Abstract 2225: Limitations on mutation detection for early detection of cancer
Authors: Haque Imran S. , Otte Gabriel , Elemento Olivier 
Published: August 2018

Introduction: Cell-free DNA (cfDNA) has potential utility for early non-invasive detection of cancer. We assess the feasibility of cfDNA mutational assays for early detection based on their physiological and economic requirements. We further review alternative biological signals of early cancer and the potential of machine learning to integrate these signals into reliable diagnostics.

Methods: A binomial model was used to assess depth and input requirements, with parameters derived from published data on cfDNA sequencing. Alternative strategies for early detection were assessed by literature review.

Results: 30,000x unique coverage is required for 95% sensitivity for 1 mutant read at 0.01% variant allele frequency, requiring 180ng cfDNA input at 50% process efficiency; current sequencing costs and reimbursement levels may make such tests economically infeasible (Table). 5th percentile plasma cfDNA concentration in the screening population is ~2.3 ng/mL, requiring &gt;140mL blood collection for test failure rate &lt;5%. Somatic mutational heterogeneity creates significant specificity challenges. Proteins, RNAs, and compartmentalized macromolecules are more abundant and may overcome cfDNA's issues of quantity, but irrelevant biological processes may confound the data. New techniques in machine learning, including latent variable modeling, may be used to integrate heterogeneous data from multiple sources to overcome these challenges.

Conclusions: Mutation-detection assays may not be feasible for early cancer detection due to limited sensitivity arising from low concentrations of cfDNA, heterogeneity leading to specificity challenges, and prohibitive cost. Integrating markers beyond mutations with modern machine learning may provide a potential route to statistically robust biomarker development for early cancer detection.

Table. Assay requirements for tumor liquid biopsy and mutation-based early cancer detection.

Sequencing cost by panel sizeVAF 95% sensitivityCorrected depthRaw depthInput volume (blood)TEC-Seq1 58 genes 81 kbRazavi et al2 508 genes 2000 KbWES ~20k genes 50,000 KbTumor liquid biopsy0.1%3000x15,000x15 mL$14$340$8300Early cancer detection0.01%30,000x150,000x150 mL$140$3400$83,0001Phallen J, et al. Sci Transl Med. 2017 Aug 16;9(403). 2Razavi P, et al. J Clin Oncol. 2017;35(suppl):abstr 11526.Model parameters: 1) No more than 5% of samples may fail because of insufficient cfDNA quantity; 2) 95% sensitivity to detect one read from any cancer-derived allele, assuming that one is present in the sample; 3) 50% process efficiency: half of the cfDNA molecules in the input blood sample are represented in the sequencer output; 4) 5x oversampling in sequencing for error correction; 5) 100% on-target rate in target enrichment; 6) “$1000 genome” sequencing costs: US $1000/(30 x 3 Gbp) of sequencing bandwidth; 7) only sequencing costs computed; all other costs (labor, equipment, facilities, depreciation, etc.) accounted at $0; 8) panel expansion neither reduces input requirements nor increases sequencing requirements.VAF = variant allele frequency; TEC-Seq = targeted error correction sequencing; WES = whole exome sequencing.

Citation Format: Imran S. Haque, Gabriel Otte, Olivier Elemento. Limitations on mutation detection for early detection of cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2225.