Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox.

ABSTRACT: Detection of somatic mutations in single cells has been severely hampered by technical limitations of whole-genome amplification. Novel technologies including primary template-directed amplification (PTA) significantly improved the accuracy of single-cell whole-genome sequencing (WGS) but still generate hundreds of artifacts per amplification reaction. We developed a comprehensive bioinformatic workflow, called the PTA Analysis Toolbox (PTATO), to accurately detect single base substitutions, insertions-deletions (indels), and structural variants in PTA-based WGS data. PTATO includes a machine learning approach and filtering based on recurrence to distinguish PTA artifacts from true mutations with high sensitivity (up to 90%), outperforming existing bioinformatic approaches. Using PTATO, we

SUBMITTER: Middelkamp S 

PROVIDER: S-EPMC10504672 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature