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Fig. 6 | Molecular Cancer

Fig. 6

From: A clinician’s handbook for using ctDNA throughout the patient journey

Fig. 6

A personal viewpoint on future plasma DNA analyses: one single dataset, an impressive number of analysis opportunities from cfDNA. In the future, there is little doubt that we will be sequencing whole patient genomes. Although current precision cancer medicine programs predominantly rely on gene panel sequencing, the decreasing cost of WGS will soon provide an attractive alternative, replacing stand-alone cancer diagnostics tests that require separate validation and standardization procedures. From a moderate sequencing coverage of 30-35x, we will be able to harvest cfDNA information from a single dataset, encompassing analysis possibilities ranging from personalized mutation tracking to tissue deconvolution. However, as methylation markers serve as the current predominant tissue-specific identifiers, it may be that whole-genome bisulfite sequencing (WGBS) provides an alternative to WGS for tissue deconvolution purposes. The complex array of data that can be obtained from diverse WGS analyses will represent multi-dimensional data to be subjected to feature extraction and various machine learning approaches. Ultimately, it will be possible to develop a model capable of distinguishing cfDNA that was derived from blood of a healthy individual and cfDNA derived from a patient with cancer. In the latter case, appropriate models may allow for tumor classification/subtyping, assessment of tumor evolution and identification of druggable targets or resistance markers. Furthermore, this would also open up exciting avenues for the analysis of cfDNA that extend beyond application in oncology

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