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

Published: 30 May 2023| Version 1 | DOI: 10.17632/c3r9chw9rb.1
Contributor:
Bioinformatics van Boxtel

Description

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 recurrency to distinguish PTA-artefacts from true mutations with high sensitivity (up to 90%), outperforming existing bioinformatic approaches. Our results show that PTATO enables studying somatic mutagenesis in the genomes of single cells with unprecedented sensitivity and accuracy.

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Institutions

Prinses Maxima Centrum voor Kinderoncologie

Categories

Genomics, Cancer, DNA, Mutation, Fanconi Anemia, DNA Mutation, Pediatric Acute Myeloid Leukemia, Genome Sequencing

Funding

New York Stem Cell Foundation

Dutch Cancer Society

12682

European Research Council

864499

Licence