Several Collaborator Presented Research Result of Different Cancers

Collaborator: Shanghai Chest Hospital

Jounral: Small methods

Cancer type: Non-small-cell Lung Carcinoma

CLAmp-seq: A Novel Amplicon-Based NGS Assay with Concatemer Error Correction for Improved Detection of Actionable Mutations in Plasma cfDNA from Patients with NSCLC

The study was chaired by Professor Jiatao Lou, director of the Department of Laboratory Medicine of Shanghai Chest Hospital. It was jointly participated by Cancer Center of the First Hospital of Jilin University, Department of Radiation Oncology of Sun Yat-sen University Cancer Center, AccuraGen Inc., etc.

This study evaluated the analytical sensitivity, specificity, and limit of detection (LOD), based on the cfDNA standard materials. The panel was then used to analyze plasma cfDNA samples from 134 NSCLC cancer patients and 50 non-cancerous controls, and ctDNA-NGS results were compared with tumor tissue ARMS and cfDNA ddPCR results.

CLAmp-seq demonstrated median detection rate of 100% at allele frequency of 0.1% for 20ng of cfDNA and zero false positive in all blank control samples. In cfDNA from plasma collected before treatment, EGFR mutations detected by ctDNA-NGS was 94.8% concordant with tumor tissue ARMS-PCR. CLAmp-seq demonstrated strong per-variant detection-rate concordance (98%) and allele frequency concordance (R² = 0.95) when compared with cfDNA ddPCR result. This study also reflected the advantages of ctDNA-NGS for detection of de novo 19 Indel mutations that multiple PCR methods cannot detected fully.

Collaborator: Zhongshan Hospital, Fudan University

Jounral: Clinical Chemistry and Laboratory Medicine

Cancer type: Colorectal Cancer

Analytical and clinical validation of a novel amplicon-based NGS assay for the evaluation of circulating tumor DNA in metastatic colorectal cancer patients

The study was chaired by Professor Wei Guo, director of the Department of Laboratory Medicine, and Tianshu Liu, director of the Department of Medical Oncology. This study deploys a novel amplicon-based next generation sequencing, targeting KRAS/NRAS/BRAF/PIK3CA mutations, to assess the analytical and clinical performance of circulating tumor DNA in metastatic colorectal cancer patients. AccuraGen provided technical support for the study.

Firefly™ assay targeting KRAS/NRAS/BRAF/PIK3CA was evaluated using cell-free DNA (cfDNA) reference standards and plasma cfDNA samples from 184 mCRC patients. Plasma results were compared to the mutation status determined by ARMS-based PCR from matched tissue. Samples with a mutation abundance below the limit of detection (LOD) were retested again by droplet digital polymerase chain reaction (ddPCR) or NGS.

Firefly™ assay demonstrated superior sensitivity and specificity with a 98.89% detection rate at an allele frequency (AF) of 0.2% for 20ng cfDNA. Generally, 40.76% and 48.37% of the patients were reported to be positive by NGS of plasma cfDNA and ARMS of FFPE tissue, respectively. The concordance rate between the two platforms was 80.11%. In the pre-treatment cohort, the concordance rate between plasma and tissue was 93.33%, based on the 17 common exons that Firefly™ and ARMS genotyped, and the positive percent agreement (PPA) and negative percent agreement (NPA) for KRAS/NRAS/BRAF/PIK3CA were 100% and 99.60%, respectively.

Total plasma cfDNA detected by Firefly™ offers a viable complement for mutation profiling in CRC patients, given the high agreement with matched tumor samples. Together, these data demonstrate that Firefly™ could be routinely applied for clinical applications in mCRC patients, such as early detection, minimal residual disease detection and disease monitoring.

Collaborator: Eastern Hepatobiliary Surgery Hospital, Second Military Medical University

Jounral: Clinics in Oncology

Cancer type: Hepatocellular Carcinoma

Detection of Tumor-Related Biomarkers in Hepatocellular Carcinoma Patients by Sequencing Circulating Cell-Free DNA

The study was chaired by Professor Heping Hu, director of the Department I of Hepatobiliary，Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, using the Firefly™ ctDNA-NGS technology independently developed by AccuraGen Group to detect 41 hepatocellular carcinoma-related gene mutation kits (Accu-Act HCC). The Firefly ™ technology based on the capturing method was used to detect the gene mutations in plasma cfDNA and matched tissues of patients with hepatocellular carcinoma in order to explore related HCC markers. This research proves that the Firefly™ system is compatible with both the small amplicon panel and the large capturing panel, and has its unique advantages. AccuraGen provided NGS testing services for this research.

In this study, we sequenced paired Cell-Free DNA (cfDNA) and tumor tissue DNA samples from 16 Hepatitis B Virus (HBV)-infected Hepatocellular Carcinoma (HCC) patients to detect tumor related biomarkers in cfDNA samples. We analyzed a panel of 41 HCC-related target genes and detected 35 mutations among 13 genes in 10 HCC samples as well as 14 mutations among 7 genes in 6 cfDNA samples. The top 6 mutant genes were TP53 (22.86%), TERT (20%), ALB (14.29%), AXIN1 (11.43%), FLT1 (5.71%) and ARID1A (5.71%). The mutation relevance ratios of matched HCC tissues and cfDNA samples were not associated with tumor size orserum α-Fetoprotein (AFP) levels. The TERT upstream gene variants, -124C>T(chr5:g.1295228G>A) is the only mutation shared by more than one case.Tumors with ALB mutations were associated with more gene mutations than tumors without ALB mutations (p=0.021407). Our study demonstrates the feasibility of cfDNA based sequencing for detecting circulating tumor DNA biomarkers in HCC patients.