate, to explain the implications of this test result, including probabilistic risk of disease and uncertainties, and the reproductive or medical options it raises. The presence or absence of cancer associated mutations does not guarantee either a positive or negative response to therapy. All test results should be interpreted in the context of patient's clinical presentation.
Additional Tests Recommended: 
Additional Comments:A "Detected" results indicates the presence of a variant. Inadequate specimen collection, processing and storage may invalidate test results. This test should not be used as the only criterion to form a clinical conclusion, instead, results should be correlated with other test results, patient symptoms and clinical presentation. The variants nomenclature used is recommended by the Human Genome Variation Society (http://www.hgvs.org/mutnomen/). The performance characteristics of this test were validated by UWHC Clinical Laboratories. The U.S. Food and Drug Administration (FDA) has not approved or cleared this test; however, FDA approval or clearance is currently not required for clinical use of this test. The UWHC Clinical Laboratories is authorized under Clinical Laboratory Improvement Amendments (CLIA) to perform high-complexity testing.
Additional Tests Performed: 

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