Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies

Two recent studies highlighted the emergence of several independent clones carrying heterogeneous patterns of KRAS and NRAS mutations associated with acquired resistance to EGFR blockade.

“two recent studies have highlighted the emergence of several independent clones carrying heterogeneous patterns of KRAS and NRAS mutations concomitantly associated with acquired resistance to EGFR blockade [40, 41].”

BRAF mutations can be detected noninvasively by ctDNA analysis in patients who objectively responded to anti-EGFR therapy but subsequently relapsed.

“BRAF mutations could be also detected noninvasively by ctDNA analysis, together with concomitant KRAS and NRAS mutations [40, 41], in patients who objectively responded to anti-EGFR therapy but subsequently relapsed.”

Two mutations in the EGFR kinase domain (codons 714 and 794) were identified as circulating mutations by cell-free DNA analysis.

“Two mutations in the EGFR kinase domain (codons 714 and 794), which were not detected before EGFR blockade, were identified as circulating mutations by cell-free DNA analysis.”

Proof of principle has been established that ctDNA analysis could complement tumor biopsy and provide an early warning of acquired resistance.

“however, the proof of principle that such an approach could complement tumor biopsy and provide an early warning of acquired resistance has been established [38, 41, 136].”

ctDNA analysis can offer a high degree of sensitivity and specificity to monitor the emergence of drug resistance during treatment.

“Such limitations could be overcome by less-invasive analysis of circulating tumor DNA, which can offer a high degree of sensitivity and specificity to monitor the emergence of drug resistance during the course of treatment [41, 135].”

The blood analyses are limited because ctDNA assays are plasma-based while TCGA blood may be whole blood/buffy coat, and mbDNA distribution among blood compartments is unknown.

“These analyses are limited by the fact that ctDNA assays are plasma-based rather than whole-blood derived45,46, and the distribution of mbDNA among blood compartments is unknown.”

After filtering out ~70% of TCGA patients with ≥1 alteration targeted by Guardant360 or FoundationOne Liquid, blood mbDNA models retained high discrimination for most remaining cancer types.

“We further used gene-lists from the Guardant360® and FoundationOne® Liquid assays45,46 to filter out TCGA patients with ≥1 targeted modification (~70%; Extended Data Figs. 8c–e) and found high discriminatory performances using the same ML approach for most remaining cancer types”

Digital PCR assays for ctDNA have high sensitivity and specificity but are typically limited to hotspot mutations in a few genes and cannot interrogate the full spectrum of acquired resistance mutations.

“Digital polymerase chain reaction assays have been developed with high sensitivity and specificity for detection of variants in ctDNA (24, 27), however, these approaches are typically limited to hotspot mutations in a few genes, and cannot interrogate the full spectrum of mutations that may emerge in the setting of acquired resistance during targeted therapy (28).”

ctDNA is readily detectable in lung cancer patient blood.

“Moreover, ctDNA is readily detectable in lung cancer patient blood (20, 27, 29, 30), and sensitivity of variant detection was recently shown to be higher in ctDNA than CTCs (25).”