1. Dan Frumkin*, Adam Wasserstrom*, Shai Kaplan, Uriel Feige & Ehud Shapiro * equal contributors Genomic variability within an organism exposes its cell lineage tree

2. An interdisciplinary slide BiologyComputer Science DNA ….ACTTCTGGCTA….. String

3. An interdisciplinary slide BiologyComputer Science DNA ….ACTTCTGGCTA….. String Sequencing

4. An interdisciplinary slide C. elegansRooted labeled binary tree BiologyComputer Science

5. Cell lineage reconstruction C. elegansRooted labeled binary tree Cell lineage tree (959 cells)

6. Organism cell lineage tree 4 6 Zygote Divided cell Dead cell Extant cell (959? XXX OR INCLUDING DEAD CELLS?)

7. “Human Cell Lineage Project” Biology Organism Human cell lineage tree (~50,000,000,000,000 cells) ?

8. “Human Cell Lineage Project” Two questions: 1.Who cares? 2.Is it possible?

9. “Human Cell Lineage Project” 1. Who cares? Developmental biology Immunology Stem-cell research Brain research Cancer research …

10. “Human Cell Lineage Project” 1.Who cares? … many biologists 2. Is it possible?

11. An imaginary organism: genomic variability encodes cell lineage

12. Reconstructing a cell sample lineage tree Actual lineage tree Reconstructed lineage tree

13. Potential problems in cell lineage reconstruction Colliding mutations Silent cell divisions

14. Genomic variability and cell lineage “the genome is the same in every cell in the body [except for some white blood cells]” (Gilbert, Developmental Biology) We discovered it has enough variability to encode cell lineage

15. Genomic variability encodes cell lineage Many types of mutations We focus on microsattelites (MS)

16. Genomic variability encodes cell lineage Many types of mutations We focus on microsattelites (MS) Fast mutators (slippage), silent phenotype, abundant (~1.5 million in Human and Mouse) In Human, each cell division induces on average ~48 MS mutations!

17. Genomic variability encodes cell lineage In Human, each cell division induces on average ~48 MS mutations! Probability of silent cell division is effectively zero (< XXX 10 -21 ) But colliding MS mutations are possible, hence further analysis is required

18. Simulation of lineage reconstruction on random trees

21. Mathematical analysis of lineage reconstruction

22. Under assumptions consistent with known biological information, the cell lineage tree of a Human (Mouse) in which no cell underwent more than 40 cell divisions, can be reconstructed from its MS mutation information with zero errors, with probability > 97.5%. Mathematical analysis of lineage reconstruction

23. “Human Cell Lineage Project” 1.Who cares? Many biologists. 2.Is it possible? Theoretically, yes. 3.Is it feasible?

24. DNA  Cell lineage tree Extraction of cell identifiers Phylogenetic Inference algorithm

25. DNA source Actual tree Reconstructed tree Result Single cells OK Discrete cell clones OK Heterogeneous tissue Problematic