Next-generation sequencing assay detects genetic variants driving cancer, resistance in NSCLC

By Marilynn Larkin

NEW YORK (Reuters Health) - 2/4/2019

A novel liquid biopsy based on ultra-deep next-generation sequencing (NGS) of plasma cell-free DNA (cfDNA) can detect oncogenic drivers and resistance mutations in non-small-cell lung cancer (NSCLC), even when tissue biopsy fails to do so, researchers say.

"This study provides further evidence that liquid biopsy for plasma circulating tumor DNA (ctDNA) may play a complementary role to tissue biopsy in the care of patients with lung cancer, including when tissue biopsy is inadequate," Dr. Bob T. Li, a medical oncologist at Memorial Sloan Kettering Cancer Center in New York City, told Reuters Health by email.

"The ultra-deep plasma NGS with clonal hematopoiesis filtering used in this study represents a novel approach for accurate detection of oncogenic drivers, with 100% specificity," he said.

"Several plasma NGS assays... are commercially available and received regulatory approval by the NYS Department of Health," he noted. "Patients with advanced NSCLC can discuss with their doctors whether a liquid biopsy may help guide or improve their treatment."

"However, the...assay used in this study is a research assay from Illumina and Grail and not clinically available," he added. The technologies "will need to be developed further for the accurate detection of early-stage cancers or molecular residual disease."

"Research is underway in this space," he said, "with even newer assays and larger studies in broader contexts."

Dr. Li and colleagues collected blood samples from 127 patients newly diagnosed with advanced NSCLC that had metastasized to other parts of the body or who had recurrent metastases.

As reported online March 20 in Annals of Oncology, 91 patients had oncogenic driver or resistance mutations identified by tissue biopsy; 19 had no mutations detected by tissue biopsy; and 17 had no tissue biopsy available or the biopsy was insufficient for analysis.

Overall, plasma NGS detected driver mutations with variant allele fractions ranging from 0.14% to 52%. In a validation subset, droplet digital PCR was used to detect EGFR or KRAS mutations. Findings were nearly identical to those of plasma NGS in 21 of 22 patients, with high concordance.

In a blinded analysis, plasma NGS detected oncogenic drivers in 68 of the 91 patients identified by tissue biopsy, for a sensitivity of 75%. In patients who were driver-negative by tissue NGS, specificity was 100% (19/19).

In the 17 patients without genotyped tissue, plasma NGS identified KRAS mutations in four. One was confirmed by tissue biopsy; the other three did not undergo tissue biopsy.

In 23 patients with EGFR mutations and acquired resistance to targeted therapy, plasma NGS detected potential resistance mechanisms, including EGFR T790M and C797S mutations and ERBB2 amplification.

Commenting by email, Dr. Vamsidhar Velcheti, director of medical thoracic oncology at NYU Langone's Perlmutter Cancer in New York City, told Reuters Health, "Precision medicine requires accurate and timely biomarker analysis. Unfortunately, nearly a third of patients with advanced lung cancer do not have adequate tumor sample for biomarker analysis."

"Liquid biopsies offer an opportunity to do tumor biomarker analysis in situations where there is inadequate tissue or where it is hard to get a repeat biopsy at the time of progression of treatments," said Dr. Velcheti, who was not involved in the study. "Despite the overall appeal for using liquid biopsies, there are several technical challenges with this approach."

"The performance of these tests is highly impacted by several pre-analytical variables such as clinical setting and timing and technique of sample collection, which can result in varying degree of ctDNA," he explained. "The quantity of ctDNA impacts the sensitivity of the assays."

"Novel technology platforms such as the ultra-deep NGS sequencing used by (the authors) can improve performance by being able to detect low levels of the ctDNA in patient blood samples," he said.

"However, the clinical utility of such highly sensitive approach to sequencing ctDNA is not yet clearly established," he noted. "This does raise some concerns of identification of rare genomic alterations at low allelic frequency with limited functional and clinical significance, and may lead to ineffective treatment decisions."

"These novel and exciting diagnostic platforms need to be further validated for clinical utility in prospective clinical trials to inform therapeutic decisions," Dr. Velcheti concluded.

The study was funded by Illumina, of which Grail is a spinout. Eleven coauthors are or were employees of these companies and 11 more received funding or fees from them.


Ann Oncol 2019.

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