Protocol for genome-wide analysis of somatic variants at single-cell resolution using primary template-directed DNA amplification
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.<sup>1</sup>.
Authors
- Vera M. Poort (ORCID: https://orcid.org/0000-0002-0933-853X)
- Ruben van Boxtel (ORCID: https://orcid.org/0000-0003-1285-2836)
- Lucca L. M. Derks (ORCID: https://orcid.org/0000-0001-9836-5558)
- Rico Hagelaar (ORCID: https://orcid.org/0000-0003-1622-6293)
- Sjors Middelkamp (ORCID: https://orcid.org/0000-0002-7027-9524)
- Mark Verheul (ORCID: https://orcid.org/0000-0002-2416-7492)
- Laurianne Trabut (ORCID: https://orcid.org/0009-0000-9618-661X)
- Alexander S. Steemers (ORCID: https://orcid.org/0000-0002-7162-7279)
- Anaïs J.C.N. van Leeuwen
- Markus J. van Roosmalen (ORCID: https://orcid.org/0000-0003-3329-1185)
Institutions
- Oncode Institute (NL)
- Princess Máxima Center (NL)
Publication Details
- Journal
- STAR Protocols
- Published
- 2024-12-20
- DOI
- https://doi.org/10.1016/j.xpro.2024.103499
- Citations
- 2
- Primary Topic
- Cancer Genomics and Diagnostics
- Type
- article
- Field-Weighted Citation Impact
- 0.57
Funders
- Stichting Kinderen Kankervrij
- Oncode Institute