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Updated: Jun 4, 2025
Detection of Copy Number Alterations Using Single Cell Sequencing
Published on: February 17, 2017
Protocol for genome-wide analysis of somatic variants at single-cell resolution using primary template-directed DNA
Lucca L M Derks1, Anaïs J C N van Leeuwen1, Alexander S Steemers1
1Princess Máxima Center for Pediatric Oncology, Utrecht 3584 CS, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands.
None:
The study of somatic mutations in single cells provides insights into aging and carcinogenesis, which is complicated by the dependency on whole-genome amplification (WGA). Here, we describe a detailed workflow starting from single-cell isolation to WGA by primary template-directed amplification (PTA), sequencing, quality control, and downstream analyses. A machine learning approach, the PTA Analysis Toolkit (PTATO), is used to filter the hundreds to thousands of artificial variants induced by WGA from true mutations at high sensitivity and accuracy. For complete details on the use and execution of this protocol, please refer to Middelkamp et al.1.
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