The Human Cell Atlas needs a pre-registered analysis plan

The Human Cell Atlas preprint came out some days ago on bioRxiv. It describes a project to collect all the cell types in the human body in one big reference map.

Our mission: To create comprehensive reference maps of all human cells—the fundamental units of life—as a basis for both understanding human health and diagnosing, monitoring, and treating disease. [from]

The contributors to the project are a Who-is-who of the leaders in single cell genomics and this will be a fantastic data set when it comes out. Because in-depth analysis of resources like this provides the foundation of all biology, as you know.

I enjoyed reading the preprint. It puts the project into a historical perspective and discusses promises as well as limitations. It even references Borges’ `On Rigor in Science’. (I love well-read scientists!) And even if all that means nothing to you, it is still worth reading as a comprehensive summary of the current state-of-the-single-cell-art.

But I kept wondering, with a project like this, how do you know whether it is a success or not? How do you know that your reference map is really comprehensive and covers all (most?) of what it is supposed to find?

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Inferring tumor evolution from single-cell genomes

Series on Tumor Evolution

Everything is better if you do it with a Nested Effects Model – even inferring tumor evolution.

Let me introduce to you Oncogenetic Nested Effects Models, or for short OncoNEMs, which we just published in the new Single Cell collection of Genome Biology (see here). They exploit the fact that tumors accumulate mutations while they evolve, which leads to (noisy) subset relations between clones – exactly the type of pattern NEMs were made for.

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