Strategies for resolving cellular phylogenies from sequential lineage tracing data
Sábháilte in:
| Foilsithe in: | bioRxiv (Jan 14, 2025) |
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| Príomhchruthaitheoir: | |
| Rannpháirtithe: | |
| Foilsithe / Cruthaithe: |
Cold Spring Harbor Laboratory Press
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| Ábhair: | |
| Rochtain ar líne: | Citation/Abstract Full text outside of ProQuest |
| Clibeanna: |
Níl clibeanna ann, Bí ar an gcéad duine le clib a chur leis an taifead seo!
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MARC
| LEADER | 00000nab a2200000uu 4500 | ||
|---|---|---|---|
| 001 | 3155458968 | ||
| 003 | UK-CbPIL | ||
| 022 | |a 2692-8205 | ||
| 024 | 7 | |a 10.1101/2025.01.14.632902 |2 doi | |
| 035 | |a 3155458968 | ||
| 045 | 0 | |b d20250114 | |
| 100 | 1 | |a Mulberry, Nicola | |
| 245 | 1 | |a Strategies for resolving cellular phylogenies from sequential lineage tracing data | |
| 260 | |b Cold Spring Harbor Laboratory Press |c Jan 14, 2025 | ||
| 513 | |a Working Paper | ||
| 520 | 3 | |a A combination of recent advancements in molecular recording devices and sequencing technologies has made it possible to generate lineage tracing data on the order of thousands of cells. Dynamic lineage recorders are able to generate random, heritable mutations which accumulate continuously on the timescale of developmental processes; this genetic information is then recovered using single-cell RNA sequencing. These data have the potential to hold rich phylogenetic information due to the irreversible nature of the editing process, a key feature of the employed CRISPR-based systems that deviates from traditional assumptions about molecular mutation processes, and recent technologies have furthermore made it possible for mutations to be acquired sequentially. Understanding the information content of these recorders remains an open area of investigation. Here, we model a sequentially-edited recording system and analyse the experimental conditions over which exact phylogenetic reconstruction occurs with high probability. We find, using simulation and theory, explicit parameter regimes over which simple and efficient distance-based reconstruction methods can accurately resolve the cellular phylogeny. We furthermore illustrate how our theoretical results could be used to help inform experimental design.Competing Interest StatementThe authors have declared no competing interest. | |
| 653 | |a Phylogenetics | ||
| 653 | |a Information processing | ||
| 653 | |a CRISPR | ||
| 653 | |a Phylogeny | ||
| 653 | |a Mutation | ||
| 653 | |a RNA editing | ||
| 653 | |a Information systems | ||
| 700 | 1 | |a Stadler, Tanja | |
| 773 | 0 | |t bioRxiv |g (Jan 14, 2025) | |
| 786 | 0 | |d ProQuest |t Biological Science Database | |
| 856 | 4 | 1 | |3 Citation/Abstract |u https://www.proquest.com/docview/3155458968/abstract/embedded/75I98GEZK8WCJMPQ?source=fedsrch |
| 856 | 4 | 0 | |3 Full text outside of ProQuest |u https://www.biorxiv.org/content/10.1101/2025.01.14.632902v1 |