GatorSeq NGS Panel

The entire coding sequences of the following genes are covered by this assay:

Genes tested for copy number alterations: ALK, ATM, ATRX, BAP1, BRAF, BRCA1, BRCA2, CCND1, CCND3, CCNE1, CDK4, CDK6, CDKN2A, CDKN2B, CHEK1, CIC, CTNNB1, EGFR, ERBB2, ERBB3, ESR1, FGF10, FGF14, FGF19, FGF23, FGF3, FGF4, FGF6, FGFR1, FGFR2, FGFR3, FGFR4, FUBP1, HRAS, IDH2, JAK2, KIT, KRAS, MDM2, MDM4, MET, MTAP, MYC, MYCN, NF1, NF2, NRAS, PDGFRA, PDGFRB, PIK3CA, PIK3CB, PTCH1, PTEN, RAF1, RB1, RET, RICTOR, SETD2, SMO, TERT, TFEB, TP53

Acceptable sample type: The samples should be specifically chosen by a pathologist to include at least 5 % tumor cells without significant necrosis or inflammation. The following are the types of samples we can accept:
a. FFPE

• i. For FFPE (formalin fixed, paraffin embedded) specimen: should have an H&E slide with the area of interest selected specifically by the pathologist.

b. Peripheral blood
c. Bone marrow aspirate
d. Buccal cells (for normal control DNA)

Blood, bone marrow aspirate: 3 to 15 mL, collected in EDTA tubes (lavender top). Transport at ambient temperature within UFPathlabs, however, at 2-8°C when coming from outside of Gainesville, FL. Pediatric collection/transport: 1 mL whole blood (lavender, EDTA), or 1 mL bone marrow (lavender, EDTA), at 2-8°C when coming from outside of Gainesville, FL. Unacceptable conditions: serum, frozen whole blood, clotted blood, or severely hemolyzed samples. Stability at ambient temperature: 24 hours; refrigerated: 5 days; frozen: unacceptable.

Formalin fixed, paraffin embedded tissue: acceptable, however, B-4 or B-5 fixed tissue will not be processed (PCR inhibition by mercuric compounds). Transport at 20-25°C.

Buccal cells: Cells collected from the inside of the patient’s cheek may be used for normal control DNA. Patients must not eat within 30 minutes of cell collection. This is the MOST IMPORTANT STEP and should be performed carefully to collect a sufficient amount of material for the analysis. For breastfeeding infants, collect specimens at least one hour after feeding. Poor specimen collection will require re-collection.

1. Open the brush packet and remove the brush. The packet must be opened according to the instructions on top of the flap.
2. Scrape the inside of the cheek wall horizontally 10 times in a back-and-forth motion, as you rotate the brush.
3. After collecting the cheek cells, place the brush directly into the correctly labeled envelope.
4. Ensure that all the specimens are clearly and appropriately labeled.
5. Close and seal the envelope after all specimens are collected. Collect 1-2 swabs per patient.
6. Place all specimen envelopes into a 4°C storage area for pickup and delivery to University of Florida Health Pathology Laboratories.
7. Storage/Transport temperature: Refrigerated
8. Stability (collection to shipping of the sample): Ambient: 24 hours Refrigerated: 1 week, Frozen: Unacceptable

Rejected samples type

1. Tissues that are not fixed in 10% formalin, or has been fixed for longer than 3days in 10% formalin.
2. Tissues that have been fixed more than three days in 10% neutral buffered formalin may not be used for DNA extraction.
3. No tumor area is indicated.
4. The tumor region is smaller than 0.5 x 0.5 mm.
5. Tumor cell content is <5%
6. Hemolysis samples
7. Clotted blood
8. Buccal swabs of insufficient quantity

10 – 14 days