Research Article

Phenotype risk scores identify patients with unrecognized Mendelian disease patterns

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Science  16 Mar 2018:
Vol. 359, Issue 6381, pp. 1233-1239
DOI: 10.1126/science.aal4043

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Hidden effects of Mendelian inheritance

Identifying the determinate factors of genetic disease has been quite successful for Mendelian inheritance of large-effect pathogenic variants. In these cases, two non- or low-functioning genes contribute to disease. However, Mendelian effects of lesser strength have generally been ignored when looking at genomic consequences in human health. Bastarache et al. used electronic records to identify the phenotypic effects of previously unidentified Mendelian variations. Their analysis suggests that individuals with undiagnosed Mendelian diseases may be more prevalent in the general population than assumed. Because of this, genetic analysis may be able to assist clinicians in arriving at a diagnosis.

Science, this issue p. 1233


Genetic association studies often examine features independently, potentially missing subpopulations with multiple phenotypes that share a single cause. We describe an approach that aggregates phenotypes on the basis of patterns described by Mendelian diseases. We mapped the clinical features of 1204 Mendelian diseases into phenotypes captured from the electronic health record (EHR) and summarized this evidence as phenotype risk scores (PheRSs). In an initial validation, PheRS distinguished cases and controls of five Mendelian diseases. Applying PheRS to 21,701 genotyped individuals uncovered 18 associations between rare variants and phenotypes consistent with Mendelian diseases. In 16 patients, the rare genetic variants were associated with severe outcomes such as organ transplants. PheRS can augment rare-variant interpretation and may identify subsets of patients with distinct genetic causes for common diseases.

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