Alias/Synonyms:
Fusions, Gene Fusions, Fusion, Gene Fusion, Gene, Sarcoma, Archer, Gatorseq, NGS, ALK, ROS, MET, KIT, NOTCH, NTRK
Additional Information:
Epic order code: LAB1230508
The Gatorseq NGS Fusions assay is a targeted next-generation sequencing assay utilizing a custom Archer® FusionPlex® reagent kit with Illumina Novaseq platform to produce high-complexity libraries for the detection of gene fusions, splicing and/or exon skipping variants. The area of tumor is localized on an H/E slide and macrodissected. Using custom reagents, the RNA extracted from the tissue is sequenced to high uniform depth. Sequence data are processed using the kit manufacturer’s analysis pipeline designed to accurately detect gene fusions and splice variants.
Genes targeted for detection of fusions, splice and/or exon-skipping variants:
ACVR2A, AKT1, AKT2, AKT3, ALK, AR, ARHGAP26, ARHGAP6, AXL, BCOR, BRAF, BRD3, BRD4, CAMTA1, CCNB3, CCND1, CD274, CIC, CRTC1, CSF1, CSF1R, DNAJB1, EGF, EGFR, EPC1, ERBB2, ERBB4, ERG, ESR1, ESRRA, ETV1, ETV4, ETV5, ETV6, EWSR1, FGF1, FGFR1, FGFR2, FGFR3, FGR, FOS, FOSB, FOXO1, FOXO4, FOXR2, FUS, GLI1, GRB7, HMGA2, IGF1R, INSR, JAK2, JAK3, JAZF1, KIT, MAML2, MAP2K1, MAST1, MAST2, MBTD1, MDM2, MEAF6, MET, MGEA5, MKL2, MN1, MSMB, MUSK, MYB, MYBL1, MYC, NCOA1, NCOA2, NCOA3, NFATC2, NFE2L2, NFIB, NOTCH1, NOTCH2, NOTCH3, NR4A3, NRG1, NTRK1, NTRK2, NTRK3, NUMBL, NUTM1, PAX3, PAX8, PDGFB, PDGFD, PDGFRA, PDGFRB, PGR, PHF1, PHKB, PIK3CA, PKN1, PLAG1, PPARG, PRDM10, PRKACA, PRKACB, PRKCA, PRKCB, PRKCD, PRKD1, PRKD2, PRKD3, RAD51B, RAF1, RELA, RET, ROS1, RSPO2, RSPO3, SRF, SS18, SS18L1, STAT6, TAF15, TCF12, TERT, TFE3, TFEB, TFG, THADA, TMPRSS2, TRIM11, USP6, VGLL2, WWTR1, YAP1, YWHAE
CPT Code(s):
81456
Specimen Requirements:
The samples should be specifically chosen by a pathologist to include at least 5 % tumor cells without significant necrosis or inflammation.
Formalin Fixed Parafin Embedded (FFPE) specimens
Must be accompanied by 1 corresponding H&E from the same block with the tumor circled by a qualified pathologist AND the estimated percentage of tumor cells present in the circled area(s).
1. Circle the area(s) on the H&E slide where tumor cells are present with a marking pen.
2. Write the percent tumor on the H&E slide with a marking pen.
OR
Unstained Slides (USS) prepared from FFPE specimens
For 10mmx10mm sized tissue or larger, send 10 USS. For smaller tissues, send 20 USS
Must be accompanied by 1 corresponding H&E from the same block with the tumor circled by a qualified pathologist AND the estimated percentage of tumor cells present in the circled area(s).
1. Circle the area(s) on the H&E slide where tumor cells are present with a marking pen.
2. Write the percent tumor on the H&E slide with a marking pen.
Unacceptable Specimens/Conditions:
Peripheral Blood (PB) or Bone Marrow Aspirate (BMA) are not acceptable for this assay.
Tissues that are not fixed in 10% formalin, or has been fixed for longer than 3 days in 10% formalin.
Tissues that have been fixed more than 3 days in 10% neutral buffered formalin may not be used for RNA extraction.
No tumor area is indicated.
The tumor region is smaller than 2.5 x 2.5 mm.
Tumor cell content is <5%
Use:
This test is used to determine a prognosis and/or treatment options for individuals with cancer at initial diagnosis or with refractory disease.
This assay is intended to detect fusions or splice variants present in tumor cells and is not to be used to determine or report germline alterations.
Reported:
10-14 days
Reference Range:
No fusions detected.
Interpretation Data:
Interpretative report provided.