Liquid Biopsy, the detection of circulating tumor DNA in peripheral blood, has been a hot topic in cancer and will keep its momentum in the foreseeable future. The majority of the liquid biopsy tests is focused on the detection of sequence variants in tumors, such as SNVs or indels. Copy number aberrations (CNAs), with its great importance in cancer genomics, is still not a main topic in liquid biospy. Here we report an article that sheds light on this exciting front: Detection of copy number alterations in cell-free tumor DNA from plasma (http://www.sciencedirect.com/science/article/pii/S2214647416300617?via%3Dihub)
In this study, SNP microarrays (Affymetrix) were used to generate whole-genome copy number profiles from plasma ccfDNA (OncoScan) and paired tumor biopsies (CytoScan) from ten patients with metastatic cancers. Nexus Copy Number software (BioDiscovery) was then used to analyze and visualize the copy number and LOH events. As shown in the picture below, the results between tumor tissue DNA (tDNA) and ccfDNA are in very good agreement. After testing several DNA input amounts, a minimum of 20ng of ccfDNA was used and the samples were correctly assessed for somatic copy number aberrations (SCNAs), ploidy, and aberrant cell fraction.
The authors then discussed the resolution in SCNAs detected in ccfDNA and in tumor biopsies, detection of clinically relevant SCNAs in ccfDNA, as well as that the presumptive non-cancerous cell apoptosis can bias the diagnostic power of ccfDNA.
They concluded that the precise detection of copy number aberrations in ccfDNA from liquid biopsies has a great potential to be implemented in the cancer diagnostics within a short time. However, more cohort studies on this front are needed to further validate this method.