Reconstruction of Cell Lineages Through CRISPR-induced DNA Mutations
"The recent advent of new CRISPR-based molecular tools allows the reconstruction of cell lineages based on the phylogenetical analysis of DNA mutations induced by CRISPR during development and promises to solve the lineage of complex model organisms at single-cell resolution (see image from McKenna et al Science 2016).
To date, however, no lineage reconstruction algorithms have been rigorously examined for their performance/robustness across diverse molecular tools, datasets, and number of cells/size of lineage trees. It also remains unclear whether new Machine-Learning algorithms that go beyond the classical ones developed for reconstructing phylogenetic trees, could consistently reconstruct cell lineages to a high degree of accuracy. The challenge - a partnership between The Allen Institute and DREAM - will comprise 3 subchallenges that consist of reconstructing cell lineage trees of different sizes and nature. In subchallenge 1, participants will be given experimental molecular data to reconstruct in vitro cell lineages of less than 100 cells. The ground truth is obtained from video-microscopy data. In subchallenge 2, participants will have to reconstruct an in silico generated tree of 1,000 cells from molecular data and using reconstructed lineages from surrogate trees of 100 cells. Finally for subchallenge 3, participants will have to reconstruct an in silico generated tree of 10,000 cells from molecular data and reconstructed cell lineages of around 1000 cells in size. Through the usage for training purposes of experimental and in silico generated data sets, the goal of this challenge is to mobilize a larger community for evaluating new optimal tree-building methods."
