Abstract 2283: Accurate and efficient Next-Generation Sequencing approach for liquid biopsy detection and monitoring

• Published in: Cancer research (Chicago, Ill.) Ill.), 2019-07, Vol.79 (13_Supplement), p.2283-2283
• Main Authors: Chen, Cai, Kasbek, Christopher, Song, Yang, Chen, Si, Almalki, Nouran, Li, Jiangyu, Wan, Yifei, Huang, Jun, Ding, Wei
• Format: Article
• Language: English
• ISSN: 0008-5472; 1538-7445
• DOI: 10.1158/1538-7445.AM2019-2283

Liquid biopsy detection using ctDNA has great potential in cancer diagnosis, monitoring, and predicting survival. However, detection sensitivity and specificity remain major challenge at the current stage. Here we utilized a targeted next-generation sequencing (NGS) approach to develop a noninvasive test to identify single nucleotide variations (SNVs), indels, fusions, copy number variations (CNVs) and microsatellite instability (MSI) present at low frequencies in different solid cancer patients. Target regions of interest were sequenced using tagging of individual molecules, followed by amplicon library generation and massive parallel sequencing using an Illumina platform. The variants were called and annotated using our in-house Actionable Genomic Interpretation System (AGIS) bioinformatics pipeline. This CLIA-approved NGS panel (LiquidGx™) detects more than 170 variants in 17 genes which were chosen mostly based on NCCN clinical actionable guidelines (AKT1, ALK, BRAF, EGFR, ERBB2, HRAS, KIT, KRAS, MAP2K1, MET, NRAS, PDGFRA, PIK3CA, PTEN, RET, ROS1 and TP53) with detection limit of 0.1%. Mutations are detected with 94% sensitivity and 99.8% specificity in a short turnaround time of 3-5 business days. To assess the performance in a clinical setting, accurate sequencing was performed on 210 lung cancer patients; the frequency of mutations identified of each gene closely mirrored the published lung cancer tissue biopsy data. Fusions are detected from exosomal RNA, which could increase the sensitivity and/or concordance to tumor. For spike-in data validation, the limit of detection (LOD) of CNV can reach 2.2 -2.5 total gene copies. In addition to actionable mutations for targeted therapy, LiquidGx™ provides MSI status, which can predict a predisposition to mutations as a result from impaired DNA mismatch repair (MMR) and help predict if a tumor will respond to anti-PD-1 therapy. The LOD of our MSI detection is 2-4%. In summary, we have developed a potent liquid biopsy platform for highly sensitive genomic biomarker test. Our technology is also available as an assay development service and can be easily adaptable to the diagnosis and monitoring of different cancer types. Note: This abstract was not presented at the meeting. Citation Format: Cai Chen, Christopher Kasbek, Yang Song, Si Chen, Nouran Almalki, Jiangyu Li, Yifei Wan, Jun Huang, Wei Ding. Accurate and efficient Next-Generation Sequencing approach for liquid biopsy detection and monitoring [abstract]