Ensemble of Nucleic Acid Absolute Quantitation Modules for Accurate Copy Number Variation Detection and Targeted RNA Profiling

Abstract Current gold standard for absolute quantitation of a specific DNA sequence is droplet digital PCR (ddPCR), which has been applied to gene copy number variation (CNV) detection. However, the number of quantitation modules in ddPCR has been limited by fluorescence channels, which thus limits the CNV sensitivity due to sampling error following Poisson distribution. Here we develop a PCR-based molecular barcoding NGS approach, quantitative amplicon sequencing (QASeq), for accurate absolute quantitation which is compatible with high multiplexing to include over 200 quantitation modules. By attaching barcodes to individual target molecules with high efficiency, 2-plex QASeq exhibits higher and more consistent conversion yield than ddPCR in absolute molecule count quantitation. Multiplexed QASeq improves CNV sensitivity to allow confident distinguishment of 2.05 ploidy from normal 2.00 ploidy. We applied multiplexed QASeq to serial longitudinal plasma cfDNA samples from patients with metastatic ERBB2+ (HER2+) breast cancer seeking association with tumor progression. We further show an RNA QASeq panel for targeted expression profiling on a wide range of RNA samples including tumor formalin-fixed, paraffin-embedded (FFPE) RNA.