Lung cancer is the leading cause of cancer related death. Squamous-cell carcinoma, a type of non-small-cell lung carcinoma (NSCLC), comprises 25–30% of all lung cancer cases and is strongly correlated with cigarette smoking. The remaining 70-75% of lung cancer cases can be described as non-squamous cell lung carcinoma (NSCC).
The US National Comprehensive Cancer Network guidelines currently recommend a minimum of EGFR, ALK, ROS1, BRAF, and PD-L1 gene mutation and expression profiling of tissue biopsies from NSCC patients. Broader profiling is recommended, if feasible, including the neurotrophic tyrosine receptor kinase (NTRK) gene. Lack of tissue may prevent this, however “liquid biopsy” of the blood is another option for additional testing.
Molecular profiling of liquid biopsy is, however, not currently routine clinical practice with questions remaining about the feasibility of in-house verses out-sourced analysis, and the interpretation of combined tissue and liquid biopsy results.
With this in mind Paul Hofman and colleagues from Pasteur Hospital, Université Côte d’Azur, Nice, France, and hospital-related biobank (BB-00033-0025) conducted a study, published in the Journal of Translational Medicine, evaluating the feasibility of implementing plasma-based next generation sequencing (NGS) in routine clinical care. Outsourced blood analysis by Foundation Medicine of Cambridge, Massachusetts, and in-house sequencing of a prospective cohort of 24 unselected NSCC patients was compared.
In the reported study 67% of cases had enough biopsy for additional NGS based studies, with the remainder having liquid biopsy as the only available option. The turnaround time for the outsourced testing was 10 days compared to 28 days for in-house. This was due to the low patient numbers in the study combined with the in-house policy of batch testing to improve cost efficiency. Under ideal circumstances, with more patients, the in-house turnaround could be 3 days.
In-house testing used unique molecular identifiers (UMIs) or barcodes to quantify the DNA/RNA species present in 2ml of plasma from the original blood samples prepared with the Thermo Fisher Oncomine cfTNA kit. The outsourced method was proprietary, requiring 17ml blood.
The concordance rate between the two panels was 73% (16/22 concordant mutations), with the in-house method detecting more mutations in this limited panel. This may be due to the use of more stringent quality control cut-offs in the outsourced pipeline. The outsourced test covered more genes and spanned more regions than the in-house test, so in total more mutations were detected in the outsourced test.
The ability to detect mutations present in the available tissue biopsies using liquid biopsy was similar in both in-house and outsourced pipelines with a success rate between 60-63%. In the present study TP53 mutations were not detectable in any liquid biopsies despite their presence in tissue biopsies.
Liquid biopsy detection of EGFR mutation allowed the initiation of targeted erlotinib treatment in two patients (8% of total), where no tissue NGS data was available (33% of total).
The study was limited in size and experienced high variability in nucleic acid extraction between patients.
“The development of novel targeted treatments in this setting [late-stage NSCC] will dramatically expand [liquid biopsy] use in daily practice. However, the importance of PD-L1 IHC [immunohistochemistry] as the only approved biomarker for the stratification of patients undergoing ICI [immune checkpoint inhibitor] treatment until the present day, as well as the currently unknown sensitivity for the testing of genomic rearrangements, makes [IHC] a mandatory addition to tissue-based testing from biopsies. In our opinion, plasma-based NGS cannot currently replace tissue testing at baseline in routine clinical and molecular pathology,” concluded the authors.