1266P - Analytical and clinical validation of a next-generation sequencing-based circulating tumor DNA (ctDNA) assay assures its clinical application

Date 11 September 2017
Event ESMO 2017 Congress
Session Poster display session
Topics Cancer in Adolescents
Diagnostics
Translational Research
Presenter Wenjin Liu
Citation Annals of Oncology (2017) 28 (suppl_5): v449-v452. 10.1093/annonc/mdx378
Authors W. Liu1, S. Mu1, J. Yao2, H. Chen3, Z. Hu4, J. Hu5, G. Chirn3, H. Kang4, K. Wang2, M. Yao5
  • 1Department Of Computational Oncology, Origimed, 200000 - Shanghai/CN
  • 2Department Of Bioinformatics, Origimed, 200000 - Shanghai/CN
  • 3Department Of Bioinformatics, OrigiMed, 200000 - Shanghai/CN
  • 4Department Of Genome Center, Origimed, 200000 - Shanghai/CN
  • 5Department Of Clinical Analysis, OrigiMed, 200000 - Shanghai/CN

Abstract

Background

To date, ctDNA has been exhibiting its unprecedented translational potential in cancer care. However, accurate identification of comprehensive genomic alternations is rigorously needed for its clinical utility.

Methods

Three biologically relevant reference materials with allele frequencies expected at 0.1%, 1% and 5% were used to analytically evaluate the accuracy and reproducibility. Clinically, 43 ctDNA samples from lung, liver, colorectal, breast and gastric cancers were genomically profiled and compared to the known alternations in their matched solid tumors, in terms of single base substitution, insertions/deletions, copy number variations and rearrangement.

Results

The analytical validation demonstrated unprecedented accuracy: near 100% specificity (99.6%, 99.9% and 100%) and 95.8%, 100% and 100% sensitivity for 3 reference materials, respectively. The actual detection limit was as low as 0.05%. The reproducibility was assessed as 0.998 (jaccard index) by sequencing 2 replicates of each reference. In clinical validation, compared to matched FFPE results, this ctDNA assay showed overall 99.9% specificity and 89% sensitivity, with > 90% sensitivity when only drug-gable hotspots were concerned. Eight events of gene rearrangements involving known targeted genes of ALK (n = 4), ROS1 (n = 3) and MET (n = 1) were detected from seven patients with 100% sensitivity and 100% specificity, confirmed either by IHC or panel sequencing (depth > 1,000X) over their matched FFPE biopsies. Due to its typically low abundance, CNV from ctDNA was detectable only for those highly amplified genes ( > =8 copies) with > =4 exons, demonstrating 72.2% sensitivity and 99.5% specificity.

Conclusions

Stringent criteria for both analytical and clinical validations are required for clinical utility of ctDNA. Our ctDNA assay has demonstrated high accuracy and reliability in comprehensively genomic profiling of ctDNA, especially in regard to druggable targets, which assures its translational utility in optimizing and monitoring targeted therapies in cancer management.

Clinical trial identification

Legal entity responsible for the study

OrigiMed Inc

Funding

OrigiMed Inc

Disclosure

W. Liu, S. Mu, J. Yao, H. Chen, Z. Hu, J. Hu, G. Chirn, H. Kang, K. Wang, M. Yao: Employee of OrigiMed Inc.