# A new way of looking at transcription factor assays

## TL;DR

This paper introduces a new high-throughput assay for studying transcription factors, demonstrated on PAX6, which improves understanding of genetic variants and outperforms computational predictions.

## Contribution

The paper presents a novel functional assay for transcription factors that enables comprehensive analysis of genetic variants with high concordance to clinical data.

## Key findings

- The assay successfully measured effects of 95% of missense variants in PAX6.
- Experimental data outperformed state-of-the-art computational variant effect predictors.
- The assay is broadly applicable to most transcription factors.

## Abstract

Advances in high-throughput functional genomics have enabled researchers to measure many thousands of individual genetic variants in a single gene in parallel using techniques such as deep mutational scanning (Fowler and Fields, 2014). The success of these approaches depends on the availability of assays that can measure a wide range of protein functions. In their recent work, Kudla and colleagues (McDonnell et al, 2024) applied deep mutational scanning to the transcription factor PAX6, which has a key role in eye development, and described a new high-throughput functional assay that could be applied to almost any transcription factor. The authors successfully measured the effects of 95% of missense variants in PAX6 and show that their assay results are highly concordant with known clinical variants. Notably, they also undertook a wide-ranging survey of computational variant effect predictors and show that their experimental data outperformed cutting-edge algorithms.

AF Rubin discusses a new high-throughput functional assay for transcription factors applied for a deep mutational scanning study of the transcription factor PAX6 by Kudla and colleagues (McDonnell et al, 2023) in this issue of Molecular Systems Biology.