Identifying facial phenotypes of genetic disorders using deep learning

Syndromic genetic conditions, in aggregate, affect 8% of the population. Many syndromes have recognizable facial features that are highly informative to clinical geneticists. Recent studies show that facial analysis technologies measured up to the capabilities of expert clinicians in syndrome identification. However, these technologies identified only a few disease phenotypes, limiting their role in clinical settings, where hundreds of diagnoses must be considered. Here we present a facial image analysis framework, DeepGestalt, using computer vision and deep-learning algorithms, that quantifies similarities to hundreds of syndromes. DeepGestalt out-performed clinicians in three initial experiments, two with the goal of distinguishing subjects with a target syndrome from other syndromes, and one of separating different genetic sub-types in Noonan syndrome. On the final experiment reflecting a real clinical setting problem, DeepGestalt achieved 91% top-10 accuracy in identifying the correct syndrome on 502 different images. The model was trained on a dataset of over 17,000 images representing more than 200 syndromes, curated through a community-driven phenotyping platform. DeepGestalt potentially adds considerable value to pheno-typic evaluations in clinical genetics, genetic testing, research and precision medicine.

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