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Updated: Jan 11, 2026
Detection of Copy Number Alterations Using Single Cell Sequencing
Published on: February 17, 2017
A medium throughput approach for single cell copy number variation sequencing towards efficient application in
Guanchuan Lin1, Caiming Chen1, Mengchang Xu1
1Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Guangdong Provincial Key Laboratory of Single Cell and Extracellular Vesicles, Southern Medical University, Guangzhou, Guangdong 510515, China; Precision Regenerative Medicine Research Centre, Medical Science Division, and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao 999078, China.
A new traceable medium-throughput single-cell copy number variation sequencing (scCNV-seq) method, msCNVS, offers a cost-effective and accurate solution for analyzing precious cells in clinical settings. This approach overcomes limitations of existing techniques, enabling reliable genomic analysis.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Single-cell copy number variation sequencing (scCNV-seq) is crucial for genomic analysis but faces challenges with high costs and biased results due to reliance on whole-genome preamplification or specialized equipment.
- These limitations are particularly problematic in clinical applications involving precious and limited cell samples.
Purpose of the Study:
- To develop a convenient, efficient, and accurate scCNV-seq method with an integrated data analysis workflow for clinical use.
- To overcome the limitations of existing scCNV-seq methods, ensuring confident and reliable output.
Main Methods:
- Developed traceable medium-throughput scCNV-seq (msCNVS) using barcode-containing modified Tn5 transposomes for direct cell labeling and early pooling, eliminating the need for preamplification.
- MsCNVS supports barcoding of 48-384 cells and uses dual indexes (i5, i7) for library construction.
- Implemented a novel bioinformatic process involving two-dimensional fitting for precise ploidy and copy number determination.
Main Results:
- MsCNVS demonstrated reliable CNV pattern distinction across 5 cell lines (292 cells) and high correlation with bulk sequencing (R=0.90-0.98).
- Achieved superior coverage uniformity compared to MDA and MALBAC, with minimal cross-contamination.
- Successfully detected CNVs in clinical samples, including abnormal blastocysts, circulating tumor cells, and patient-derived xenograft nuclei, distinguishing confident CNVs from ambiguous regions.
Conclusions:
- msCNVS provides a robust and highly efficient CNV-seq approach suitable for precious and rare cells.
- The method is particularly promising for applications in reproductive and cancer clinics.
