title: Base-Position Error Rate Analysis of Next-Generation Sequencing Applied to Circulating Tumor DNA in Non-Small Cell Lung Cancer: A Prospective Study.
abstract: BACKGROUND
  Circulating tumor DNA (ctDNA) is an approved noninvasive biomarker to test for the presence of EGFR mutations at diagnosis or recurrence of lung cancer. However, studies evaluating ctDNA as a noninvasive "real-time" biomarker to provide prognostic and predictive information in treatment monitoring have given inconsistent results, mainly due to methodological differences. We have recently validated a next-generation sequencing (NGS) approach to detect ctDNA. Using this new approach, we evaluated the clinical usefulness of ctDNA monitoring in a prospective observational series of patients with non-small cell lung cancer (NSCLC).
  
  
  RESULTS
  We recruited 124 patients with newly diagnosed advanced NSCLC for ctDNA monitoring. The primary objective was to analyze the prognostic value of baseline ctDNA on overall survival. ctDNA was assessed by ultra-deep targeted NGS using our dedicated variant caller algorithm. Common mutations were validated by digital PCR. Out of the 109 patients with at least one follow-up marker mutation, plasma samples were contributive at baseline (n = 105), at first evaluation (n = 85), and at tumor progression (n = 66). We found that the presence of ctDNA at baseline was an independent marker of poor prognosis, with a median overall survival of 13.6 versus 21.5 mo (adjusted hazard ratio [HR] 1.82, 95% CI 1.01-3.55, p = 0.045) and a median progression-free survival of 4.9 versus 10.4 mo (adjusted HR 2.14, 95% CI 1.30-3.67, p = 0.002). It was also related to the presence of bone and liver metastasis. At first evaluation (E1) after treatment initiation, residual ctDNA was an early predictor of treatment benefit as judged by best radiological response and progression-free survival. Finally, negative ctDNA at E1 was associated with overall survival independently of Response Evaluation Criteria in Solid Tumors (RECIST) (HR 3.27, 95% CI 1.66-6.40, p < 0.001). Study population heterogeneity, over-representation of EGFR-mutated patients, and heterogeneous treatment types might limit the conclusions of this study, which require future validation in independent populations.
  
  
  CONCLUSIONS
  In this study of patients with newly diagnosed NSCLC, we found that ctDNA detection using targeted NGS was associated with poor prognosis. The heterogeneity of lung cancer molecular alterations, particularly at time of progression, impairs the ability of individual gene testing to accurately detect ctDNA in unselected patients. Further investigations are needed to evaluate the clinical impact of earlier evaluation times at 1 or 2 wk. Supporting clinical decisions, such as early treatment switching based on ctDNA positivity at first evaluation, will require dedicated interventional studies.
authors.affiliation: INSERM UMR-S1147, CNRS SNC 5014, Equipe labélisée Ligue Contre le Cancer, Université Sorbonne Paris Cité, Paris, France.|Department of Medical Oncology, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique-Hôpitaux de Paris, Paris, France.
authors.forename: Nicolas
authors.identifier: http://orcid.org/0000-0002-3321-5791
authors.initials: N
authors.lastname: Pécuchet
authors.affiliation: INSERM UMR-S1147, CNRS SNC 5014, Equipe labélisée Ligue Contre le Cancer, Université Sorbonne Paris Cité, Paris, France.
authors.forename: Eleonora
authors.initials: E
authors.lastname: Zonta
authors.affiliation: INSERM UMR-S1147, CNRS SNC 5014, Equipe labélisée Ligue Contre le Cancer, Université Sorbonne Paris Cité, Paris, France.
authors.forename: Audrey
authors.initials: A
authors.lastname: Didelot
authors.affiliation: Department of Medical Oncology, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique-Hôpitaux de Paris, Paris, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Combe
authors.affiliation: Department of Medical Oncology, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique-Hôpitaux de Paris, Paris, France.
authors.forename: Constance
authors.initials: C
authors.lastname: Thibault
authors.affiliation: Department of Pathology, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique-Hôpitaux de Paris, Paris, France.
authors.forename: Laure
authors.initials: L
authors.lastname: Gibault
authors.affiliation: Department of Biochemistry, Pharmacogenetics and Molecular Oncology, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique-Hôpitaux de Paris, Paris, France.
authors.forename: Camille
authors.initials: C
authors.lastname: Lours
authors.affiliation: MERIT-UMR IRD 216, Université Sorbonne Paris Cité, Paris, France.
authors.forename: Yves
authors.identifier: http://orcid.org/0000-0002-3907-5101
authors.initials: Y
authors.lastname: Rozenholc
authors.affiliation: INSERM UMR-S1147, CNRS SNC 5014, Equipe labélisée Ligue Contre le Cancer, Université Sorbonne Paris Cité, Paris, France.
authors.forename: Valérie
authors.initials: V
authors.lastname: Taly
authors.affiliation: INSERM UMR-S1147, CNRS SNC 5014, Equipe labélisée Ligue Contre le Cancer, Université Sorbonne Paris Cité, Paris, France.|Department of Biochemistry, Pharmacogenetics and Molecular Oncology, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique-Hôpitaux de Paris, Paris, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Laurent-Puig
authors.affiliation: INSERM UMR-S1147, CNRS SNC 5014, Equipe labélisée Ligue Contre le Cancer, Université Sorbonne Paris Cité, Paris, France.|Department of Biochemistry, Pharmacogenetics and Molecular Oncology, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique-Hôpitaux de Paris, Paris, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Blons
authors.affiliation: INSERM UMR-S1147, CNRS SNC 5014, Equipe labélisée Ligue Contre le Cancer, Université Sorbonne Paris Cité, Paris, France.|Department of Medical Oncology, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique-Hôpitaux de Paris, Paris, France.
authors.forename: Elizabeth
authors.identifier: http://orcid.org/0000-0002-1244-873X
authors.initials: E
authors.lastname: Fabre
mesh_terms: D000328:Adult; D000368:Aged; D014408:Biomarkers, Tumor / Q000235:genetics; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics*; D004273:DNA, Neoplasm / Q000235:genetics* / Q000378:metabolism; D018572:Disease-Free Survival; D005260:Female; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D009154:Mutation; D009360:Neoplastic Cells, Circulating / Q000378:metabolism*; D011379:Prognosis; D011446:Prospective Studies
chemical_list: D014408:Biomarkers, Tumor; D004273:DNA, Neoplasm