CMOCO Panels by Tumor Type*

* All mutational panels are performed as part of a 169 gene (full-coding) hybrid capture-based next generation sequencing (NGS) assay  

Current CMOCO Panels available (updated 11/18/2024):

Lung Panels
Gastrointestinal (GI) Panels

Initial presentation/testing

Mutations: EGFR, KRAS, BRAF, ERBB2, METex14

Fusions: ALK, ROS1, METex14, RET, NTRK1/2/3

Amplifications: ERBB2, MET by FISH

IHC: PD-L1 (SP263) (if not previously done)


Colorectal Carcinoma

Microsatellite instability analysis

Mutations:  BRAF, KRAS, NRAS, POLE

If negative for RAS/RAF, reflex to:

FISH:  ERBB2 

Fusions:  NTRK1/2/3, RET

     If MSI-H and MLH1/PMS2 loss (by IHC),

        MLH1 promoter hypermethylation

Resistance to targeted therapy

Mutations:  BRAF, EGFR, ERBB2, KRAS, METex14

PLUS kinase domain relevant driver (ALK, RET, ROS1) as indicated by clinical history

Fusions:  ALK, METex14, NTRK1/2/3, RET, ROS1

      Amplifications:  ERBB2, MET by FISH

Pancreatic Carcinoma

Microsatellite instability analysis (requires paired normal tissue)

Mutation:  BRCA1, BRCA2, KRAS

If driver negative, reflex to:

Fusions:  NRG1, NTRK1/2/3

Relatedness of multiple lesions

Mutations:  All genes in assay (169)

Fusion (as appropriate):  ALK, METex14, NTRK1/2/3, RET, ROS1

GIST

Mutations:  BRAF, KIT, NF1, PDGFRA

If negative for the above genes, reflex to:

      Fusions:  NTRK1/2/3

Rapid EGFR/KRAS/ALK panel *

Mutations:  Rapid EGFR, Rapid KRAS

IHC:  ALK, PD-L1 (if not previously done)

      If negative, will reflex to initial lung panel

Cholangiocarcinoma

Microsatellite instability analysis (requires paired normal tissue)

Fusions:  FGFR2/3, ROS1

   Mutations:  BRAF, IDH1, KRAS

Rapid KRAS reflex to panel *

Mutations:  Rapid KRAS

      If negative, will reflex to initial lung panel

Gastric/Gastroesophageal/GE junction Carcinoma *

 

Mutations: BRAF, ERBB2, KRAS

 

Fusions: NTRK1/2/3, RET

 

Microsatellite instability analysis (requires paired normal

tissue)

 

FISH ERBB2 (If IHC equivocal or not performed)

 

* Can be ordered without mutational/fusion NGS

* Rapid panels are offered with the intent of expediting therapy decisions in the setting of severely/acutely ill patients. Rapid testing is performed at the discretion of the molecular pathologist and may be deferred to prioritize more comprehensive testing.Rapid KRAS (non-NGS)
 Rapid MSI (available for colorectal carcinomas only)
 

Relatedness of multiple lesions (multiple primary vs metastasis)

  Mutations: All genes in assay (169)

 

 

Genitourinary (GU) Panels 

Urothelial (bladder)

        Mutations: ERBB2, FGFR2/3, PIK3CA

        If negative for the above genes, reflex to:

               Fusions: FGFR1/2/3

Prostatic Adenocarcinoma/Homologous Recombination Deficiency (HRD) 

 

Microsatellite Instability analysis (requires paired normal tissue)

 

Mutations: ATMBARD1BRCA1BRCA2, CDK12, CHEK2, FANCAPALB2, RAD51D

 

Renal Cell Carcinoma (RCC)

 

Mutations: BAP1PBRM1SETD2VHL*

 

 

*Priority reportable genes variable depending on differential diagnosis/tumor type suspicion. Other reportable genes include (but are not limited to): ELOC (TCEB1), FHSDHA/B/C/D, and SMARCB1.

 

 
Non-lung/Non-GI/Non-GU Panels 

Melanoma

 - Cutaneous

    Mutation: BRAF, KIT, MAP2K1, NF1, NRAS 

     If negative for the above genes, reflex to:

        Fusions: ALK, BRAF, NTRK1/2/3, ROS1

 - Uveal

    Mutations: GNA111, GNAQ 

    If negative for the above genes, reflex to:

      Fusions: ALK, BRAF, NTRK1/2/3, ROS1

- Rapid BRAF reflex to panel

   Mutations: Rapid BRAF

    If negative, will reflex to appropriate panel above

Glioma Panel*

 

Mutations: BRAF, IDH1, IDH2, TERT promoter

Option to add Fusions: FGFR2/3, NTRK1/2/3, RET

Option to add: MGMT promoter methylation

*Adult diffuse glioma panel listed. Priority reportable genes variable depending on differential diagnosis/tumor type suspicion. Other reportable genes include: FGFR1, H3F3A, and MAP2K1. Other fusions include: BRAF, FGFR1 kinase domain duplication, and MYB


Desmoid Fibromatosis

 

Mutations: CTNNB1APC


Meningioma Panel

 

Mutations: BAP, NF2, TERT

Losses: 1p &CDKN2A (by FISH)



 

Breast

    Mutations: AKT1, ERBB2, ESR1, PIK3CA, PTEN


 

Endometrial

    Mutations: CTNNB1, POLE, TP53

    If MSI-H and MLH1/PMS2 loss (by IHC),

        MLH1 promoter hypermethylation

 



Thyroid

  - Differentiated Thyroid Cancer

      Mutation: BRAF

      If negative for BRAF, reflex to:

        Mutations: RAS

        Fusions: NTRK, PAX8-PPARg, RET

  - Anaplastic Thyroid Cancer

      Mutations: BRAF

      If negative for BRAF, reflex to:

        Mutations: RAS, TERT

        Fusions: NTRK, PAX8-PPARg, RET

  - Medullary Thyroid Cancer

      Mutations: RET

      If negative for RET, reflex to:

        Mutations: RAS



Pathology (SOM)

CU Anschutz

Academic Office One

12631 East 17th Avenue

2nd Floor

Aurora, CO 80045


303-724-3704

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