Liquid Biopsy Field Moves Forward But Faces Hurdles

Advancements are rapidly expanding the potential uses for blood-based liquid biopsies, but broad clinical adoption in cancer care hinges on improving the knowledge base of practicing oncologists and gathering prospective data to validate assays, according to experts.

Overall, the field is brimming with discovery and enthusiasm for possible new applications, including plasma-based next-generation sequencing (NGS) assays.

On August 26, 2020, the FDA approved Foundation Medicine’s FoundationOne Liquid CDx for all solid tumors, with multiple companion diagnostic indications.¹ FoundationOne Liquid is an NGS sequencing test that analyzes more than 300 genes and gene signatures, such as microsatellite instability, in cell-free and circulating tumor DNA (ctDNA) from plasma, and can be used to inform therapy selection and clinical trial options for patients.^1-3

It is now indicated as a companion diagnostic for rucaparib (Rubraca) for assessing BRCA1/2 mutation status for patients with metastatic castration-resistant prostate cancer, as well as for gefitinib (Iressa), osimertinib (Tagrisso), and erlotinib (Tarceva) for detecting EGFR exon 19 deletions or exon 21 L858R substitutions in patients with non–small cell lung cancer (NSCLC).

Earlier in August, the FDA approved Guardant360 CDx, also an NGS liquid biopsy, to detect EGFR mutations in circulating cell-free DNA from patients with NSCLC who are candidates for osimertinib therapy.⁴

The approvals come amid continuing development of assays that analyze cell-free ctDNA in 3 key clinical settings: precancer diagnosis and risk monitoring; measuring minimal residual disease (MRD); and guiding therapy choices in recurrent and/or metastatic settings. An international assortment of prospective clinical trials evaluating the use of ctDNA testing in these areas are ongoing (Table).⁵

“Liquid biopsy approaches are potentially transformative in nearly all aspects of oncologic care. There’s potential for these approaches to really improve treatment for just about every patient with cancer,” Maximilian Diehn, MD, PhD, who focuses on developing genomics-based biomarkers, said in an interview with OncologyLive®.

However, more progress must be made before plasma-based assays can be integrated more thoroughly into oncology practice, Diehn and other experts agreed. The crux of these efforts will be physician education, according to Andrew McKenzie, PhD, director of personalized medicine at Sarah Cannon in Nashville, Tennessee. He said that fostering a more comprehensive understanding of liquid biopsy’s utilities and limitations in oncology is a prerequisite for using the information that can be derived from plasma NGS, such as tumor heterogeneity and the presence or absence of subclonal mutations, to the fullest degree.

“I think liquid biopsy is being used a lot more widely in the community oncology setting than most people appreciate, but I don’t know if it’s being used most judiciously in those settings [because] the research is somewhat outpacing the general medical oncologist’s understanding of what these tests are actually doing and showing,” McKenzie said. “I think there’s a significant education gap right now, and if we solve that education gap, we would be able to make a lot more sense out of what these tests are showing us.”

Specifically, a more complete knowledge base would be particularly beneficial in instances of serial liquid biopsies where treating oncologists are looking for resistance mechanisms or new actionable mutations that could have evolved over time, McKenzie explained. “This area is one where we just don’t know enough now to know if that’s the right thing to do or not. I think there’s a place for that, but I would put a word of caution out for doing serial biopsies in spaces where there’s just not documented evidence that it is worth the time or the money,” he said. Closing this “education gap” would also be advantageous as the FDA approves more assays.

More extensive prospective data also are needed to validate assay efficacy, noted Diehn, an associate professor of radiation oncology at Stanford Cancer Institute in Palo Alto, California. “This is the age-old challenge of having a very promising new technology that has a lot of compelling preliminary data, but doesn’t yet have the highest level of evidence for its clinical utility,” Diehn said. “We need data from prospective studies applying liquid biopsy technologies that prove that patients benefit from having liquid biopsies compared with control arms where it is not done. The biggest hurdle to moving liquid biopsies forward faster is our need to generate more prospective evidence of the utility beyond just a noninvasive genotyping in patients with advanced disease.”

The “good news,” Diehn said, is that several prospective studies are already under way. Although these trials typically take years to complete, data from these investigations—if positive—will pave the way for standardization and payer support. “Nearly all of the data we have come from preliminary retrospective studies, which isn’t the level of evidence usually required to get [a new modality] into the standard of care [SOC] or have payers cover it,” Diehn explained.

The exception, McKenzie said, is NSCLC, where prospective data establishing liquid biopsy’s clinical suitability are available. For example, findings from the NILE study (NCT03615443), published in 2019, demonstrated that the Guardant360 CDx assay was as effective as SOC tissue genotyping for the detection of guideline-recommended biomarkers in previously untreated patients with metastatic NSCLC. Additionally, investigators were significantly more likely to complete evaluation for the full biomarker panel with ctDNA testing (268 vs 51 patients; P < .0001). When both liquid and tissue results were available, the concordance rate was greater than 98.2%, with a 100% positive predictive value for ctDNA.⁶

Meredith McKean, MD, MPH, also emphasized that much of the data available on plasma-based tests’ applications has been exploratory. McKean agreed that more prospective data are required to refine liquid biopsy’s various roles in the oncology space, and she noted that findings from these investigations, when available, will help close the educational gap addressed by McKenzie. “This information is going to help clinicians understand how to implement liquid biopsy and how it can change therapy,” said McKean, an investigator for the Melanoma and Skin Cancer Research Program for Sarah Cannon Research Institute at Tennessee Oncology.

As more robust data emerge, McKean expects to see insurance coverage standardized for plasma-based NGS. In the short-term, McKean said, securing coverage has not been as much of an impediment as some might expect. “I have been impressed with the customer support that the companies provide and think they have developed very patient-centric financial assistance programs to help patients,” McKean said. “As a provider, it’s always uncomfortable to order a test for a patient that you’re hoping they can benefit from, not knowing what the financial implications might be, but I think most companies have been very helpful in making sure there is no financial toxicity.”

A recent examination of insurance trends shows a dramatic increase in coverage for ctDNA-based testing panels from 2015, the first instance of payer coverage, to July 2019. Investigators found that 38% of private payer policies (28 of 73) covered ctDNA panel testing for some clinical indications while Medicare local coverage determinations grew to 8 final, 2 draft, and 2 scheduled decisions. Additionally, the number of cancers covered by testing increased to 12 solid tumor types and from single-gene EGFR testing to large panels.⁷

Although the growth in coverage is encouraging the policies are complex and gaps do arise.¹ For instance, investigators noted that policies may not reflect testing that is recommended in guidelines or in research reports. They also pointed out that although there is “a plethora of coverage for the use of ctDNA testing in NSCLC from both private payers and Medicare, the coverage has been primarily for treatment selection, with only 11% of payers with positive coverage including any monitoring indications.”⁷ Notably, FoundationOne Liquid CDx will be covered across all solid tumors for eligible Medicare and Medicare Advantage beneficiaries.¹

Companion Diagnostics

Besides the FoundationOne Liquid CDx and Guardant360 CDx assays, the FDA has approved 2 ctDNA-based companion diagnostics: the cobas EGFR Mutation Test v2, manufactured by Roche, and the therascreen PIK3CA RGQ PCR Kit, developed by Qiagen.

The cobas test, approved on June 1, 2016, was the first plasma-based assay approved as a companion diagnostic in oncology; it is indicated to detect EGFR mutations in patients with NSCLC who are candidates for therapy with erlotinib, gefitinib, and osimertinib.^8,9 The therascreen assay, approved on May 24, 2019, is indicated to identify PIK3CA mutations in patients with advanced breast cancer who are being considered for treatment with alpelisib (Piqray).¹⁰

Although companion diagnostics point to the immediate clinical utility of a test, liquid biopsy results can still shape a patient’s course of treatment, even if the test uncovers an alteration for which no targeted therapy currently exists, explained Irene M. Ghobrial, MD. “Even if the mutation is not targetable, it could be predictive of responses to certain therapies. For example, knowing that someone with multiple myeloma has a 17p deletion or a biallelic p53 deletion, that would be predictive, and you know that this person needs a different approach. You could say, ‘Maybe that patient needs immunotherapy because I know my usual targeted therapy would not work in this case.’ You can still do precision interception even if the target is not targetable yet.”

Discovery of an alteration without an immediate target can also help direct a patient to an appropriate umbrella study or other novel clinical trial where participants are grouped by their mutations and copy number alterations, added Ghobrial, director of the Clinical Investigator Research Program and of the Michele & Stephen Kirsch Laboratory at the Dana-Farber Cancer Institute in Boston, Massachusetts.

Testing for the presence of MRD, the small number of cancer cells that remain in the body during and after treatment and can cause disease recurrence, is another application of liquid biopsy technology that Diehn envisions as “the next major crest” in the modality’s use in oncology.

“In my mind, the next wave for liquid biopsies is going to be detection of MRD after curative-intent treatment. This is a big area of interest with a lot of activity in publications as well as medical meetings,” Diehn said. Notably, Adaptive Biotechnologies’ clonoSEQ Assay, which uses PCR and NGS technology to analyze DNA extracted from bone marrow, was approved in September 2018 to detect MRD in patients with B-cell acute lymphoblastic leukemia or multiple myeloma.¹¹ In August 2020, the assay’s indication was expanded to detect and monitor MRD in the blood or bone marrow of patients with chronic lymphocytic leukemia, making clonoSEQ the first and only in vitro diagnostic to receive FDA clearance to monitor MRD in this disease.¹²

The Push to Change Standard Practice

Although liquid biopsies present less invasive and potentially more informative alternatives to tissue or bone marrow biopsies, they also come with certain limitations. Lower volumes of available cellular content are a complicating factor of liquid biopsy’s potential to detect disease early, according to Diehn. “Cancer screening is a very exciting but also very difficult area because the tumors that you want to detect are small. And, of course, you also need high specificity,” Diehn said. Nevertheless, there is “a lot of promise for liquid biopsy utility in this context,” he added.

False positives are another complication of liquid biopsies and are mainly driven by clonal hematopoiesis of indeterminate potential (CHIP) mutations. CHIP refers to a common, aging-related process in which hematopoietic stem cells acquire mutations that catalyze the formation of a distinct subpopulation of blood cells that carry these mutations. During ctDNA-based liquid biopsy analyses, it is necessary to differentiate between CHIP-associated alterations and tumor-associated mutations to ensure that ctDNA test results do not display a false-positive based on the presence of CHIP in nontumor white blood cells rather than cancerous tumors with genomic aberrations.¹³

A high rate of false negatives in studies of ctDNA testing is noted as a disadvantage of the testing modality in the National Comprehensive Cancer Network guidelines for NSCLC. The guidelines state that ctDNA testing should not be used instead of a histologic tissue diagnosis. However, the guidelines panel said it can be considered if the patient is not able to undergo invasive sampling or if there is insufficient material for molecular analysis in the initial diagnostic setting and follow-up tissue testing is planned. Additionally, the panel noted that study findings suggest that ctDNA testing can detect mutations not otherwise identified in metastatic NSCLC.¹⁴

McKenzie believes the guidelines open the door for broader use of ctDNA testing. The guidelines “indicate that you should be testing for BRAF, ALK, ROS, and the rest of the [known drivers] as part of a broad panel, but they don’t specify if that’s tissue- or plasma-based,” he said. The result, he added, is “a little bit of a gray area within those guidelines, for example, that may be spurring doctors on to whatever is easiest or most convenient for them to quickly get the answers.” As the field continues to move liquid biopsy technology forward, McKenzie is “hopeful that [liquid biopsy] tests will become a part of guidelines.”

Meanwhile, the portfolio of molecularly targeted treatment options for NSCLC continues to expand, making liquid biopsy become an increasingly attractive diagnostic option for clinicians to use to identify patients with actionable alterations and subsequently select suitable precision therapies, Charu Aggarwal, MD, MPH, said during a presentation at the virtual 4th Annual International Congress on Oncology and Pathology™.¹⁵

“Plasma NGS is a powerful tool for targeted therapy. [It] is an easy, fast, and minimally invasive way to rule in a mutation. I suggested an algorithm which I use in my clinic in case of inadequate or unavailable tissue. [This has] truly given us an [alternate testing] option and a way to offer personalized therapy to our patients,” said Aggarwal, the Leslye M. Heisler Associate Professor for Lung Cancer Excellence at the Perelman School of Medicine at the University of Pennsylvania.

The prospective TRACERx study (NCT01888601) has played a pivotal role in illustrating the potential of plasma-based NGS in NSCLC. Findings published in 2017 demonstrated that MRD indicative of recurrence could be detected in plasma at a median of 70 days before relapse could be confirmed via CT imaging, supporting the use of liquid biopsy technology in this setting.¹⁶

Data from other clinical investigations of liquid biopsy’s benefit in NSCLC have further underscored its diagnostic utility. Notably, results from a prospective single-center study authored by Aggarwal and colleagues showed that the addition of ctDNA liquid biopsy to tissue-based testing markedly improved investigators’ ability to identify targetable mutations in patients with stage IV NSCLC, facilitating better delivery of molecularly guided therapy. Actionable mutations were detected in 20.5% of 229 patients who first underwent tissue testing. When plasma-based NGS was added to the diagnostic sequence, 35.8% of patients had a targetable alteration identified.¹⁷

Expanding the Tool Kit

Moving forward, liquid biopsy approvals are expected to increase as the demand for plasma- based technologies rises in oncology. To date, liquid biopsy has been used primarily to detect circulating tumor cells and ctDNA. Other biomarkers of clinical interest include circulating RNA, circulating microRNAs, exosomes, platelets, and plasma/serum metabolites.^18,19

In terms of FDA oversight, the companion diagnostic category is among several pathways for gaining the agency’s approval to market an assay. Tests also can be approved for marketing through the FDA’s 510(k) program and through a third-party reviewer, the New York State Department of Health (NYSDOH).²⁰

The FDA also has started the Breakthrough Devices Program, which enables tests to be reviewed on a priority basis if they offer new technology or significant advantages over existing methods. One such assay with breakthrough status is Signatera, a ctDNA test that facilitates treatment monitoring and MRD assessment in patients previously diagnosed with cancer.

The NGS assay, manufactured by Natera, demonstrated its efficacy in the phase 2 INSPIRE trial (NCT02644369) that evaluated pembrolizumab (Keytruda) monotherapy in 70 patients with advanced cancer.

Investigators used Signatera to assess ctDNA at baseline and again at the start of the third treatment cycle. Findings showed that Signatera detected molecular traces of ctDNA in 68 of 70 patient blood samples at baseline for a 97% sensitivity rate. Results demonstrated a strong correlation between changes in ctDNA amount and overall survival (adjusted HR, 0.38; P = .004), progression-free survival (adjusted HR, 0.47; P = .006), and overall clinical response rate, indicating that ctDNA could be a clinically meaningful biomarker in immunotherapy-receiving patients with various cancers.²¹

Data presented at the 2020 American Society of Clinical Oncology Virtual Scientific Program further affirmed Signatera’s high-fidelity detection of ctDNA, demonstrating that the test identified patients with a high risk of recurrence with a sample-level specificity higher than 99.8% in postoperative ctDNA analyses. The assay was used in a prospective, multicenter cohort study of 193 patients with resected stage I to III colorectal cancer. Preoperative ctDNA was detected in 90% (166 of 185) of patients. Serial ctDNA evaluation captured MRD up to a median of 9.08 months ahead of radiologic relapse with a 79.1% sensitivity and 99.0% specificity.²²

Signatera is currently available for clinical and research use. In August 2019, Medicare issued a positive draft local coverage determination approving Signatera for patients with stage II or stage III colorectal cancer.^23,24 A final decision on the proposed coverage is due this year, according to Natera.²³ The draft decision indicates that advances in coverage can be achieved without prospective study data, although these data are often necessary to secure clinical guideline support and insurance coverage, according to Diehn. “This is an extremely exciting time in this field, which is very young, and I think we’re just starting to scratch the surface of what is possible,” Diehn concluded.

References

1. FDA approves Foundation Medicine’s FoundationOne Liquid CDx, a comprehensive pan-tumor liquid biopsy test with multiple companion diagnostic indications for patients with advanced cancer. News release. Foundation Medicine. August 26, 2020. Accessed August 26, 2020. https://bit.ly/2EFrbhu

2. Provider FAQs. Foundation Medicine. Accessed August 17, 2020. https://www.foundationmedicine.com/faq/provider-faqs 

3. FoundationOne Liquid. Foundation Medicine. Accessed August 17, 2020. https://www.foundationmedicine.com/test/foundationone-liquid 

4. FDA approves first liquid biopsy next-generation sequencing companion diagnostic test. FDA. August 7, 2020. Accessed August 17, 2020. https://bit.ly/31AAEi0

5. Cescon DW, Bratman SV, Chan SM, Siu LL. Circulating tumor DNA and liquid biopsy in oncology. Nat Cancer. 2020;1:276-290. doi:10.1038/s43018-020-0043-5

6. Leighl NB, Page RD, Raymond VM, et al. Clinical utility of comprehensive cell-free DNA analysis to identify genomic biomarkers in newly diagnosed metastatic non–small cell lung cancer. Clin Cancer Res. 2019;25(15):4691-4700. doi:10.1158/1078-0432.CCR-19-0624

7. Douglas MP, Gray SW, Philips KA. Private payer and Medicare coverage for circulating tumor DNA testing: a historical analysis of coverage policies from 2015 to 2019. J Natl Compr Canc Netw. 2020;18(7):866-872. doi:10.6004/jnccn.2020.7542

8. FDA grants first liquid biopsy test approval to the Roche cobas EGFR Mutation Test v2. News release. FDA; June 1, 2016. Accessed August 3, 2020. https://diagnostics.roche.com/us/en/news-listing/2016/fda-grants-first-liquid-biopsy-approval-to-the-roche-cobas-egfr-mutation-test-v21.html

9. The cobas EGFR Mutation Test v.2. Cobas. Updated December 23, 2019. Accessed August 5, 2020. http://cobasegfrtest.com/

10. The therascreen PIK3CA RGQ PCR Kit – P190001 and P190004. FDA. Updated June 11, 2019. Accessed August 3, 2020. https://www.fda.gov/medical-devices/recently-approved-devices/therascreen-pik3ca-rgq-pcr-kit-p190001-and-p190004

11. Evaluation of automatic class II designation for clonoSEQ Assay. decision summary. FDA. September 28, 2018. Accessed August 18, 2020.

12. Adaptive Biotechnologies receives expanded FDA clearance for the clonoSEQ Assay to assess minimal residual disease (MRD) in patients with chronic lymphocytic leukemia. News release. Adaptive Biotechnologies Corporation; August 6, 2020. Accessed August 6, 2020. https://investors.adaptivebiotech.com/news-releases/news-release-details/adaptive-biotechnologies-receives-expanded-fda-clearance

13. Koo KM, Mainwaring PN. The role of circulating tumor DNA testing in breast cancer liquid biopsies: getting ready for prime time. Future Med. 2020;9(1). doi:10.2217/bmt-2020-0003

14. NCCN. Clinical Practice Guidelines in Oncology. Non-small cell lung cancer, version 6.2020. Accessed August 17, 2020. https://www.nccn.org/professionals/physician_gls/pdf/nscl.pdf

15. Aggarwal C. ctDNA and the “Liquid First” Concept. Presented at: 4th Annual International Congress on Oncology and Pathology™; June 20, 2020; virtual. Accessed August 6, 2020.

16. Abbosh C, Birbak NJ, Wilson GA. Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature. 2017;545(7655):446-451. doi:10.1038/nature22364

17. Aggarwal C. Thompson JC, Black TA, et al. Clinical implications of plasma-based genotyping with the delivery of personalized therapy in metastatic non–small cell lung cancer. JAMA Oncol. 2019;5(2):173-180. doi:10.1001/jamaoncol.2018.4305

18. Alix-Panabières C. The future of liquid biopsy. Nature. 2020;579(7800):S9. doi:10.1038/d41586-020-00844-5

19. Revelo AE, Martin A, Velasquez R, et al. Liquid biopsy for lung cancers: an update on recent developments. Ann Transl Med. 2019;7(15):349. doi:10.21037/atm.2019.03.28

20. FDA unveils a streamlined path for the authorization of tumor profiling tests alongside its latest product action. News release. FDA; November 15, 2017. Accessed August 18, 2020. https://bit.ly/2O6cYN9

21. Data presented at ASCO shows Natera’s Signatera test detects immunotherapy treatment response in metastatic cancers. News release. Natera; June 3, 2019. Accessed August 5, 2020. https://www.natera.com/press-releases/data-presented-asco-shows-nateras-signatera-test-detects-immunotherapy-treatment

22. Tarazona N, Henriksen TV, Carbonell-Asins JA, et al. Circulating tumor DNA to detect minimal residual disease, response to adjuvant therapy, and identify patients at high risk of recurrence in patients with stage I-III CRC. J Clin Oncol. 2020;38(suppl 15; abstr 4009). doi:10.1200/JCO.2020.38.15_suppl.4009

23. New study shows benefit of using Signatera technology for personalized monitoring in gastrointestinal cancer. News release. Natera; April 2, 2020. Accessed August 5, 2020. https://www.natera.com/press-releases/new-study-shows-benefit-using-signatera™-technology-personalized-monitoring

24. Medicare issues positive draft local coverage determination for Natera’s Signatera MRD test in colorectal cancer. News release. Natera; August 22, 2019. Accessed August 6, 2020. https://www.natera.com/press-releases/medicare-issues-positive-draft-local-coverage-determination-nateras-signatera™-mrd