Shannon Lu

Introduction. Lung cancer is the most common global cancer and cause of cancer death.¹  Circulating tumor DNA (ctDNA), a subset of cell-free DNA (cfDNA), are extracellular DNA fragments released from tumor cells into the bloodstream. Detection and testing of ctDNA can potentially be used for early screening and diagnosis and personalized targeted therapy of lung cancer. Higher ctDNA levels are correlated to disease progression so the development of a ctDNA assay with increased sensitivity would be required for improved diagnostic ability.^2,3  Methods. Cancer personalized profiling by deep sequencing (CAPP-Seq) utilized a specifically designed probe and deep sequencing to detect and analyze ctDNA in non-small cell lung cancer (NSCLC) patients. The probe consisting of introns and exons that contain known driver mutations, predicted mutations, and breakpoints of common mutations was used for hybridization-based capture method of next-generation sequencing (NGS).⁴  An error suppression model, integrated digital error suppression (iDES), was developed to improve sensitivity of CAPP-Seq. A molecular barcoding technique used to distinguish artifacts produced ex vivo during PCR from somatic in vivo mutations was combined with a computational model that suppresses recurrent background errors in silico.⁵  CAPP-Seq and iDES performance was assessed on blood samples from participating NSCLC patients.^4,5  Results. CAPP-Seq had an area under the curve (AUC) of 0.95 with 85% sensitivity and 96% specificity for all samples from untreated patients. Of those patients, there was 50% sensitivity for stage I tumors and 100% sensitivity for stage II-IV tumors. With both pre- and post-treatment samples, CAPP-Seq achieved an AUC of 0.89.4 iDES with CAPP-Seq reduced the detection limit of ctDNA down to 0.0025 (2.5 in 105 molecules) which is about 10-fold lower than that of the CAPP-Seq approach alone. iDES improved sensitivity of CAPP-Seq to 92% of all untreated patients including ctDNA detection in 3/3 stage I tumors and maintained 96% specificity. Pre- and post-treatment samples had 73% sensitivity and 100% specificity using iDES.⁵  Conclusion. CAPP-Seq and iDES highlight the newer methods that increase sensitivity of ctDNA detection techniques while decreasing rates of false positives. Liquid body and ctDNA analysis are being utilized in tracking disease progression and in assessing the effectiveness of therapy.^6,7  The expansion of ctDNA to screening, diagnosis, assessing response to therapy management alone or in conjugation with existing tissue biopsy techniques could be instrumental to improving morbidity and mortality of lung cancer.

1. Bade BC, Dela Cruz CS. Lung Cancer 2020: Epidemiology, Etiology, and Prevention. Clin Chest Med. 2020;41(1):1-24.
2. Pellini B, Szymanski J, Chin RI, Jones PA, Chaudhuri AA. Liquid Biopsies Using Circulating Tumor DNA in Non-Small Cell Lung Cancer. Thorac Surg Clin. 2020;30(2):165-177.
3. Herbst RS, Morgensztern D, Boshoff C. The biology and management of non-small cell lung cancer. Nature. 2018;553(7689):446-454.
4. Newman AM, Bratman SV, To J, et al. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat Med. 2014;20(5):548-554.
5. Newman AM, Lovejoy AF, Klass DM, et al. Integrated digital error suppression for improved detection of circulating tumor DNA. Nat Biotechnol. 2016;34(5):547-555.
6. Abbosh C, Birkbak NJ, Wilson GA, et al. Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature. 2017;545(7655):446-451.
7. Anagnostou V, Forde PM, White JR, et al. Dynamics of Tumor and Immune Responses during Immune Checkpoint Blockade in Non-Small Cell Lung Cancer. Cancer Res. 2019;79(6):1214-1225.