Robust Reconstruction of CRISPR and Tumor Lineage Using Depth Metrics

Abstract

Lineage reconstruction using CRISPR edited barcodes are becoming wide-spread and methods robust against noise are in need. Neighbor-Joining (NJ) algorithm is a robust distance based algorithm extensively used in phylogeny eld. NJ is also used for CRISPR-encoded-lineage (CEL) reconstruction with proper re-rooting since NJ is unrooted algorithm. However, we found NJ works without re-rooting for reconstructing CEL when the lineage contains multiple trees but not for a single tree. Examining why this is the case leads to the idea of depth metrics. The notion of depth metrics also naturally explains why Russell-Rao metric, previously found best metric for CEL reconstruction, works well. Furthermore, based on the probabilistic model of CEL, we constructed a new metric that performs better than Russell-Rao metric. We also propose inferring ancestral code during reconstruction instead of using a linkage method. These, together with Nearest-Neighbor-Interchange resulted in a new robust method for reconstructing CEL or tumor-cell-lineages which share same assumptions as CEL.

Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts

“…At the end of the lineage tracing experiment, the indel alleles are collected from individual cells by sequencing and paired with single-cell expression profiles of the cell state (22,23). Then, as in retrospective tracing approaches, computational approaches (29)(30)(31)(32)(33)(34) can reconstruct a phylogenetic tree that best models subclonal cellular relationships (e.g., by maximum-parsimony) from the observed shared or distinguishing alleles. Thus far, Cas9-enabled tracing has been successfully applied to study the cellular progenitor landscape in early mammalian embryogenesis (23,35), hematopoiesis (36), and neural development in zebrafish (22).…”

Theoretical Guarantees for Phylogeny Inference from Single-Cell Lineage Tracing

“…end while 16: end procedure (We note a similar algorithm has been presented in Sugino et. al [37], although no theoretical guarantees on accuracy are given in that work. )…”

“…Over time, characters may mutate from their unedited states at instantaneous rate λ according to an exponential distribution. While previous models have assumed a per-generation mutation rate [10,37,17], in our model, mutations occur independently from cell division. We believe this is a more accurate representation of current experimental regimes.…”

Dense reconstruction of elongated cell lineages: overcoming suboptimum lineage encoding and sparse cell sampling

“…This does not appear to limit our ability to track 100 serial cell cycles. In fact, we have previously observed that the number of alleles per unit is much less important compared to the rate of editing and the number of coding units [37,38]. A recent study on cell phylogenic analysis has also concluded similarly about the Cas9 base-editor's advantage in having many more targets despite limited edit outcomes [39].…”