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Transcriptomics and machine learning predict diagnosis and severity of growth hormone deficiency.

ABSTRACT: The effect of gene expression data on diagnosis remains limited. Here, we show how diagnosis and classification of growth hormone deficiency (GHD) can be achieved from a single blood sample using a combination of transcriptomics and random forest analysis. Prepubertal treatment-naive children with GHD (n = 98) were enrolled from the PREDICT study, and controls (n = 26) were acquired from online data sets. Whole blood gene expression was correlated with peak growth hormone (GH) using rank regression and a random forest algorithm tested for prediction of the presence of GHD and in classification of GHD as severe (peak GH <4 μg/l) and nonsevere (peak ≥4 μg/l). Performance was assessed using area under the receiver operating characteristic curve (AUC-ROC). Rank regression identified 347 probe sets in which gene expression correlated with peak GH concentrations (r = ± 0.28, P < 0.01). These 347 probe sets yielded an AUC-ROC of 0.95 for prediction of GHD status versus controls and an AUC-ROC of 0.93 for prediction of GHD severity. This study demonstrates highly accurate diagnosis and disease classification for GHD using a combination of transcriptomics and random forest analysis. NCT00256126 and NCT00699855. Merck and the National Institute for Health Research (CL-2012-06-005).

SUBMITTER: Murray PG

PROVIDER: S-EPMC5928867 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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Transcriptomics and machine learning predict diagnosis and severity of growth hormone deficiency.

Murray Philip G PG Stevens Adam A De Leonibus Chiara C Koledova Ekaterina E Chatelain Pierre P Clayton Peter E PE

JCI insight 20180405 7

<h4>Background</h4>The effect of gene expression data on diagnosis remains limited. Here, we show how diagnosis and classification of growth hormone deficiency (GHD) can be achieved from a single blood sample using a combination of transcriptomics and random forest analysis.<h4>Methods</h4>Prepubertal treatment-naive children with GHD (n = 98) were enrolled from the PREDICT study, and controls (n = 26) were acquired from online data sets. Whole blood gene expression was correlated with peak grow ...[more]

PMID: 29618660

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Project description:BackgroundThere have been few longitudinal studies assessing the effect of preoperative phenotypic severity on long-term esthetic outcomes in metopic craniosynostosis. This study evaluates the relationship between metopic severity and long-term esthetic outcomes using interfrontal angle (IFA) and CranioRate, a novel metopic synostosis severity measure.MethodsPatients with metopic craniosynostosis who underwent bifrontal orbital advancement and remodeling between 2012 and 2017 were reviewed. Preoperative computed tomography head scans were analyzed for IFA and CranioRate, a machine learning algorithm which generates quantitative severity ratings including metopic severity score (MSS) and cranial morphology deviation (CMD). Long-term esthetic outcomes were assessed by craniofacial surgeons using blinded 3-rater esthetic grading of clinical photos. Raters assessed Whitaker score and the presence of temporal hollowing, lateral orbital retrusion, frontal bone irregularities and/or "any visible irregularities."ResultsPreoperative scans were performed at a mean age of 7.7±3.4 months, with average MSS of 6/10, CMD of 200/300, and IFA of 116.8±13.8 degrees. Patients underwent bifrontal orbital advancement and remodeling at mean 9.9±3.1 months. The average time from operation to esthetic assessment was 5.4±1.0 years. Pearson correlation revealed a significant negative correlation between MSS and age at computed tomography ( r =-0.451, P =0.004) and IFA ( r =-0.371, P =0.034) and between IFA and age at surgery ( r =-0.383, P =0.018). In multinomial logistic regression, preoperative MSS was the only independent predictor of visible irregularities (odds ratio=2.18, B =0.780, P =0.024) and preoperative IFA alone significantly predicted Whitaker score, with more acute IFA predicting worse Whitaker score (odds ratio=0.928, B =-0.074, P =0.928).ConclusionsMore severe preoperative phenotypes of metopic craniosynostosis were associated with worse esthetic dysmorphology. Objective measures of preoperative metopic severity predicted long-term esthetic outcomes.

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Transcriptomics and machine learning predict diagnosis and severity of growth hormone deficiency.

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Transcriptomics and machine learning predict diagnosis and severity of growth hormone deficiency.

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