Ensemble of nucleic acid absolute quantitation modules for copy number variation detection and RNA profiling

Lucia Ruojia Wu; Peng Dai; Michael Xiangjiang Wang; Sherry Xi Chen; Evan N. Cohen; Gitanjali Jayachandran; Jinny Xuemeng Zhang; Angela V. Serrano; Nina Guanyi Xie; Naoto T. Ueno; James M. Reuben; Carlos H. Barcenas; David Yu Zhang

doi:10.1038/s41467-022-29487-y

Ensemble of nucleic acid absolute quantitation modules for copy number variation detection and RNA profiling

Lucia Ruojia Wu, Peng Dai, Michael Xiangjiang Wang, Sherry Xi Chen, Evan N. Cohen, Gitanjali Jayachandran, Jinny Xuemeng Zhang, Angela V. Serrano, Nina Guanyi Xie, Naoto T. Ueno, James M. Reuben, Carlos H. Barcenas, David Yu Zhang

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6 Scopus citations

Abstract

Current gold standard for absolute quantitation of a specific DNA sequence is droplet digital PCR (ddPCR), which has been applied to copy number variation (CNV) detection. However, the number of quantitation modules in ddPCR is 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 scalable to 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 allowing confident distinguishment of 2.05 ploidy from normal 2.00 ploidy. We apply 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.

Original language	English (US)
Article number	1791
Journal	Nature communications
Volume	13
Issue number	1
DOIs	https://doi.org/10.1038/s41467-022-29487-y
State	Published - Dec 2022

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

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Wu, L. R., Dai, P., Wang, M. X., Chen, S. X., Cohen, E. N., Jayachandran, G., Zhang, J. X., Serrano, A. V., Xie, N. G., Ueno, N. T., Reuben, J. M., Barcenas, C. H., & Zhang, D. Y. (2022). Ensemble of nucleic acid absolute quantitation modules for copy number variation detection and RNA profiling. Nature communications, 13(1), Article 1791. https://doi.org/10.1038/s41467-022-29487-y

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title = "Ensemble of nucleic acid absolute quantitation modules for copy number variation detection and RNA profiling",

abstract = "Current gold standard for absolute quantitation of a specific DNA sequence is droplet digital PCR (ddPCR), which has been applied to copy number variation (CNV) detection. However, the number of quantitation modules in ddPCR is 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 scalable to 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 allowing confident distinguishment of 2.05 ploidy from normal 2.00 ploidy. We apply 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.",

author = "Wu, {Lucia Ruojia} and Peng Dai and Wang, {Michael Xiangjiang} and Chen, {Sherry Xi} and Cohen, {Evan N.} and Gitanjali Jayachandran and Zhang, {Jinny Xuemeng} and Serrano, {Angela V.} and Xie, {Nina Guanyi} and Ueno, {Naoto T.} and Reuben, {James M.} and Barcenas, {Carlos H.} and Zhang, {David Yu}",

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year = "2022",

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doi = "10.1038/s41467-022-29487-y",

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AU - Jayachandran, Gitanjali

AU - Zhang, Jinny Xuemeng

AU - Serrano, Angela V.

AU - Xie, Nina Guanyi

AU - Ueno, Naoto T.

AU - Reuben, James M.

AU - Barcenas, Carlos H.

AU - Zhang, David Yu

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Ensemble of nucleic acid absolute quantitation modules for copy number variation detection and RNA profiling

Abstract

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