Abstract 111P
Background
Immunohistochemistry (IHC)/in situ hybridization (ISH) are widely used methods in many pathology laboratories to assess human epidermal growth factor receptor 2 (HER2) status in gastric cancer (GC) patients. Nowadays, next generation sequencing (NGS) technologies are adopted to precisely predict absolute gene amplification levels. However, these tissue-based tests are suffering from intratumoral heterogeneity and inter-laboratory technical biases.
Methods
We set up a novel probe-based Absolute Q digital PCR assays for quantitative measurement of HER2 amplification using the formalin-fixed paraffin embedded (FFPE) tissue samples and the results were compared with IHC/ISH and NGS results in 184 gastric adenocarcinoma samples. HER2 amplifications were determined with HER2 TaqMan® probe hydrolysis assays within exon 22 and was multiplexed by the ratios of HER2 copy number (CN) to reference gene CN (HER2/RNaseP ratio).
Results
With digital PCR, the median HER2 CN were 1.79 copies/μL (ranged from 0.02 to 48.87 copies/μL). With NGS, HER2 amplifications were detected in 28 cases (15.2%). By IHC, HER2 positive (3+) was found in 25 cases (13.6%) and equivocal (2+) cases were observed in 15 cases (8.2%), in which ISH conformed amplifications in 13 cases. The concordance rate between IHC (3+ or 2+ and HER2 amplified) and NGS was 71.3%. In HER2-amplified cases by NGS, the median CN measured with digital PCR were 9.7 copies/μL (ranged from 1.95 to 48.87 copies/μL). In statistical analyses, Pearson correlation coefficients between NGS and digital PCR was 0.916, suggesting strong correlation. Given HER2 amplification by NGS as the standard reference, digital PCR predicted HER2 amplification with a 98.7% specificity, 92.9% sensitivity, 92.9% positive predictive value, and 98.7% negative predictive value. The AUC values for predicting HER2 amplification by digital PCR were 0.989.
Conclusions
With newly designed novel probes, digital PCR accurately measured HER2 CN with high sensitivity and specificity.
Editorial acknowledgement
Clinical trial identification
Legal entity responsible for the study
The authors.
Funding
The Ministry of Health & Welfare, Republic of Korea.
Disclosure
All authors have declared no conflicts of interest.
Resources from the same session
103P - MSI detection by NGS using tumor samples and liquid biopsy for patients with solid tumors: A single institution experience
Presenter: Alexandra Lebedeva
Session: Cocktail & Poster Display session
Resources:
Abstract
104P - Hypomethylated immune gene promoters as potential biomarkers in oral and oropharyngeal cancer
Presenter: Petra Anić
Session: Cocktail & Poster Display session
Resources:
Abstract
105P - Implementation of technical improvements in cfMeDIP-Seq library preparation
Presenter: Martina Dameri
Session: Cocktail & Poster Display session
Resources:
Abstract
106P - Clinical application of next-generation sequencing in metastatic colorectal cancer (mCRC): Experience from a comprehensive cancer centre
Presenter: David Lluís Garulo
Session: Cocktail & Poster Display session
Resources:
Abstract
107P - Unveiling mismatch repair deficiency (dMMR) and microsatellite-instability high (MSI-H) detection in cancer patients (pt) using a next-generation sequencing (NGS)-based molecular pre-screening program (MPP)
Presenter: Lucia Notario Rincon
Session: Cocktail & Poster Display session
Resources:
Abstract
108P - Validation and implementation of a large NGS panel to test liquid biopsies from patients with suspected advanced non-small cell lung cancer (NSCLC) in an NHS genomic laboratory for the QuicDNA biomarker study
Presenter: Rachel Dodds
Session: Cocktail & Poster Display session
Resources:
Abstract
109P - A multiomic, single-cell measurable residual disease (scMRD) assay for phasing DNA mutations and surface immunophenotypes
Presenter: Simone Formisano
Session: Cocktail & Poster Display session
Resources:
Abstract
110P - Multicellular three-dimensional tumor spheroid of nasopharyngeal carcinoma
Presenter: Shiau Chuen Cheah
Session: Cocktail & Poster Display session
Resources:
Abstract
112P - A novel methylation-sensitive assay for early detection of hepatocellular carcinoma to improve surveillance
Presenter: Jeong Sil Ha
Session: Cocktail & Poster Display session
Resources:
Abstract
113P - Evaluation of effects of tissue preservation methods on the proteome abundance through deep proteomics of breast cancer tissue
Presenter: Shashwati parihari
Session: Cocktail & Poster Display session
Resources:
Abstract