All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons.
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 sensitivi...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2022-04-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1009487 |
| _version_ | 1828119663606759424 |
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| author | Vivekananda Sarangi Yeongjun Jang Milovan Suvakov Taejeong Bae Liana Fasching Shobana Sekar Livia Tomasini Jessica Mariani Flora M Vaccarino Alexej Abyzov |
| author_facet | Vivekananda Sarangi Yeongjun Jang Milovan Suvakov Taejeong Bae Liana Fasching Shobana Sekar Livia Tomasini Jessica Mariani Flora M Vaccarino Alexej Abyzov |
| author_sort | Vivekananda Sarangi |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T13:51:37Z |
| format | Article |
| id | doaj.art-848e1df22c1148058be996edd1e34985 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-04-11T13:51:37Z |
| publishDate | 2022-04-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-848e1df22c1148058be996edd1e349852022-12-22T04:20:34ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582022-04-01184e100948710.1371/journal.pcbi.1009487All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons.Vivekananda SarangiYeongjun JangMilovan SuvakovTaejeong BaeLiana FaschingShobana SekarLivia TomasiniJessica MarianiFlora M VaccarinoAlexej AbyzovAccurate 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.https://doi.org/10.1371/journal.pcbi.1009487 |
| spellingShingle | Vivekananda Sarangi Yeongjun Jang Milovan Suvakov Taejeong Bae Liana Fasching Shobana Sekar Livia Tomasini Jessica Mariani Flora M Vaccarino Alexej Abyzov All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons. PLoS Computational Biology |
| title | All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons. |
| title_full | All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons. |
| title_fullStr | All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons. |
| title_full_unstemmed | All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons. |
| title_short | All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons. |
| title_sort | all2 a tool for selecting mosaic mutations from comprehensive multi cell comparisons |
| url | https://doi.org/10.1371/journal.pcbi.1009487 |
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