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We hypothesized that a polygenic score for height (PGS<jats:sub>height<\/jats:sub>) could identify children with non-familial idiopathic short stature (ISS-NF) who carry a polygenic predisposition to shorter height that is not accounted for by existing measures.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Methods<\/jats:title>\n            <jats:p>We studied 534 pediatric participants in an electronic health record (EHR)-linked DNA biobank (BioVU) who had been evaluated for short stature by an endocrinologist. Participants were classified as having one of five short stature subtypes: primary growth disorders, secondary growth disorders, idiopathic short stature (ISS), which was sub-classified into familial (ISS-F) and non-familial (ISS-NF), and constitutional delay of puberty (ISS-DP). Differences in polygenic predisposition between subtypes were analyzed using a validated PGS<jats:sub>height<\/jats:sub> which was standardized to a standard deviation score (SDS). Adult height predictions were generated using the PGS<jats:sub>height<\/jats:sub> and mid-parental height (MPH). Within-child differences in height predictions were compared across subtypes. Logistic regression models and AUC analyses were used to test the ability of the PGS<jats:sub>height<\/jats:sub> to differentiate ISS-NF from growth disorders. The incremental improvement (\u0394AUC) of adding the PGS<jats:sub>height<\/jats:sub> to prediction models with MPH was also estimated.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Among the 534 participants, 29.0% had secondary growth disorders, 24.9% had ISS-F, 20.2% had ISS-NF, 17.2% had ISS-DP, and 8.6% had primary growth disorders. Participants with ISS-NF had similar PGS<jats:sub>height<\/jats:sub> values to those with ISS-F (difference [\u0394] in PGS<jats:sub>height<\/jats:sub> SDS [95% CI]\u2009=\u20090.19 [\u2212\u20090.31 to 0.70], <jats:italic>p<\/jats:italic>\u2009=\u20090.75). Predicted heights generated by the PGS<jats:sub>height<\/jats:sub> were lower than the MPH estimate for children with ISS-NF (\u0394[PGS<jats:sub>height<\/jats:sub>\u2009\u2212\u2009MPH]\u2009=\u2009\u2009\u2212\u20090.37 SDS; <jats:italic>p<\/jats:italic>\u2009=\u20093.2\u2009\u00d7\u200910<jats:sup>\u22129<\/jats:sup>) but not for children with ISS-F (\u0394\u2009=\u2009\u2009\u2212\u20090.07; <jats:italic>p<\/jats:italic>\u2009=\u20090.56). Children with ISS-NF also had lower PGS<jats:sub>height<\/jats:sub> than children with primary growth disorders (\u0394PGS<jats:sub>height<\/jats:sub>\u2009=\u2009\u2009\u2212\u20090.53 [\u2212\u20091.03 to\u2009\u2212\u20090.04], <jats:italic>p<\/jats:italic>\u2009=\u20090.03) and secondary growth disorders (\u0394\u2009=\u2009\u2009\u2212\u20090.45 [\u2212\u20090.80 to\u2009\u2212\u20090.10], <jats:italic>p<\/jats:italic>\u2009=\u20090.005). The PGS<jats:sub>height<\/jats:sub> improved model discrimination between ISS-NF and children with primary (\u0394AUC,\u2009+\u20090.07 [95% CI, 0.02 to 0.17]) and secondary growth disorders (\u0394AUC,\u2009+\u20090.03 [95% CI, 0.01 to 0.10]).<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Some children with ISS-NF have an unrecognized polygenic predisposition to shorter height, similar to children with ISS-F and greater than those with growth disorders. A PGS<jats:sub>height<\/jats:sub> could aid clinicians in identifying children with a benign, polygenic predisposition to shorter height.\n<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/s13073-025-01455-3","type":"journal-article","created":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T16:04:45Z","timestamp":1742400285000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["A polygenic score for height identifies an unmeasured genetic predisposition among pediatric patients with idiopathic short stature"],"prefix":"10.1186","volume":"17","author":[{"given":"John P.","family":"Shelley","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingjian","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Josh F.","family":"Peterson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara L.","family":"Van Driest","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jill H.","family":"Simmons","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan D.","family":"Mosley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,3,19]]},"reference":[{"key":"1455_CR1","doi-asserted-by":"publisher","unstructured":"Polygenic Risk Score Task Force of the International Common Disease Alliance, Adeyemo A, Balaconis MK, et al. 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