The Solid Tumor Profile Plus test combines the analysis of 434 DNA genes with targeted transcriptome sequencing (RNA) of more than 1600 genes to provide a comprehensive evaluation of cancer that includes detection of single-nucleotide variation, copy-number variation, gene expression levels, and fusions irrespective of their partner genes. In addition, the test is designed to detect microsatellite instability (MSI), tumor mutation burden (TMB), homologous recombination repair (HRR) mutations, and homologous recombination deficiency (HRD). Other notable features include evaluation for MET exon 14 skipping, EGFRvIII, AR-V7, TERT promoter mutations, DYPD gene polymorphism for prediction of toxicity to fluoropyrimidine therapy, and RNA levels of CTLA4, PD-L1, and PD-L2. The provided information helps in determining prognosis, designing a therapeutic approach, and predicting response to immunotherapies, targeted therapies, and precision medicines. It may also aid in biomarker discovery.
Targeted transcriptome sequencing can also detect:
Epstein-Barr Virus (EBV): Important for diagnosis and classification of lymphoid neoplasms and some solid tumors.
Human Papillomavirus (HPV): Chronic infection with high-risk HPV subtypes is associated with increased risk of anogenital and oropharyngeal cancer. Detection of HPV mRNA suggests active (productive) infection.
Torque Teno Virus (TTV): This virus was first discovered in a patient with non-A-E hepatitis and is now regarded as a part of the human virome. In general, TTV does not cause pathology in immunocompetent individuals. This virus is considered as a marker of the degree of immune competence in patients with immunological impairment and inflammatory disorders. High TTV load is associated with increased risk of infection. In patients with organ transplant, low TTV load is associated with an increased risk of rejection.
T-cell and B-cell Clonality Detection: The detection of T- and B-cell clonality is important because it can help diagnose and monitor certain types of malignancies. When a malignant transformation occurs in a T- or B-cell, the cells can undergo uncontrolled clonal expansion, resulting in the accumulation of many cells with the identical T- or B-cell receptor.
MGMT Methylation: This assay is available as an add-on for brain cancer patients. MGMT methylation is predictive of response to radiotherapy and prognostic for glioblastoma.
Sensitivity is 3% for non-hotspot and 1% for hotspots. It is at 0.001 for cases with prior Hx.