Multi-cancer early detection (MCED) in circulating tumor DNA (ctDNA) using an ultrasensitive mutation-based amplicon next-generation sequencing (NGS) assay.
Authors: Poh Jonathan , Ang Yong Chai , Ho Jia Min , Chen Hao , Cher Chae Yin , Pek Michelle , Chang Mei Mei , Loke Sau Yeen , Pinweha Pannapa , Kwong Ee Wern , Hum Yee Fang , Lim Chwee Ming , Tan Min-Han 
Published: June 2024

e15042

Background: Cancer remains a leading cause of mortality globally. For most cancers, routine screening options are still unavailable. Blood-based MCED has emerged as a promising strategy to bridge this gap. Mutation-based NGS in ctDNA detects highly specific cancer signals, an attribute critical for MCED assays. We developed an ultrasensitive mutation-based NGS assay optimized to detect cancer signals in 50 cancers and predict tissue-of-origin (TOO) for up to 21 cancer classes. Methods: An amplicon-based NGS assay incorporating mirror barcodes for error correction was designed to detect cancer-associated alterations (CAAs), including single nucleotide variants (SNVs), insertion-deletion mutations (indels), and viral DNA (EBV and 20 genotypes of HPV), in 50 cancers. Analytical validation was performed using reference standards and clinical validation was performed in a retrospective case-control cohort of 601 subjects comprising cell-free DNA (cfDNA) from 313 self-declared healthy donors and 288 cancer patients (30.9% early-stage, 50.3% late-stage and 9.4% hematolymphoid cancers). Tissue-of-origin (TOO) was predicted for 21 cancer classes using a weighted sum model. Where relevant, matched buffy coat genomic DNA (gDNA) was analyzed to rule out clonal hematopoiesis. Results: Analytical validation demonstrated a limit of detection (LoD) of 0.05% variant allele frequency (VAF) for indels and 0.07% VAF for SNVs in cfDNA. LoD was matched in gDNA (0.04% and 0.05% VAF for indels and SNVs respectively). In clinical validation, the assay demonstrated a specificity of 99.0% (310/313) and an overall sensitivity of 80.9% (233/288), with sensitivities of 64.0%, 91.7%, and 85.2% in early-stage, late-stage, and hematolymphoid cancers respectively. The mean number of CAAs detected in early-stage, late-stage, and hematolymphoid CAA-positive cancers was 2.1, 3.1, and 4.6. Inclusion of viral targets aided the detection of nasopharyngeal (NPC), cervical, and p16+ oropharyngeal (oPSCC) cancers. EBV DNA was detected in 91.7% of NPC cases. In cervical cancer and p16+ oPSCC, HPV DNA (genotypes 16, 18, 33 and 39) was detected in 71.4% and 90.9% of cases respectively. Conversely, none of the p16- oPSCC cancers had detectable HPV DNA. Across the 21 TOO classes, a high confidence prediction could be made in 62.4% (mean 73.6%, range 26.7%-100%) of cases with an overall accuracy of 87.7% (mean 84.9%, range 33.3%-100%). Overall TOO prediction performance was modeled in a simulated cohort based on cancer incidence in Singapore and Hong Kong, giving an accuracy of 87.3% and 88.7% respectively. Conclusions: The mutation-based NGS assay sensitively detects cancer signals and accurately predicts the tumor origin for early-stage, late-stage, and hematolymphoid cancers. Inclusion of viral targets additionally enables early detection of virus-associated cancers.