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Correlation of Next-Generation Sequencing and PCR Analysis of ctDNA with Clinical Outcomes and Emerging Mutations Linked to Drug Resistance

2020 Year in Review: Cholangiocarcinoma — December 19, 2020

Preclinical data indicate that genetic analysis of ctDNA from patients with advanced CCA harboring IDH mutations was concordant with those of tissue samples and could detect emerging mutations associated with treatment resistance.

One of the challenges faced by clinicians when trying to diagnose CCA is obtaining enough tumor tissue to conduct molecular-profiling studies. A repeated biopsy could potentially be performed. However, some tumors may be difficult or dangerous to reach to obtain the necessary tissue. An alternative to obtaining tumor tissue is to perform blood testing for circulating tumor DNA (ctDNA), which identify important molecular markers that could be missed if a repeat biopsy is difficult to perform.

It can be difficult to detect DNA variations in the blood when the amount of ctDNA is too low. This can be a drawback of ctDNA testing. However, oncologists and pathologists recognize the benefit of this ctDNA testing for a number of reasons. Primary cancers or cancer recurrence can be screened for and detected early, the effectiveness of the cancer treatment can be assessed, and treatment-resistant genetic variations can be identified.

At this year’s annual meeting of the American Association for Cancer Research, Morten Lapin, PhD, MS, Department of Investigational Cancer Therapeutics, M.D. Anderson Cancer Center, Houston, TX, and colleagues presented their recent study results. They sought to determine whether the ctDNA from patients with advanced CCA and isocitrate dehydrogenase (IDH) mutation was concordant with tissue samples of the same patients. Dr Lapin and colleagues also sought to establish whether ctDNA could be associated with clinical outcomes and could detect emerging mutations associated with therapeutic resistance.

A total of 32 patients with an IDH1 or IDH2 mutation were included in the study. The detection of ctDNA in these study patients was performed at baseline, while the patients were receiving therapy with an IDH inhibitor, and at disease progression during active therapy. Droplet digital polymerase chain reaction (ddPCR) was used to perform molecular profiling of ctDNA; this produces more precise, reproducible, and statistically significant results than quantitative PCR. Targeted digital next-generation sequencing was used to test baseline and disease progression ctDNA samples for oncogenic aberrations in 74 genes.

The baseline results from the ctDNA analysis were compared with those of the molecular profiles of archival biopsy tissue specimens to establish concordance and sensitivity. Patients’ clinical outcomes were compared with the variant allele frequency, which is a surrogate measure of the proportion of DNA molecules carrying a specific DNA variant.

Samples from patients with progressive disease were analyzed for the emergence of mutations possibly associated with treatment resistance. Researchers also analyzed the rates of known simultaneous mutations other than IDH.

The detection of IDH1 and IDH2 mutations was well aligned between patients who had ddPCR and those who had next-generation sequencing testing (84% and 83%, respectively). Patients with variant allele frequency values less than the median had longer times to treatment nonresponse than did those patients with higher than the median variant allele frequency based on samples examined at baseline for IDH mutation–positive ctDNA. Similarly, patients with a low amount of ctDNA for all detected molecular alterations via variant allele frequency at baseline had longer times to treatment nonresponse than did patients with high combined variant allele frequency.

In addition, in serially collected samples evaluated by ddPCR, changes in the quantity of IDH mutation–positive ctDNA showed that patients with a decreased variant allele frequency of IDH-positive ctDNA versus patients with no change or an increase in IDH-positive ctDNA had a trend toward longer survival (P = .06). However, longer time to treatment nonresponse (P = .4) was not evident.

No IDH isoform switching was detected in patients with disease progression during therapy. However, mutations that were not detected at baseline in these patients were exposed via next-generation sequencing of ctDNA. The mutations most often detected were TP53 and ARID1.

Source: Lapin M, et al. Cancer Res. 2020;80(16_suppl). Abstract 734.

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