Cell-free tumour DNA

Cell-free or circulating tumour DNA (ctDNA) is tumour DNA circulating freely in the blood of a cancer patient. Analysis of the fraction of mutant-alleles from ctDNA compared to normal-alleles from the patients normal genome provides opportunities for minimally-invasive cancer diagnosis, prognosis and tumour monitoring.[1]

ctDNA originates from dying tumour cells[2] and can be present in a wide range of cancers but at varying levels and mutant allele fractions.[3] The ctDNA is highly fragmented to around 170 bp and is cleared rapidly after surgery to remove tumours or chemotherapeutic treatment.[1]

ctDNA testing

Protocols to extract ctDNA generally aim to reduce contamination with normal DNA from leukocytes. This is achieved by rapid processing of whole blood by centrifugation to remove all cells, and analysis of the remaining plasma. The utility of circulating tumor DNA in cancer detection and monitoring has recently been shown via targeted sequencing of plasma.[4] In an oncology setting these recommendations, when combined with the use of a cell stabilisation fluid, such as that found in special ctDNA blood collection tubes can increase the chances of detecting mutations present in ctDNA.[5]

Technologies used for detection of ctDNA[6]
Principle Method Name
PCR based Nested real-time PCR
ARMS / Scorpion PCR
PCR - SSCP
Mutant allele specific PCR
Mass spectrometry
Bi-PAP-A amplification
Digital PCR BEAMing
Droplet-based digital PCR
Microfluidic digital PCR
Targeted Deep Sequencing SafeSeq
TamSeq
Ion-AmpliSeq
CAPP-Seq
OnTarget
Whole genome sequencing Digital karyotyping
PARE

Cell-free DNA was first used medically for Down's syndrome screening using cell-free foetal DNA.

As of March 2016 the US FDA is considering issuing guidance for the licensing of ctDNA tests.[7] At least 5 companies are developing ctDNA tests for cancer diagnosis or screening.[7]

References

  1. 1 2 Kelly, Janis C. (18 November 2014). "ctDNA 'Liquid Biopsy' Could Revolutionize Cancer Care". Medscape.
  2. ↑ Burke, Elizabeth (February 2014). "Circulating tumor DNA: A new generation of cancer biomarkers". National Human Genome Research Institute.
  3. ↑ Karachaliou, Niki; Mayo-de-las-Casas, Clara; Molina-Vila, Miguel Angel; Rosell, Rafael (March 2015). "Real-time liquid biopsies become a reality in cancer treatment". Annals of Translational Medicine. 3 (3): 36. doi:10.3978/j.issn.2305-5839.2015.01.16. PMC 4356857Freely accessible. PMID 25815297.
  4. ↑ Newman, Aaron M.; Bratman, Scott V.; To, Jacqueline; Wynne, Jacob F.; Eclov, Neville C. W.; Modlin, Leslie A.; Liu, Chih Long; Neal, Joel W.; Wakelee, Heather A.; Merritt, Robert E.; Shrager, Joseph B.; Loo, Billy W., Jr.; Alizadeh, Ash A.; Diehn, Maximilian (2014). "An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage". Nature Medicine. 20 (5): 548–554. doi:10.1038/nm.3519. PMC 4016134Freely accessible. PMID 24705333.
  5. ↑ Sherwood, James L.; Corcoran, Claire; Brown, Helen; Sharpe, Alan D.; Musilova, Milena; Kohlmann, Alexander (26 February 2016). "Optimised Pre-Analytical Methods Improve KRAS Mutation Detection in Circulating Tumour DNA (ctDNA) from Patients with Non-Small Cell Lung Cancer (NSCLC)". PLOS ONE. 11 (2): e0150197. doi:10.1371/journal.pone.0150197. PMC 4769175Freely accessible. PMID 26918901.
  6. ↑ Qin, Zhen; Ljubimov, Vladimir A.; Zhou, Cuiqi; Tong, Yunguang; Liang, Jimin (2016-01-01). "Cell-free circulating tumor DNA in cancer". Chinese Journal of Cancer. 35: 36. doi:10.1186/s40880-016-0092-4. ISSN 1944-446X. PMC 4823888Freely accessible. PMID 27056366.
  7. 1 2 Philippidis, Alex (7 March 2016). "Getting Testy Over Liquid Biopsies: CtDNA Tests Attract Interest from Companies, Institutions, and Regulators". Genetic Engineering & Biotechnology News.

Further reading


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