Completeness estimation of large-scale single-cell sequencing projects

During embryonic development, cells undergo differentiation into highly specialized cell types. Taking advantage of single-cell RNA sequencing, substantial resources have been invested towards cataloguing these differentiated cell types by their transcriptomic profiles. Despite the extensive efforts to profile different organs and their cellular compositions, metrics to assess the completeness of such datasets have been lacking. In this cellular biodiversity analysis, we used the increasingly available single-cell data together with statistical methods, originally developed for assessing the species richness of ecological communities, to provide cellular diversity estimates for any organ based on single-cell RNA sequencing data, as well as estimating how cell types are distributed along different organ systems. Deriving from such cellular richness estimates, we establish a statistical framework that allows estimation of the completeness of any large-scale single-cell profiling projects, after which additional sequencing efforts do not anymore reveal new insights into an organ’s cellular composition. Such estimates can serve as stoppage-points for the ongoing sequencing projects for more cost-efficient completion of the remaining profiling on various human tissues.