Validation of a computational phenotype for finding patients eligible for genetic testing for pathogenic PTEN variants across three centers

Exploring the Prevalence of Oral Features for Early Detection of PTEN Hamartoma Tumour Syndrome

AIMS

Patients with PTEN hamartoma tumour syndrome (PHTS) have an increased risk of developing cancer due to a pathogenic germline variant in the PTEN tumour suppressor gene. Early recognition of PHTS facilitates initiation of cancer surveillance which is highly effective in preventing the development of advanced malignancies. PHTS is rare and due to its varied phenotype, even within families, oral abnormalities may be a valuable tool in the identification of these patients at an early stage before cancer development.

MATERIALS AND METHODS

Between 1997 and 2020, phenotypic characteristics were evaluated in 81 paediatric (median age: 9 years) and 86 adult (median age: 40 years) PHTS patients by one of 2 medical experts during yearly surveillance visits at a Dutch PHTS expertise centre. Oral features evaluated included gingival hypertrophy, oral papillomas, and high palate (in adults).

RESULTS

Within adults, gingival hypertrophy was present in 94%, oral papillomas in 88%, and a high palate in 89%. All adult patients had at least one of these oral features, and 99% showed at least 2 oral features. Oral features were less common in paediatric patients, especially under 11 years of age. Gingival hypertrophy was observed in 44% and oral papillomas in 54% of paediatric patients.

CONCLUSIONS

The presence of 2 or 3 oral features may indicate PHTS in adults or adolescents, especially if macrocephaly is present. Dental professionals are well-positioned to recognise these oral manifestations could be related to PHTS. They can initiate an overall clinical assessment of the patient by alerting the patient's medical practitioner of the findings and the possible need for genetic testing. This could significantly improve outcomes, including life expectancy, for patients and possibly for their relatives.

CLINICAL RELEVANCE

Dental professionals are ideally placed to recognise oral features and initiate early assessment of PHTS which could significantly improve patient outcomes.

Phenotypic presentation of Mendelian disease across the diagnostic trajectory in electronic health records

PURPOSE

To investigate the phenotypic presentation of Mendelian disease across the diagnostic trajectory in the electronic health record (EHR).

METHODS

We applied a conceptual model to delineate the diagnostic trajectory of Mendelian disease to the EHRs of patients affected by 1 of 9 Mendelian diseases. We assessed data availability and phenotype ascertainment across the diagnostic trajectory using phenotype risk scores and validated our findings via chart review of patients with hereditary connective tissue disorders.

RESULTS

We identified 896 individuals with genetically confirmed diagnoses, 216 (24%) of whom had fully ascertained diagnostic trajectories. Phenotype risk scores increased following clinical suspicion and diagnosis (P < 1 × 10-4, Wilcoxon rank sum test). We found that of all International Classification of Disease-based phenotypes in the EHR, 66% were recorded after clinical suspicion, and manual chart review yielded consistent results.

CONCLUSION

Using a novel conceptual model to study the diagnostic trajectory of genetic disease in the EHR, we demonstrated that phenotype ascertainment is, in large part, driven by the clinical examinations and studies prompted by clinical suspicion of a genetic disease, a process we term diagnostic convergence. Algorithms designed to detect undiagnosed genetic disease should consider censoring EHR data at the first date of clinical suspicion to avoid data leakage.

Phenotypic convergence: a novel phenomenon in the diagnostic process of Mendelian genetic disorders

Introduction

The study of Mendelian disease has yielded a large body of knowledge about the phenotypic presentation of disease. Less is known about the way the diseases are reflected in the electronic health record (EHR).

Aim

To develop an EHR-based model of the diagnostic trajectory and investigate data availability and the longitudinal distribution of signs and symptoms of a Mendelian disorder within EHRs.

Methods

We created a conceptual model to specify key time points of the diagnostic trajectory and applied it to individuals with genetically confirmed hereditary connective tissue diseases (HCTD). Using the model, we assessed EHR data availability within each time interval. We tested the performance of phenotype risk scores (PheRS), an algorithm that detects Mendelian disease patterns and assessed the phenotypic expression of HCTD over the diagnostic trajectory.

Results

We identified 251 individuals with HCTD; 79 (35%) of these patients had a fully ascertained diagnostic trajectory. There were few documented signs and symptoms prior to clinical suspicion that evoked an HCTD disorder (median PheRS 0.14); once suspicion was documented, median PheRS increased to 1.87 (SD). The majority (72%) of phenotypic features were identified post clinical suspicion.

Discussion

Using a novel conceptual model for the diagnostic trajectory of Mendelian disease, we demonstrated that phenotype ascertainment is, in part, driven by the diagnostic process and that many findings are only documented following clinical suspicion and diagnosis, a process we term phenotypic convergence. Therefore, algorithms that aim to detect undiagnosed Mendelian disease should censor EHR data to avoid data leakage.