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Liquid Biopsies: Non-Invasive Cancer Detection

  • Writer: sdshinghal
    sdshinghal
  • Jan 5, 2021
  • 4 min read

Note: This is a republication of a blog post I wrote for Strand Life Sciences, published on 5/1/2021. The original can be found here.


When it comes to diagnosing a cancer, clinicians typically choose to biopsy the tumour. This involves an invasive surgery in which a sample of the tumour tissue is resected for analysis. While beneficial, this surgery can take a toll on the patient, especially if they are older or have other co-morbidities. In some situations surgery may not even be an option.


This is where liquid biopsies come in. As a tumour grows, it tends to shed old cells to replace them with new ones. Some of these cells degrade and ‘leak’ their contents — including their DNA — into their surroundings. The fluid (e.g. blood, saliva, cerebro-spinal fluid, and so on) surrounding the tumour will then circulate these shed cells and degraded contents around the body. These shed cancerous cells are called circulating tumour cells or CTCs, and the shed DNA is known as cell-free circulating tumour DNA or ctDNA [1]. By assaying and sequencing CTCs and ctDNA, researchers can detect the type of cancer the DNA encodes for.



Unfortunately, the central issue to this is the process of obtaining and recognizing the ctDNA. When taking a biopsy from a patient, the tissues can contain as low as 5% tumour content [2]. This may also change depending on the site of biopsy and biopsy method. However, ctDNA percentage depends on both the size and stage of the tumour. For instance, a patient with a stage 1 disease may have less than 10 copies of tumour mutations per 5ml of plasma, whereas a patient at a later stage can have up to 100 copies of tumour mutations. A 10ml blood draw (of which ~5.5ml is plasma) contains only about 10 copies of the cancer mutations. However, these 10 copies are buried within ~100 ng of ctDNA. [3]. Furthermore, tumour tissues tend to be made up of different subpopulations of cancerous cells. Therefore, depending on the variant allele frequency (VAF) — how common the cancer variant of interest is — this number can drastically decrease. These VAFs can be as low as 0.1% in some cases, although are typically a little higher — around 2% [4].

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This means that at a lower limit (in early stage cancers), we are trying to detect variants present at <1% frequency (detecting a mutant at 2% VAF from the low concentration of mutations present within the ctDNA — 10 copies per 5ml ). For instance, patients with Non-Small Cell Lung Cancers (NSCLC), typically have a ctDNA concentration of <0.5% [5]. These microscopic levels mean that you will require a high coverage to detect such variants. However, high depth sequencing will also mean lots of noise!



References

  1. Bettegowda, C., Sausen, M., Leary, R. J., Kinde, I., Wang, Y., Agrawal, N., Bartlett, B. R., Wang, H., Luber, B., Alani, R. M., Antonarakis, E. S., Azad, N. S., Bardelli, A., Brem, H., Cameron, J. L., Lee, C. C., Fecher, L. A., Gallia, G. L., Gibbs, P., Le, D., … Diaz, L. A., Jr (2014). Detection of circulating tumor DNA in early- and late-stage human malignancies. Science translational medicine, 6(224), 224ra24. https://doi.org/10.1126/scitranslmed.3007094

  2. Izumchenko, E., Hasina, R., Hariharan, A., Shanmugam, A., Irusappan, S., & Maji, S. et al. (2020). Detection of somatic mutations in saliva of patients with oral cavity squamous cell carcinoma. Journal Of Clinical Oncology, 38(15_suppl), 6562–6562. https://doi.org/10.1200/jco.2020.38.15_suppl.6562

  3. Chen, M., Zhao, H. Next-generation sequencing in liquid biopsy: cancer screening and early detection. Hum Genomics 13, 34 (2019). https://doi.org/10.1186/s40246-019-0220-8

  4. Dagogo-Jack, I., Shaw, A. Tumour heterogeneity and resistance to cancer therapies. Nat Rev Clin Oncol 15, 81–94 (2018). https://doi.org/10.1038/nrclinonc.2017.166

  5. Newman, A. M., Bratman, S. V., To, J., Wynne, J. F., Eclov, N. C., Modlin, L. A., Liu, C. L., Neal, J. W., Wakelee, H. A., Merritt, R. E., Shrager, J. B., Loo, B. W., Jr, Alizadeh, A. A., & Diehn, M. (2014). An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nature medicine, 20(5), 548–554. https://doi.org/10.1038/nm.3519

Further Reading

  1. Paliogiannis, P., Attene, F., Cossu, A., Defraia, E., Porcu, G., Carta, A., Sotgiu, M. I., Pazzola, A., Cordero, L., Capelli, F., Fadda, G. M., Ortu, S., Sotgiu, G., Palomba, G., Sini, M. C., Palmieri, G., & Colombino, M. (2015). Impact of tissue type and content of neoplastic cells of samples on the quality of epidermal growth factor receptor mutation analysis among patients with lung adenocarcinoma. Molecular medicine reports, 12(1), 187–191. https://doi.org/10.3892/mmr.2015.3347

  2. Palmirotta, R., Lovero, D., Cafforio, P., Felici, C., Mannavola, F., Pellè, E., Quaresmini, D., Tucci, M., & Silvestris, F. (2018). Liquid biopsy of cancer: a multimodal diagnostic tool in clinical oncology. Therapeutic advances in medical oncology, 10, 1758835918794630. https://doi.org/10.1177/1758835918794630

  3. Kustanovich, A., Schwartz, R., Peretz, T., & Grinshpun, A. (2019). Life and death of circulating cell-free DNA. Cancer biology & therapy, 20(8), 1057–1067. https://doi.org/10.1080/15384047.2019.1598759

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