Clinical Applications

The Liquid Biopsy

  • Monitoring for cancer recurrence
  • Cancer screening market

Diagnostics on Cancer Tissue

  • Targeted Chemotherapy
  • Specific Immunotherapy (Check Point Inhibitors)
  • Micro-satellite instability

The co-development of companion diagnostics for new targeted chemotherapy

Patient selection for Clinical Trials

MutantDx Assays for Solid Tumors

Colorectal Cancer

  1. Braf pV600E/K
    Significant negative prognostic factor in patients with Stage II and III colorectal carcinoma.
  2. Micro satellite instability MSI-H (MMRD)
    MSI is a tumor screening test for all new diagnosed colorectal cancer patients to identify patients who may have an inherited form of colorectal cancer (Hereditary Nonpolyposis Colon Cancer or Lynch Syndrome. Markers-BAT-25, BAT-26, NR-21, NR-24 and MONO-27). Samples with instability in two or more of these mononucleotide markers are designated MSI-High (MSI-H), whereas those with one unstable marker are designated MSI-Low (MSI-L).  Samples with no detectable alterations are MSI-stable (MSS).  These designations are in accordance with the National Cancer Institute’s Bethesda guidelines
  3. Colon Cancer Panel (Braf, Kras, Nras)
    CPT Code(s): 81210 (Braf)8127581403 (Kras)81404 (Nras)

Non-Small Cell Lung Cancer

  1. EGFR (Exons 18, 19, 20 & 21)
    CPT Code(s): 81235 • 81479
    Activating mutations in EGFR are present in approximately 10-12% of non-small cell carcinomas of the lung (primarily adenocarcinomas). Based on several Phase II and III trials, most EGFR mutations predict a good response to treatment with EGFR inhibitors such as gefitinib and erlotinib1. The exceptions are insertion mutations in exon 20 and the T790M substitution, which correlate with resistance to these drugs.
  2. ALK Resistance
    CPT Code: 81479
    ALK gene fusions are important oncogenic drivers in several cancer types, including non-small cell lung cancer, anaplastic large cell lymphoma, inflammatory myo-fibroblastic tumor, and renal medullary carcinoma.  The use of ALK kinase inhibitors to treat these cancers is associated with the development of resistance due to selection of new mutations in the kinase domain that interfere with drug activity. Sequencing the ALK kinase domain can be used to identify mutations associated with drug resistance. In addition, this sequencing can identify primary activating mutations of ALK that occur in some cases of neuroblastoma.
  3. ROS1 kinase markers ROS 1
    CPT Code: 88368
    Gene fusions involving ROS1 are present in 1-2% of non-small cell lung carcinomas, primarily adenocarcinomas. Several partner genes (FIG, SLC34A2, CD74) have been identified.  Resulting activation of ROS1 kinase activity appears to be a principal growth driver in these tumors. This kinase is sensitive to crizotinib, and patients with ROS1-fusion positive tumors have shown responses to this inhibitor. A break-apart FISH probe to the ROS1 locus can be used to screen for these fusions by FISH. The ROS1 FISH test is recommended for screening NSCLC cases that are negative for EGFR mutation and ALK fusion.

Malignant Melanoma

  1. Braf (exon 15)
    CPT Code: 81210
    Mutations in the BRAF gene are the most common oncogenic alterations in malignant melanoma, present in approximately 45% of tumors arising from cutaneous sites and occurring in melanomas at other locations. The V600E mutation is the most common BRAF alteration, and this mutation is the target for BRAF kinase inhibitors such as vemurafenib
  2. Nras (exons 1 & 2)
    CPT Code(s): 81404
    Activating mutations in NRAS are present in approximately 20% of malignant melanomas. Based on pre-clinical data, the presence of a mutation may predict for sensitivity to RAF and/or MEK kinase inhibitors. Clinical trials for the treatment of NRAS-positive melanomas with these compounds are ongoing.
  3. KIT (cKIT) (exons 11, 13, & 17)
    CPT Code: 81272
    Activating mutations of the KIT tyrosine kinase are present in some cases of malignant melanoma. The frequency varies with primary site, as indicated below.
  4. GNAQ • GNA11 (Melanoma, choroid, uveal)
    CPT Code(s): 81479 • 81403
    The most common oncogenic mutations associated with ocular (choroidal/uveal) melanomas occur in the genes for two related GTP-binding proteins, GNAQ and GNA11. Rarely, these genes are mutated in cutaneous melanomas. Both gene products are involved in signal transduction from transmembrane receptors through the MAP kinase pathway. Pre-clinical studies have shown that mutations in GNA11 induced spontaneously metastasizing tumors in a mouse model. And a melanoma cell line harboring a GNAQ Q209L mutation has been shown to be sensitive to a MEK inhibitor. Screening for GNAQ and GNA11 mutations may be useful in subtyping melanomas for potential targeted therapy in clinical trials.

GI Stromal Tumor (GIST)

  1. KIT (cKIT) (exons 9, 11, 13, 17) reflexed to PDGFRA
    CPT Code: 81272
    Approximately 80% of gastrointestinal stromal tumors (GISTs) have an oncogenic mutation in the gene encoding KIT tyrosine kinase. Another 5-7% of GISTs have a mutation in the gene encoding the related kinase PDGFRA (platelet-derived growth factor receptor alpha).  KIT and PDGFRA mutations are mutually exclusive in GISTs.  In both genes, the observed mutations are invariably in-frame and result in expression of a mutant kinase isoform that has constitutive tyrosine kinase activity. Approximately 10-15% of GISTs have no detectable KIT or PDGFRA gene mutation.
  2. BRAF (wild-type GIST) (exon 15)

Breast Cancer

  1. PIK3CA P13 Kinase
    CPT Code(s):81479
    Screening for mutations in oncogenes and tumor suppressor genes is increasingly important in delivering personalized cancer care. In both pre-clinical studies and recent clinical trials, mutations in the PIK3CA gene have been associated with increased sensitivity to inhibitors of the PI3 kinase pathway. This test is used to screen for the most common activating mutations in the alpha subunit of PI3 kinase.
  2. AKT1 c.49G>A (E17K)
    The E17K mutation results in an amino acid change at position 17 in AKT1, from a glutamic acid (E) to a lysine (K). This mutation occurs within the pleckstrin homology domain (PHD) of AKT1 (Figure 1) and results in activation of the phosphatidylinositol 3-kinase (PI3K) pathway. In vitro studies suggest that the AKT1 E17K mutation is less sensitive than wild type AKT1 to inhibition by the experimental AKT inhibitor VIII, a non-ATP competitive agent which requires a functional pleckstrin homology domain.
  3. PTEN c.697C>T (R233*)
    The R233* mutation results in the introduction of a premature stop codon into the PTEN gene. This mutation occurs within exon 7, which encodes a portion of the C2 domain. C2 domains are known to be involved in targeting proteins to cell membranes. In vitro studies have shown that inactivating mutations in the PTEN gene confer sensitivity to PI3K-AKT inhibitors as well as FRAP/mTOR inhibitors.

Endometrial Cancer

  1. PIK3CA P13 Kinase
    CPT Code(s):81479
    Screening for mutations in oncogenes and tumor suppressor genes is increasingly important in delivering personalized cancer care. In both pre-clinical studies and recent clinical trials, mutations in the PIK3CA gene have been associated with increased sensitivity to inhibitors of the PI3 kinase pathway. This test is used to screen for the most common activating mutations in the alpha subunit of PI3 kinase.
  2. PTEN c.697C>T (R233*)
    The R233* mutation results in the introduction of a premature stop codon into the PTEN gene. This mutation occurs within exon 7, which encodes a portion of the C2 domain. C2 domains are known to be involved in targeting proteins to cell membranes.

Gliomas

  1. MGMT – Methylation
    CPT Code: 81287
    O6-methylguanine methyltransferase (MGMT) gene encodes a DNA repair enzyme that de-alkylates guanines in DNA. Methylation of CpG sites in the promoter region of the MGMT gene leads to decreased expression of this enzyme, allowing accumulation of alkylguanines that, following incorrect base pairing with thymine, cause DNA damage signaling and cell death.  MGMT promoter methylation predicts for increased sensitivity of glioblastomas to alkylating agents like BCNU (carmustine), and also correlates with prolonged progression-free survival in temozolomide treated patients.
  2. AML • Isocitrate dehydrogenase isoforms
    CPT Code: 81403
    Mutations in isocitrate dehydrogenase enzyme isoforms 1 (IDH1) and 2 (IDH2) have been found in 70% of grade II-IV gliomas and in approximately 15% of acute myeloid leukemias (AML).   These mutations alter arginine 132 (R132) in IDH1, and either R140 or R172 in IDH2.  In AML, presence of these mutations confers an adverse prognosis and will likely be the target for drugs in development.

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