All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons

Vivekananda Sarangi, Yeongjun Jang, Milovan Suvakov, Taejeong Bae, Liana Fasching, Shobana Sekar, Livia Tomasini, Jessica Mariani, Flora M. Vaccarino, Alexej Abyzov

Research output: Contribution to journalArticlepeer-review

Abstract

Accurate discovery of somatic mutations in a cell is a challenge that partially lays in immaturity of dedicated analytical approaches. Approaches comparing a cell’s genome to a control bulk sample miss common mutations, while approaches to find such mutations from bulk suffer from low sensitivity. We developed a tool, All2, which enables accurate filtering of mutations in a cell without the need for data from bulk(s). It is based on pair-wise comparisons of all cells to each other where every call for base pair substitution and indel is classified as either a germline variant, mosaic mutation, or false positive. As All2 allows for considering dropped-out regions, it is applicable to whole genome and exome analysis of cloned and amplified cells. By applying the approach to a variety of available data, we showed that its application reduces false positives, enables sensitive discovery of high frequency mutations, and is indispensable for conducting high resolution cell lineage tracing.

Original languageEnglish (US)
Article numbere1009487
JournalPLoS computational biology
Volume18
Issue number4
DOIs
StatePublished - Apr 2022

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Ecology
  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Cellular and Molecular Neuroscience
  • Computational Theory and Mathematics

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