Trends in Cancer
ReviewTechnical and biological constraints on ctDNA-based genotyping
Section snippets
The emerging clinical need for ctDNA profiling in metastatic prostate cancer
Cell-free ctDNA in peripheral blood is an important new biomarker source in oncology. Early detection of plasma ctDNA promises to improve cancer diagnosis, while quantification of ctDNA in people with cancer can prognosticate and monitor the response to therapeutic interventions (Figure 1A,B, Key figure) [1., 2., 3., 4., 5., 6., 7., 8., 9., 10.]. Characterization of genomic alterations in ctDNA is enabling a greater understanding of metastatic disease biology and beginning to help predict drug
Assay design: a tradeoff between breadth and cost
The methodology for cell-free DNA (cfDNA) profiling must match the intended clinical application. Early diagnosis of cancer, the detection of minimal residual disease or treatment response, and the characterization of genomic alteration status are each associated with different optimal approaches that can also differ by cancer type and patient population.
DNA-sequencing approaches can be described by their depth and breadth (Figure 1C). Depth refers to the average redundant read support per
ctDNA% influences results interpretation
Independent of panel design, per-sample ctDNA% is a determinant of sensitivity, specificity, and limits of detection, which may differ for different types of genomic alterations (Figure 2A,B). Accurate ctDNA% estimates are particularly important for distinguishing true from false negatives. True negatives (i.e., the absence of a given alteration despite sufficient ctDNA% to detect the alteration) do not require further confirmatory testing. However, potential false negatives due to low ctDNA%
cfDNA sequencing without a matched normal
Unlike most research tools, clinical assays rarely incorporate patient germline samples into analysis [37,66,67]. Without a matched normal, germline and somatic variants are less easily distinguished [37,66]. Failure to discriminate germline from somatic status is not a major issue for individual variants (e.g., pathogenic BRCA2 mutations), since the clinical relevance of any single-lesion biomarker usually stems from its functional effect. Rather, this failure is liable to reduce the accuracy
Signature approaches
As described above, results of testing for individual mutations or CNVs may be unreliable. However, alterations to some classes of genes are associated with patterns of genome-wide ‘scarring’ (i.e., mutation signatures), creating orthogonal opportunities for detection [83,84]. For example, signatures of HRR deficiency may indicate vulnerability to PARP inhibitors, while signatures of defective DNA mismatch repair are a putative predictive biomarker for immune-checkpoint inhibitor response [40,47
Concluding remarks
In metastatic cancers with expanding therapeutic options, ctDNA screening offers a practical strategy to determine genomic biomarker status. Despite the excitement, the integration of ctDNA testing into routine clinical care for people with metastatic prostate or other cancers is encumbered by technical and biological complexities (Box 3). In particular, low ctDNA% is common and magnifies the known technical limitations of sequencing and bioinformatic methods, which are usually less relevant in
Declaration of interests
A.W.W. has served on advisory boards and/or received honoraria from AstraZeneca, Astellas, Janssen, and Merck. A.W.W.’s laboratory has contract research agreements with Janssen and ESSA Pharma. C.H. has no interests to declare.
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