Evaluation

Overview

Teams will be evaluated based on the ranked ordering of enhancers that have been screened in enhancer AVVs in-vivo at the Allen Institute for Brain Science.

Validation data

Each enhancer AAV in our collection has been scored to determine specificity of the enhancer element with respect to a target cell type as well as density and intensity of cell labeling.

Briefly, each enhancer is screened as follows:

• Enhancer elements were cloned upstream of a minimal beta-globin promoter driving fluorescent protein SYFP2 and packaged in PHP.eB-serotype viruses that enable crossing of the blood brain barrier.
• Mice were injected retroorbitally (RO) with the enhancer AAV, sliced sagittally, and imaged confocally.
• Enhancer specificity was scored by manually evaluating SYFP2 fluorescence in serial brain slices. We defined enhancer specificity based on the density (relative to the expected distribution; from 0 to 2) and fluorescence intensity (from 0 to 2) of labeling. We also provide a combined score (0 - 3) of these values.

In total, the Allen Institue has experimentally validated hundreds of enhancer elements selected to be specific for a given cortical cell population. For further details of the Allen Institues enhancer screening efforts please refer to Graybuck and Daigle et al. 2021 or Mich et al. 2021.

Evaluation metrics

Metrics for evaluating cell type-specific functional enhancer prediction aim to characterize how well the ranked list of enhancers correspond to experimentally validated enhancer collections.