Liquid Trace™ Solid Tumor

Pan-Tumor Assay for Solid Tumors 

GTC’s Liquid Trace Solid Tumor is a pan-cancer highly sensitive test evaluating cfRNA and cfDNA providing highly informative data that can be used for diagnoses, evaluating the host immune response, and identifying biomarkers for predicting responses to various therapies. 

Furthermore, Liquid Trace Solid Tumor may provide additional information not detected by tissue biopsies including information on the presence of germline mutations or mutations in the subclones not present in the tissue sample (heterogeneity).

Types of solid tumors Liquid Trace can detect:

• Lung
• Breast
• Thyroid
• Colon
• Oropharyngeal tumors
• Pancreatic
• Ovarian
• Prostate
• HPV
• Cancer of unknown primary (CUP)

Liquid biopsy in its current form is dependent on cfDNA analysis; this method likewise presents multiple challenges. These include variations in DNA shedding between tumors as well as low sensitivity (especially in early-stage cancer), difficulty in detecting fusion genes (i.e., chromosomal translocations leading to the expression of chimeric mRNA from two genes), and inability to reflect the numerous biological processes that modify RNA expression levels, such as alternative splicing, stability, and allele-specific methylation. The latter limitation is critically important as recent studies have shown that RNA testing provides another level of biological information regarding the tumor and its microenvironment.

The Benefits of cfRNA

RNA sequencing has proven to be more sensitive for some types of mutations. Cancer cells typically contain one copy of mutated DNA but numerous copies of RNA.  This research is consistent with GTC’s findings that cfRNA has increased sensitivity over cfDNA alone. More specifically, cfRNA allowed GTC’s Liquid Trace to detect more mutations and fusions in hematologic and solid tumor samples, which may be undetected by conventional cfDNA.

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 a large number of identical cells with the same T or B cell receptor.

HLA genotyping is now part of Liquid Trace and is useful for identifying patients who may be candidates for immunotherapy.

GTC evaluates HLA class I and class II level of expression (available upon request).

GTC uses AI in every step of our analysis and it makes a difference in helping make a new discovery daily that improve patient care.

Once the data is offloaded from the sequencer, our AI:

1. Assists with mutation analysis, identifying non-mutations and artifacts
2. Compares various data sets to explore disease biology
3. Provides support for clinical decision making and classification of the disease
4. It helps with matching patients to therapeutics and presents clinical trial options
5. Aggregates data for report generation and simplifies the results so they are easily understood

Case Study: Prostate Cancer

Background 

Prostate cancer is one of the most common solid tumors among men. Multiple therapies have been introduced to improve survival and symptom control. Analysis of circulating tumor DNA and RNA in the blood using liquid biopsies, has become an important tool in the management of prostate cancer. In localized disease, it can distinguish between low-and high-grade cancers and can guide the decision to proceed with or defer tissue biopsy. In advanced tumor states, liquid biopsy has a prognostic value and has been used in clinical trials to assess response. 

Clinical History 

• 75-year-old male  
• With history of prostate cancer presenting for monitoring

Figure 1

Molecular Profiling Findings 

• Androgen receptor splice variant 7 (AR-V7) is detected (figure 1)
• t(21;21)(q22;q22) ERG-TMPRSS2 mRNA fusion
  
• Mutations in TP53, CDK12, and GATA2 genes
  
• Chromosomal structural analysis shows +7, +8, -11, +12, -13, -14, and others
  
• Increased PSA mRNA
  
• Increased Keratin 19 mRNA
  
• No evidence of germline BRCA1/2, BARD1, BRIP1, CDK12, CHEK1/2, FANCL, PALB2 or RAD mutations
   

Discussion 

Although serum Prostate-Specific Antigen (PSA) is being used for monitoring prostate cancer, PSA levels has often failed to precisely reflect disease burden and extent, and multiple therapies impact patient survival and symptoms without corresponding changes in serum PSA levels. As such, comprehensive analysis of cfDNA and cfRNA using liquid biopsies provides another level of biological information regarding the tumor and its microenvironment. This technique is simple, safe, and easily repeatable throughout disease course and can serve as a prognostic and predictive biomarker as well as a ready tissue source for molecular profiling. In this specific case we were able to evaluate the patient’s AR-V7 (on the RNA level) and Homologous Recombination Repair Gene Mutations status. Men with AR-V7 expression have a shorter progression-free survival, and overall survival when treated with Enzalutamide or Abiraterone, suggesting a possible means of predicting response to these therapies through cfDNA and cfRNA profiling.

Download Case Study Brochure (PDF)

References 

1. Siegel, R. L., Miller, K. D., & Jemal, A. (2019). authors. Cancer statistics, 2019. CA Cancer J Clin, 69, 7-34.
2. Albitar, M., Zhang, H., Charifa, A., Ip, A., De Dios, I., Ma, W., ... & Goy, A. (2022). Cell-free RNA in liquid biopsy and biomarkers profiling of hematologic and solid tumors.
3. Albitar, M., Zhang, H., Charifa, A., Ip, A., De Dios, I., Ma, W., ... & Goy, A. (2022). Combining cell-free RNA (cfRNA) with cell-free total nucleic acid (cfTNA) as a new paradigm for liquid biopsy.

Case Study: ESR1

Background 

Circulating tumor DNA and RNA (cfDNA, cfRNA) is cell-free DNA/RNA released by tumor cells in the blood. cfDNA and cfRNA can be detected in the plasma of patients with cancer, and their analysis represents a minimally invasive tool for detecting and monitoring key gene mutations and alterations. In breast cancer, detection of ESR1 and PIK3CA mutations is very important, since recently there have been specific targeted therapies developed.

Clinical History 

• 62-year-old female  
• With relapsing (ER+/HER2 -) breast cancer 

Molecular Profiling Findings 

• Mutations in ESR1, PIK3CA, MAP3K1, PRKDC, KMT2C, MYC, ROS1, NOTCH2, and EP300 genes 

Discussion 

Endocrine therapy is the main treatment option for Estrogen receptor-positive (ER+) breast cancer (BC). Compared with other clinical subtypes, ER+ BC patients usually have a more favorable prognosis. However, almost all ER+ BC patients develop endocrine resistance and disease progression eventually. Mutations in Estrogen Receptor 1 (ESR1) play a key role in resistance to Aromatase Inhibitors but may retain sensitivity to selective estrogen receptor degraders (SERD). Recently, Elacestrant, an oral SERD, was approved for patients with ER+/HER2- ESR1 mutant metastatic breast cancer. Detection of PIK3CA mutations is important as well, since recently Alpelisib in combination with Fulvestrant with HR+/HER2- PIK3CA mutant metastatic breast cancer. Detection of ESR1 and PIK3CA could also have important clinical applications for the follow-up of these patients. In this case the patient breast cancer tissue was sequenced initially and treated accordingly. ESR1 mutation was not detected in the diagnostic tissue sample. Later on, the patient’s disease progressed and relapsed. A minimally invasive liquid biopsy was performed and ESR1 mutation was detected indicating endocrine resistance.   
In summary, novel selective estrogen receptor degraders (SERDS) and PIK3CA inhibitors are emerging as new therapeutic options in metastatic breast cancer. The analysis of cfDNA and cfRNA allows for non-invasive monitoring of these mutations over time, providing clinicians with valuable information about treatment response, disease progression, and the emergence of resistance. This approach reduces the need for invasive tissue biopsies and enables real-time monitoring of the tumor's genetic profile, facilitating personalized treatment decisions. Furthermore, Trace liquid biopsy can be used as tissue informed test for monitoring response and minimal residual disease with high sensitivity but at the same time detecting clonal evolution of the development of new mutations. 

Download Case Study Brochure (PDF)

References 

1. Combining cell-free RNA (cfRNA) with cell-free total nucleic acid (cfTNA) as a new paradigm for liquid biopsy. Maher Albitar, Hong Zhang, Ahmad Charifa, Andrew Ip, Ivan De Dios, Wanlong Ma, James K. McCloskey, Michele Donato, David Samuel DiCapua Siegel, Stanley E. Waintraub, Martin Gutierrez, Andrew L Pecora, Andre Goy. DOI: 10.1200/JCO.2022.40.16_suppl.3048 Journal of Clinical Oncology 40, no. 16_suppl (June 01, 2022) 3048-3048. 
2. Detection of ESR1 Mutations Based on Liquid Biopsy in Estrogen Receptor-Positive Metastatic Breast Cancer: Clinical Impacts and Prospects. Liao H, Huang W, Pei W, Li H. Front Oncol. 2020 Dec 15;10:587671. doi: 10.3389/fonc.2020.587671.  

• Peripheral blood: 10 mL. EDTA tube is required.

Specimen Preparation and Shipping Guidelines

Use the Hematology Transport Kit

• Complete Requisition, making sure all sections are completed in their entirety including client information, patient Information, specimen Information and test Selection.  Missing information may delay reporting of test results.
• Diagnosis/patient history is extremely important in rendering the correct interpretation of results and should also be filled out as completely as possible. A copy of a Path report should be included.
• Ensure the specimen is labeled with patient name and number.  A minimum of two patient identifiers is required for each specimen.

For blood samples:

• Ship using a cold pack. The cold pack should not directly contact the blood tube. Ship as soon as sample collected with overnight delivery.

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Genes validated and tested for Mutations in cfDNA testing