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bioRxiv · 10.1101/091595

SiFit: A Method for Inferring Tumor Trees from Single-Cell Sequencing Data under Finite-site Models

Zafar, H.·Tzen, A.·Navin, N.·Chen, K.·Nakhleh, L.
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Abstract

Single-cell sequencing (SCS) enables the inference of tumor phylogenies that provide insights on intra-tumor heterogeneity and evolutionary trajectories. Recently introduced methods perform this task under the infinite-sites assumption, violations of which, due to chromosomal deletions and loss of heterozygosity, necessitate the development of inference methods that utilize finite-site models. We propose a statistical inference method for tumor phylogenies from noisy SCS data under a finite-sites model. The performance of our method on synthetic and experimental datasets from two colorectal cancer patients to trace evolutionary lineages in primary and metastatic tumors suggest that employing a finite-sites model leads to improved inference of tumor phylogenies.

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Zafar, H., Tzen, A., Navin, N., Chen, K., Nakhleh, L.. 2016-12-04. SiFit: A Method for Inferring Tumor Trees from Single-Cell Sequencing Data under Finite-site Models. https://doi.org/10.1101/091595

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