Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 Mar 6:3:PO.18.00211.
doi: 10.1200/PO.18.00211. eCollection 2019.

Real-World Utility of an Amplicon-Based Next-Generation Sequencing Liquid Biopsy for Broad Molecular Profiling in Patients With Advanced Non-Small-Cell Lung Cancer

Jordi Remon  1 , Ludovic Lacroix  2 , Cecile Jovelet  2 , Caroline Caramella  1 , Karen Howarth  3 , Vincent Plagnol  3 , Nitzan Rosenfeld  3   4 , Clive Morris  3 , Laura Mezquita  1 , Chloe Pannet  1 , Maud Ngocamus  1 , Cecile Le Pechoux  1 , Julien Adam  1 , Alina-Miruna Grecea  1 , David Planchard  1 , Gilles Vassal  1   5 , Jose Carlos Benitez  1 , Anas Gazzah  1 , Emma Green  3 , Jean-Charles Soria  1   5 , Benjamin Besse  1   5
Affiliations

Real-World Utility of an Amplicon-Based Next-Generation Sequencing Liquid Biopsy for Broad Molecular Profiling in Patients With Advanced Non-Small-Cell Lung Cancer

Jordi Remon et al. JCO Precis Oncol. .

Abstract

Purpose: To assess the feasibility and utility of circulating tumor DNA (ctDNA) by amplicon-based next-generation sequencing (NGS) analysis in the daily clinical setting in a cohort of patients with advanced non-small-cell lung cancer (NSCLC), as an alternative approach to tissue molecular profiling.

Patients and methods: In this single-center prospective study, treatment-naïve and previously treated patients with advanced NSCLC were enrolled. Clinical validation of ctDNA using amplicon-based NGS analysis (with a 36-gene panel) was performed against standard-of-care tissue molecular analysis in treatment-naïve patients. The feasibility, utility, and prognostic value of ctDNA as a dynamic marker of treatment efficacy was evaluated. Results of tissue molecular profile were blinded during ctDNA analysis.

Results: Of 214 patients with advanced NSCLC who were recruited, 156 were treatment-naïve patients and 58 were pretreated patients with unknown tissue molecular profile. ctDNA screening was successfully performed for 91% (n = 194) of all patients, and mutations were detected in 77% of these patients. Tissue molecular analysis was available for 111 patients (52%), and tissue somatic mutations were found for 78% (n = 87) of patients. For clinically relevant variants, concordance agreement between ctDNA and tumor tissue analysis was 95% among 94 treatment-naïve patients who had concurrent liquid and tumor biopsy molecular profiles. Sensitivity and specificity were 81% and 97%, respectively. Of the 103 patients with no tissue available, ctDNA detected potential actionable mutations in 17% of patients; of these, 10% received personalized treatment. ctDNA kinetics correlated with response rate and progression-free survival in 31 patients treated with first-line platinum-based chemotherapy.

Conclusion: These real-world data from a prospective study endorse ctDNA molecular profile by amplicon-based NGS as an accurate and reliable tool to detect and monitor clinically relevant molecular alterations in patients with advanced NSCLC.

PubMed Disclaimer

Conflict of interest statement

The following represents disclosure information provided by authors of this manuscript. All relationships are considered compensated. Relationships are self-held unless noted. I = Immediate Family Member, Inst = My Institution. Relationships may not relate to the subject matter of this manuscript. For more information about ASCO's conflict of interest policy, please refer to www.asco.org or ascopubs.org/po/author-center.Jordi RemonConsulting or Advisory Role: Pfizer, Bristol-Myers Squibb, Boehringer Ingelheim, MSD Oncology Travel, Accommodations, Expenses: Roche, Genentech, Inivata, OSE ImmunotherapeuticsCaroline CaramellaConsulting or Advisory Role: Bristol-Myers Squibb, PfizerKaren HowarthEmployment: Inivata Stock and Other Ownership Interests: Inivata Research Funding: Inivata Patents, Royalties, Other Intellectual Property: Patents and patent applications relating to cancer classifications, detection or analysis of microRNA and circulating tumor DNA, detection of rare sequence variants, applications in molecular diagnosticsVincent PlagnolEmployment: Inivata Stock and Other Ownership Interests: Inivata Patents, Royalties, Other Intellectual Property: Inivata patentsNitzan RosenfeldEmployment: Storm Therapeutics (I), Inivata Leadership: Inivata Stock and Other Ownership Interests: Inivata, Mission Therapeutics (I) Research Funding: AstraZeneca (Inst) Patents, Royalties, Other Intellectual Property: Patents and patent applications relating to cancer classifications, detection or analysis of microRNA and circulating tumor DNA, detection of rare sequence variants, applications in molecular diagnosticsClive MorrisEmployment: Inivata Leadership: Inivata Stock and Other Ownership Interests: InivataCecile Le PechouxConsulting or Advisory Role: AstraZeneca, Lilly, Nanobiotix, AmgenJulien AdamConsulting or Advisory Role: Roche, Bristol-Myers Squibb, AstraZeneca, Merck Sharp & Dohme Research Funding: Sanofi (Inst), Pierre Fabre (Inst), Merck Sharp & Dohme (Inst)David PlanchardConsulting or Advisory Role: AstraZeneca, Boehringer Ingelheim, Bristol-Myers Squibb, Novartis, Roche, Pfizer, MSD Oncology, CelgeneGilles VassalConsulting or Advisory Role: Bayer, Roche, Genentech, AstraZeneca, Bristol-Myers Squibb, Celgene, Lilly, Servier, Takeda, Incyte, Ipsen, Novartis, Merck Serono Travel, Accommodations, Expenses: Bristol-Myers Squibb, RocheEmma GreenEmployment: Inivata Stock and Other Ownership Interests: Inivata Travel, Accommodations, Expenses: InivataJean-Charles SoriaEmployment: MedImmune Stock and Other Ownership Interests: AstraZeneca, Gritstone Oncology Honoraria: Roche, AstraZeneca, Sanofi, Servier, Pierre Fabre, Abbvie, Pharmamar-ZeltiaBenjamin BesseResearch Funding: AstraZeneca (Inst), Roche (Inst), Genentech (Inst), Pfizer (Inst), Boehringer Ingelheim (Inst), Lilly (Inst), Servier (Inst), Onxeo (Inst), Bristol-Myers Squibb (Inst), Ose Pharma (Inst), Inivata (Inst), Novartis (Ins), OncoMed (Inst), Loxo (Inst) Travel, Accommodations, Expenses: Roche, Pfizer, Bristol-Myers Squibb, Medarex, Novartis, Pierre Fabre No other potential conflicts of interest were reported.

Figures

FIG 1.
FIG 1.
Liquid biopsy circulating tumor DNA (ctDNA) molecular profiles of treatment-naïve cohort with successful plasma-based testing by InVisionSeq (n = 142).
FIG 2.
FIG 2.
Liquid biopsy circulating tumor DNA (ctDNA) molecular profiles of the previously treated rescue cohort that had unknown tissue molecular profiles from primary tissue, with successful plasma-based testing by InVisionSeq (n = 52).
FIG 3.
FIG 3.
No. of patients with advanced NSCLC in whom molecular analysis was performed for tissue and liquid biopsy, which shows positive mutations detected. This analysis demonstrates the utility of plasma to support broader testing in patients with no or limited tissue analysis for actionable and clinically relevant mutations.
FIG 4.
FIG 4.
Concordance of amplicon-based assay (InVisionSeq) for liquid biopsy compared with tissue biopsy.
FIG 5.
FIG 5.
Liquid biopsy mutation correlation to response rate as calculated by change in radiologic response (RECIST 1.1) versus change in mutation molecules, representative of tumor mutation burden, after first-line platinum-based chemotherapy in an unselected cohort with advanced non–small-cell lung cancer (n = 31). Data from 20 patients are shown; others lacked baseline genomic alterations or RECIST data. (*) Two data points, with overlapping data. ctDNA, circulating tumor DNA. D42, day 42.
FIG 6.
FIG 6.
Progression-free survival plot in unselected patients with advanced non–small-cell lung cancer treated with first-line platinum-based chemotherapy; plot compares circulating tumor DNA (ctDNA) mutations at baseline. Negative, those with mutations of low (< 2% mutation allele fraction [MAF]) and high (> 2% MAF) allele fractions, as defined by median allele fraction of baseline mutations across the cohort (n = 31).
FIG A1.
FIG A1.
Flowchart of enrollment and cohorts for analysis: patients with advanced non–small-cell lung cancer (NSCLC) were eligible for the study if they were treatment naïve and expected to receive first-line platinum-based chemotherapy (treatment-naïve cohort) or were previously treated but did not have tissue-based molecular profile of a primary tissue sample available. Patients with concurrent tissue and blood-based testing comprised the validation cohort. Patients without tissue molecular profiles comprised the utility cohort. QC, quality control.
FIG A2.
FIG A2.
InVision (Inivata, Research Triangle Park, NC, and Cambridge, United Kingdom) gene panels: Indicated is the coverage per gene, including hotspots, comprehensive or full coverage of coding regions (70% to 100% tiling coverage), and copy number variants (CNVs). In this study, two versions of the InVision gene panel were used (InvCore versions 1.4 and 1.5). (A) InVision liquid biopsy tumor profiling panel (InvCore version 1.4). (B) InVisionSeq Lung liquid biopsy tumor profiling panel (InvCore version 1.5). indels, short insertions or deletions; SNVs, single nucleotide variants.
FIG A3.
FIG A3.
Agreement and complementary testing of liquid biopsy to tissue molecular profiling in the validation cohort (concurrent tissue and liquid biopsy) for clinically relevant core gene variants. CNVs, copy number variants; indels, short insertions or deletions; SNVs, single nucleotide variants.
See this image and copyright information in PMC

References

    1. VanderLaan PA, Rangachari D, Majid A, et al. Tumor biomarker testing in non–small-cell lung cancer: A decade of change. Lung Cancer. 2018;116:90–95. - PMC - PubMed
    1. Reck M, Rabe KF. Precision diagnosis and treatment for advanced non–small-cell lung cancer. N Engl J Med. 2017;377:849–861. - PubMed
    1. Barlesi F, Mazieres J, Merlio J-P, et al. Routine molecular profiling of patients with advanced non–small-cell lung cancer: Results of a 1-year nationwide programme of the French Cooperative Thoracic Intergroup (IFCT) Lancet. 2016;387:1415–1426. - PubMed
    1. Novello S, Barlesi F, Califano R, et al. Metastatic non–small-cell lung cancer: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up. Ann Oncol. 2016;27:v1–v27. - PubMed
    1. Kalemkerian GP, Narula N, Kennedy EB, et al. Molecular testing guideline for the selection of patients with lung cancer for treatment with targeted tyrosine kinase inhibitors: American Society of Clinical Oncology endorsement of the College of American Pathologists/International Association for the Study of Lung Cancer/Association for Molecular Pathology clinical practice guideline update. J Clin Oncol. 2018;36:911–919. - PubMed