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Multiplex Solid Tumor Panel

Overview: The Pathology Translational Research Laboratory has developed a panel of multiplexed assays to screen for 649 mutations across 53 genes. The panel is designed to facilitate rapid identification of mutations that can be targeted with therapeutics now in clinical development or already FDA-approved.

The panel includes all of the common mutations and many of the rare mutations in these genes, but is not inclusive of all possible genetic alterations in these genes. Therefore, it is possible that a submitted tumor sample will contain one or more mutations that are not included on the panel. The sensitivity of the assays in the panel averages approximately 10% mutant allele. A list of the specific mutations covered by the panel is available upon request.

AKT1FESKDRPDGFRA
AKT2FGFR1KITPIK3CA
AKT3FGFR2KRASPIK3R1
ALKFGFR3MAP2K1PIK3R4
BRAFFRGR4MAP2K2PIK3R5
CDK4FOXL2MAP2K7PKHD1
CSF1RGNA11METPRKCB1
CTNNB1GNAQMYCRAF1
EGFRGNASNEK9RET
ERBB2HRASNRASSMO
ERCC6IDH1NTRK1SOS1
FBX4IDH2NTRK2STAT1
FBXW7IGF1RNTRK3TEC
   TP53*
*TP53 – only approximately 30% of potential mutations covered.

Methods: DNA is extracted and purified from material containing a minimum of 50% tumor cellularity, and mutations in the genes listed above are screened using a Sequenom MassARRAY system. This system involves the following steps: 1) multiplex PCR amplification of gene exons of interest; 2) primer extension reactions using TYPLEX chemistry; and 3) readout of the primer extension products by mass spectrometry (MALDI-TOF MS). All mutations detected by mass spectrometry are confirmed by conventional bi-directional sequencing.

Shipping Address:

Knight Diagnostic Laboratory
2525 SW 3rd Ave.
Ste. 350
Portland, OR 97201
Ph: 503-494-5400

Submission Form

Please fill out the DNA Sample Submission Information Form and email to warricka@ohsu.edu.

Specimen Fixation and Shipping Methods:

SpecimenFixationShipping Method
Bone Marrow CoresFormalin-Fixed is OK. Do not use fixative such as Zenker's, B5, Hollande's.Room Temperature
Bone Marrow ClotFormalin-Fixed is OK. Do not use fixative such as Zenker's, B5, Hollande's.Room Temperature
Bone Marrow AspirateNo heparin tubes.Ship within 24 hours. Please avoid shipping on Friday, if unavoidable please contact lab for instructions prior to shipment.
BloodEDTA or citrate tubes only. No heparin tubes.Room Temperature. Please avoid shipping on Friday, if unavoidable please contact lab for instructions prior to shipment.
Blocks and SlidesFormalin-Fixed is OK. Do not use fixative such as Zenker's, B5, Hollande's.Room Temperature
DNAn/aIce packs or dry ice preferred.
Fresh TissueFlash frozen.Ship on dry ice. Weekday delivery to laboratory only.

CPT codes: Coming soon

For additional information, contact Knight Diagnostic Laboratory Services Center at 503-494-5400.

Links: Back to Knight Diagnostic PTRL, Research Tests Available, GIST Test Descriptions, GIST Background Information