Solid Tumor OncoPanel Hotspot and Fusion on RNA by NGS

CPT Code(s)

81455, G0452


Solid tumor, NGS, next generation sequencing, fusion, translocation, RNA, single nucleotide variant, SNV, hotspot


Molecular Diagnostics Laboratory

Clinical Indication and Relevance

The assay can identify molecular genomic alterations that may help provide a diagnosis and/or therapeutic information. Genomic alterations that can be identified include gene fusions, hotspot single nucleotide variants, small indels (<20bp), and a select number of oncogenic splicing variants.


The Solid Tumor HotSpot and Fusion OncoPanel is a custom-designed targeted RNA sequencing assay, created to detect gene fusions, exon skipping events, and select expressed hotspot mutations in solid tumors (see table 1 and 2 for gene lists). Selected gene targets represent recurrently altered genes expressed in solid tumors.  Anchored Multiplex PCR chemistry is used for Archer FusionPlex library preparation with molecular barcoding from specimen RNA or total nucleic acid (TNA) targeting regions of interest in the Solid Tumor HotSpot and Fusion OncoPanel. After sequencing on the Illumina MiSeq, the Archer Analysis Bioinformatics Pipeline is used to detect relevant alterations, and uses the molecular barcodes for read deduplication and error correction.

Alterations are assessed as Tier I, Tier II, Tier III or Tier IV (benign or likely benign) based on professional guidelines (Li M et. al, 2017, PMID 27993330), and Tier I-III alterations are reported here after being assessed using public databases (such as COSMIC, OncoKB, Quiver Fusion Database, CIViC, and others).


AKT1                      BCOR                     BRAF                     CCND1                  CIC                         CTNNB1

DICER1                  EGFR                      ERBB2                   FGFR1                   FGFR2                    FGFR3

GNA11                  GNAQ                     GNAS                    H3F3A                   HIST1H3B             HRAS

IDH1                      IDH2                       KIT                         KRAS                     MAP2K1                MED12

MET                       MTOR                     NFE2L2                 NRAS                     NTRK1                   NTRK3

PDGFRA                PPP2R1A                RAC1                     RAF1                      RET                        SF3B1

SMO                      TP53


AKT1                      AKT3                      ALK                        AR                          ARHGAP26            ATRX

AXL                        BCAR4                   BCL2                      BCL2L1                  BCOR                     BRAF

CAMTA1               CCND1                   CD274                   CDK6                      CDKN2B-AS1        CIC

CTNNB1               DNAJB1                  EGFR                      ERBB3                    ERBB4                   ERG

ESR1                      ETV1                       ETV4                      ETV5                       ETV6                      EWSR1

FGFR1                   FGFR2                     FGFR3                   FGFR4                     FLI1                       FOS

FOSB                     FOXA1                    FOXO1                  FUS                          GLI1                      HMGA2

JAZF1                     KIT                          MAML2                 MAML3                   MAST1                  MAST2

MET                       MRTFB                   MN1                       MYB                        MYBL1                  NCOA1

NCOA2                  NDRG1                  NOTCH1                NOTCH2                 NR4A3                  NRG1

NTRK1                   NTRK2                   NTRK3                    NUMB                    NUTM1                 PAX3

PDGFD                  PDGFB                   PDGFRA                 PHF1                       PIK3CA                 PLAG1

PPARG                  PRKCA                    RAF1                       RELA                       RET                       ROS1

RSPO2                   RSPO3                   SLC45A3                 SS18                       SS18L1                 STAT6

TAF15                    TCF12                    TCF7L1                    TCF7L2                   TERT                     TFE3

TFEB                      TFG                        THADA                     TMPRSS2               TP53                     TRIO

USP6                     VGLL2                    YWHAE                     WWTR1                 YAP1

SNV Hotspot Regions
Fusion and Oncogenic Isoform Targets

Minimum Specimen Requirements


  • Formalin Fixed Paraffin Embedded (FFPE) tissue; should not be more than 5 years old. Tumor percentage should be 40% in one area.
    • Tissue blocks, including core needle biopsies. The Histology lab will cut 10 unstained slides at 5-10 microns and 1 H&E.
    • Unstained FFPE tissue slides (10 slides at 5-10 microns thickness). And 1 H&E.
    • Fine needle aspirate (FNA) processed as FFPE cell block (cytospin). The Histology lab will cut 10 unstained slides at 5-10 microns and 1 H&E.

Less desired:

  • Cells grown in tissue culture or cells preserved by Cytogenetics. A corresponding H&E from the submitted sample is desired.
  • Fresh or frozen tissue, at least 0.5 x 0.5 cm. Frozen tissue should be stored at -80C. An H&E slide is also required.
  • Frozen tissue preserved in OCT (Optimal Cutting Temperature) and stored at -80C. An H&E slide is also required.



  • Formalin-fixed paraffin embedded (FFPE) tissue blocks and slides can be delivered at controlled temperatures, not to exceed 30C.
  • Fresh tissue samples should be delivered at room temperature in RPMI culture medium to the lab within 3 hours of collection, or snap frozen in liquid nitrogen at -70°C and packed in dry ice for delivery. Please do not allow frozen tissues to thaw.

Unacceptable Samples

  • Tissue samples fixed in Zenker’s, B5, or Bouin’s fixatives
  • Samples decalcified with strong acids
  • Hematopathologic samples
  • FFPE tissue scrolls are not desired, as they cannot be macrodissected. They require pathologist approval.
  • Tumor percentage less than 40% on one area is not ideal. Tumor content between 5-40% in one area may be approved by a pathologist on a case-by-case basis.
  • Frozen or fresh tissue samples or samples from cytogenetics must be accompanied by an H&E. In special situations, this may be approved by a pathologist.

Turnaround time

Seven to 15 working days.

View Requisition Sheet