Improving cancer outcomes- it’s written in blood

Genome sequencing of tumor biopsy tissue can identify the mutations that cause cancer and indicate treatments. However, genomic sequencing can also be used to detect DNA shed by the tumor into the blood.

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Authors: Donald J. Johann, Ira Deveson, Timothy Mercer, Joshua Xu

The ability to use a routine blood draw, termed a liquid biopsy, to provide the same diagnostic information included in a tissue biopsy has tremendous ramifications.  In our referenced paper an international team reports the findings of a proficiency study utilizing five commercially available assays for liquid biopsy testing.  This study helps lay the foundation for a transformation in oncology practice, clinical trials and drug development with the analytical validation of assays based on circulating tumor DNA (ctDNA). 

In our study, the accuracy and reproducibility of ctDNA assays is reported using a unique set of reference materials, associated analytical framework, and suggested best practices.  Generally, the earlier a cancer can be detected the better the outcome.  Likewise, poor clinical outcomes are linked to an inability to detect cancer at an early stage.  Our study also begins to lay the foundation for additional applications including a potential cancer screening assay.

“Progress in science depends on new techniques, new discoveries and new ideas, probably in that order”, is a quote credited to Sydney Brenner, the 2002 Nobel Laureate for work on the genetic code.  In a stepwise fashion, the ability to analyze DNA by sequencing eventually led to the Human Genome Project, an enormously successful public – private partnership that has resulted in over a one million fold reduction in the price and time associated with sequencing [1].  Next, research from The Cancer Genome Atlas (TCGA) continues to reveal the molecular basis of cancer and provide a basic science framework for improved molecular diagnostics and therapeutics [2, 3].  Today, Next Generation Sequencing (NGS) assays are tools of clinical medicine due to their price (about the cost of a CT scan) and turn-around-time allowing for medical decision making.

The Sequencing Quality Control Phase 2 (SEQC2) consortium sponsored this liquid biopsy proficiency study.  SEQC2 builds on the foundation and frameworks put forth by the Human Genome Project and the many studies from TCGA.   SEQC2 is an international group, composed of members from academia, industry, and led by the FDA [4].  The aims of this group are the development of best practices, protocols, and quality metrics for NGS-based diagnostic assays, which support precision medicine and regulatory science.  SEQC2 is funded by United States Congressional 21st Century Cures Act [5].  It is intended to support cancer research, such as the development of more sensitive diagnostic tests along with research that has the potential to transform the scientific field.  This liquid biopsy proficiency study was conducted by a SEQC2 dedicated subgroup.

We are learning that the blood contains informative DNA molecules that reflect the ongoing physiologic state of tissues, especially when a cancerous process is present.  As cells turnover a record or signature is left on nucleic acid material and is shed into the blood [6].  The specificity of these signatures can now be used for diagnostic monitoring and therapeutic assignment purposes.  What may have been thought of as cellular waste is really a diagnostic treasure trove.  In essence, a liquid biopsy is an application of deep sequencing using nucleic acids obtained from a routine blood draw. CtDNA is a tumor shed product [7].  The speed, safety, reduction in costs, and potential for repeat/longitudinal analyses for liquid biopsies verses conventional tumor tissue biopsies are significant and transformational.

An illustration of how ctDNA assays may be used to guide medical decision making is shown in Figure 1.  Depicted is the pattern of tumor growth over time measured by ctDNA found in the blood.  This is shown following diagnosis (Dx), initial treatment, response to treatment and, relapse with the acquisition of resistance mutations.  Currently, the state/phase of ctDNA-based clinical application is located on the right most portion of the diagram (shaded yellow), principally under “Metastasis & Relapse”, since there are FDA approvals for these indications.  Given the results of this proficiency study and further maturation of ctDNA assay development, there is an opportunity to shift applications of ctDNA to early diagnosis stages of the cancer disease process (light blue shaded).  Using ctDNA as part of the consideration for Adjuvant Therapy, Surveillance for cancer recurrence, and more effective Minimal Residual Disease strategies, will allow for deeper and more durable remissions.  Guidance to avoid “over treatment” of patients and reductions of severe toxicities and treatment related malignancies are critical needs that liquid biopsies may help to address.

Prospective clinical trials to assess the association of ctDNA with therapeutic response in early stage cancers are rapidly emerging.  Combination immune checkpoint inhibitor (ICI) with chemotherapy for resected stage II/III non-small cell lung cancer (MERMAID-1 and 2) are phase III studies [8, 9].  The COBRA study is a phase II/III surveillance study for resected stage IIA colon cancer [10].  The IMvigor011 study involves ICI therapy vs placebo for muscle invasive bladder cancer having ctDNA assay positive results [11]. These are just a few of the new and advanced clinical trials that are already employing innovative liquid biopsy approaches. Additionally, consortia such as BloodPAC [12] and ctMoniTR [13] are actively engaged in the dynamic liquid biopsy field.

Our liquid biopsy study advances the understanding of analytical performance involving ctDNA NGS assays.  Best practice guidelines are provided.  Ultimately clinical utility is required and this study is a deliberate step in that direction through the establishment and use of a unique set of reference materials along with a corresponding analytical framework involving standardized proficiency testing.

References

  1. Lander, E.S., et al., Initial sequencing and analysis of the human genome. 2001.
  2. Tomczak, K., P. Czerwińska, and M. Wiznerowicz, The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge. Contemporary oncology, 2015. 19(1A): p. A68.
  3. Weinstein, J.N., et al., The cancer genome atlas pan-cancer analysis project. Nature genetics, 2013. 45(10): p. 1113-1120.
  4. SEQC2. Sequencing Quality Control Phase II (SEQC2). 2021 [cited 2021 March 25, 2021]; Available from: https://www.fda.gov/science-research/bioinformatics-tools/microarraysequencing-quality-control-maqcseqc.
  5. US_Congress. 21st Century Cures Act. 2016 [cited 2021; Available from: https://www.congress.gov/114/bills/hr34/BILLS-114hr34enr.pdf
  6. Diehl, F., et al., Circulating mutant DNA to assess tumor dynamics. Nature medicine, 2008. 14(9): p. 985-990.
  7. Bettegowda, C., et al., Detection of circulating tumor DNA in early-and late-stage human malignancies. Science translational medicine, 2014. 6(224): p. 224ra24-224ra24.
  8. MERMAID-1. Phase III Study to Determine the Efficacy of Durvalumab in Combination With Chemotherapy in Completely Resected Stage II-III Non-small Cell Lung Cancer (NSCLC) (MERMAID-1). [cited 2021 March 25, 2021]; Available from: https://clinicaltrials.gov/ct2/show/NCT04385368?term=MERMAID-1&draw=2&rank=1.
  9. MERMAID-2. Phase III Study to Determine Efficacy of Durvalumab in Stage II-III Non-small Cell Lung Cancer (NSCLC) After Curative Intent Therapy. (MERMAID-2). March 25, 2021]; Available from: https://clinicaltrials.gov/ct2/show/NCT04642469?term=MERMAID-2&draw=2&rank=1.
  10. COBRA. Circulating Tumor DNA Testing in Predicting Treatment for Patients With Stage IIA Colon Cancer After Surgery. March 25, 2021]; Available from: https://clinicaltrials.gov/ct2/show/NCT04068103?term=COBRA&cond=Colon+Cancer+Stage+II&draw=2&rank=1.
  11. IMvigor011. A Study of Atezolizumab Versus Placebo as Adjuvant Therapy in Patients With High-Risk Muscle-Invasive Bladder Cancer Who Are ctDNA Positive Following Cystectomy (IMvigor011). March 25, 2021]; Available from: https://clinicaltrials.gov/ct2/show/NCT04660344?term=IMvigor011&cond=Bladder+Cancer&draw=2&rank=1.
  12. BloodPAC. Blood Profiling Atlas in Cancer. 2021]; Available from: https://www.bloodpac.org/.
  13. FoCR. Friends of Cancer Research Launches ctMoniTR, New Project Aims to Harmonize ctDNA for Monitoring Treatment Response. 2019 March 25, 2021]; Available from: https://friendsofcancerresearch.org/news/friends-cancer-research-launches-ctmonitr.

Donald Johann

Associate Professor, University of Arkansas for Medical Sciences