Liquid Trace™ Hematology

Pan-Tumor Assay for Hematologic Malignancies

GTC’s Liquid Trace Hematology 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. 

GTC’s Liquid Trace can significantly reduce the need for bone marrow biopsies for hematology patients. Furthermore, the test can detect, chromosomal abnormalities, translocations, and gene amplifications.

Liquid Trace can detect all types if hematologic cancers including:

• Multiple myeloma
• Lymphoma
• Acute Lymphoblastic Leukemia
• Acute myeloid leukemia
• MDS
• CMML
• MPN
• MRD
• VEXAS syndrome
• EBV - related neoplasms
• Hypersinophilia

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.

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: Multiple Myeloma

Background

Multiple myeloma is a malignancy originating in plasma cells. It is characterized by bone marrow infiltration, excessive production of monoclonal proteins, bone destruction, plasma cell aggregates, renal involvement, and associated anemia and immunodeficiency.
Multiple myeloma is heterogeneous in its genetic abnormalities and shows molecular evolution during disease progression and treatment. In addition, there is molecular diversity between subclones in the same or different bone marrow (BM) sites, between BM and the extramedullary sites, and between individuals. These features may explain why despite improving and longer overall median survival over the past few years, some patients survive for decades, whereas others succumb to the disease rapidly. As a result of these characteristics, optimal management of this malignancy requires testing modalities capable of capturing a comprehensive profile of the mutational and chromosomal landscape of the disease, enabling new risk stratification systems and individual therapy options previously unavailable.
Liquid biopsy has emerged as a promising non-invasive diagnostic tool frequently used in solid tumors but rarely used in multiple myeloma. While bone marrow biopsy, supplemented by flow cytometry, immunohistochemistry, cytogenetics and Fluorescent In Situ Hybridization (FISH) has traditionally been the gold standard for diagnosis and follow-up of multiple myeloma patients, liquid biopsy is emerging as a one-stop source, capable of not only supplementing, but increasingly replacing and surpassing many facets of traditional bone marrow biopsy. It offers several advantages over traditional bone marrow biopsy for evaluation of multiple myeloma, including but not limited to ease of sampling, real-time monitoring, identification of potential molecular targets, drug resistance and enhanced detection of chromosomal abnormalities, translocations, gene amplifications and assessment of B-cell as well as T-cell clonality.
Liquid biopsy also has the potential to be used as an ultimate tool for measuring minimal residual disease because it provides information on b-cell clonality as well as mutations.

Clinical History

• 61 year old male with hypercalcemia, anemia, and new lytic bone lesions involving the left iliac bone and the right 9th rib.
• The patient has a free kappa light chain of 1195 mg/L and a free lambda light chain of 3.2 mg/L with a kappa to lambda ratio of 373. Immunofixation shows an IgG monoclonal protein with kappa light chain specificity.

Molecular Profiling Findings

• Mutations in KMT2C (2 mutations), PTPN11 (2 mutations), WHSC1, PRKAR1A, TP53 (low level), CCNE1, TSHR, POLD1, EGFR, and DNMT3A genes.
• No detectable autosomal chromosomal structural gain or loss by Copy Number Variation (CNV analysis)
• Increased plasma cell mRNA markers CD138 and BCMA.
• Marked increase in CCND1 mRNA, reflecting promoter hijacking, characteristic of t(11;14) CCND1-IgH.
• No evidence of high risk chromosomal abnormalities consisting of t(4;14)(FGFR3/NSD2), t(14;16)(MAF), t(14;20)(MAFB), 1q21 + , del(1p), and del(17p) by RNA fusion or CNV analysis.
• No evidence of mutations in KRAS, NRAS, ATM, ATR, MYC and DIS3.
• Positive B-cell clonality detection (IgHV3.65/IgKV8.61), see figure 1.

Discussion

The mutational profile, elevated mRNA marker levels for plasma cells, and a positive B-cell clonality test are diagnostic of multiple myeloma.
The detection of t (11;14) CCND1-IgH by fusion mRNA is considered an intermediate risk category in multiple myeloma and confers a worse outcome compared to standard-risk myeloma. In addition, t(11;14) myeloma cases have been shown to be particularly sensitive to Bcl-2 inhibitors, making Bcl-2 a potential target in this subtype of myeloma.
This case also showed absence of poor prognostic chromosomal abnormalities consisting of t(4;14), t(14;16), t(14;20), 1q21 + , del(1p), and del(17p), as well as high risk mutations consisting of KRAS, NRAS, ATM, ATR, MYC and DIS3, all of which are typically associated with poor risk multiple myeloma.
The aggregate findings in this case provide comprehensive genomic profiling that is superior to single-site tissue biopsy for diagnosis, prognostic profiling, treatment and longitudinal management due to its less invasiveness and better representation of up-to-date tumor genome abnormalities and tumor genomic diversity.

Download Case Study Brochure (PDF)

References
1. Davies FE, Walker BA. What Is Genomic High-Risk Myeloma? Hemato. 2022; 3(2):287-297. https://doi.org/10.3390/hemato3020021
2. Ferreira, B., Caetano, J., Barahona, F. et al. Liquid biopsies for multiple myeloma in a time of precision medicine. J Mol Med 98, 513–525 (2020). https://doi.org/10.1007/s00109-020-01897-9
3. Liu Y, Guo J, Yi Y, Gao X, Wen L, Duan W, Wen Z, Liu Y, Guan Y, Xia X, Ma L, Fu R, Liu L, Huang X, Ge Q, Lu J. Circulating Tumor DNA: Less Invasive, More Representative Method to Unveil the Genomic Landscape of Newly Diagnosed Multiple Myeloma Than Bone Marrow Aspirates. Cancers (Basel). 2022 Oct 7;14(19):4914. doi: 10.3390/cancers14194914. PMID: 36230837; PMCID: PMC9563595.
4. Li S, Zhang E, Cai Z. Liquid biopsy by analysis of circulating myeloma cells and cell-free nucleic acids: a novel noninvasive approach of disease evaluation in multiple myeloma. Biomark Res. 2023 Mar 8;11(1):27. doi: 10.1186/s40364-023-00469-6. PMID: 36890597; PMCID: PMC9997021.

• 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