Targeted/exome sequencing identified mutations in ten Chinese patients diagnosed with Noonan syndrome and related disorders

Phenotypic and genotypic spectrum of noonan syndrome: A retrospective analysis of 46 consecutive pediatric patients presented at a regional cardiac center in China

Background

Noonan syndrome (NS) is relatively common but poorly recognized. We aimed to describe the phenotypic and genotypic spectrum of NS in a Chinese cohort.

Method

The study retrospectively investigated consecutive pediatric patients who presented at the Guangdong cardiovascular institute between 2018 and 2020 with confirmed known NS-relevant mutations determined by exome sequencing. Dates of genetic testing, Age, sex, institution of genetic testing, mutated gene (related to NS) and its classification, heterozygosity, and parental origin were identified from the sequencing reports. Facial features, cardiac defect and other clinical characteristics were also assessed. Comparisons of categorical variables between groups were examined by Chi-square test or Fisher's exact test when appropriate. Intraclass correlation coefficient (ICC) was performed to evaluate the reliability of evaluation of facial features between different evaluators.

Results

The most prevalent mutated genes were PTPN11 (37.0%) and RAF1 (19.6%), and most mutations were pathogenic (67.4%) and de novo (87.0%). Most patients were with NS-relevant facial features (97.4%) and cardiac defects (92.7%), where ventricular hypertrophy, pulmonary valve stenosis, and atrial septal defect were the most prevalent. Patients with mutated RAF1 appeared to be diagnosed at an older age than those with mutated PTPN11, and with higher prevalence of mitral regurgitation, hypertrophic cardiomyopathy, and ventricular hypertrophy, but lower prevalence of pulmonary valve stenosis and pulmonary artery stenosis. Patients presented at an age ≥2 years appeared to be with fewer NS-relevant facial features and cardiac defects than those aged <2 years.

Conclusions

These findings indicated featured distributions of phenotypic and genotypic spectrum in Chinese pediatric patients, which might be helpful for early NS diagnosis.

RAF1 mutation leading to hypertrophic cardiomyopathy in a Chinese family with a history of sudden cardiac death: A diagnostic insight into Noonan syndrome

BACKGROUND

Hypertrophic cardiomyopathy (HCM) is predominantly caused by mutations in sarcomeric genes. However, a subset of cases is attributed to genetic disorders unrelated to sarcomeric genes, such as Noonan syndrome (NS) and other RASopathies. In this study, we present a family with a history of sudden cardiac death (SCD) and focus on two adults with syndromic left ventricular hypertrophy (LVH).

METHODS

Clinical evaluations, including echocardiography, were conducted to assess cardiac manifestations. Whole-exome sequencing was performed to identify potential genetic variants underlying syndromic LVH in the study participants.

RESULTS

Whole-exome sequencing revealed a missense variant in the RAF1 gene, c.782C>T (p.Pro261Leu). This variant confirmed the diagnosis of NS in the affected individuals.

CONCLUSION

The findings of this study underscore the importance of family history investigation and genetic testing in diagnosing syndromic LVH. By identifying the underlying genetic cause, clinicians can better understand the etiology of RAS-HCM and its association with SCD in young adults.

Clinical Exome Sequencing Identifies NDP Gene Variants in Two Chinese Families with X-Linked Norrie Disease

Purpose: To explore the genetic defects in two Chinese families with X-linked Norrie disease (ND). Methods: We analyzed two Chinese families with ND at molecular level through clinical exome sequencing and the variations were identified by Sanger sequencing. Results: Two genetic variations were found in the NDP gene by clinical exome sequencing, a partial deletion of 801 bp contained the whole exon 2 and a missense variant (164G>A) within codon 55 that resulted in the interchange of cysteine by phenylalanine. Clinical findings were more severe in the patients who presented the missense variant. Conclusion: We report two genetic variations in the NDP gene in Chinese that extend the mutational and phenotypic spectra of NDP gene, and also demonstrate the feasibility of clinical exome sequencing in application of molecular diagnosis.

Effects of Noonan Syndrome-Germline Mutations on Mitochondria and Energy Metabolism

Noonan syndrome (NS) and related Noonan syndrome with multiple lentigines (NSML) contribute to the pathogenesis of human diseases in the RASopathy family. This family of genetic disorders constitute one of the largest groups of developmental disorders with variable penetrance and severity, associated with distinctive congenital disabilities, including facial features, cardiopathies, growth and skeletal abnormalities, developmental delay/mental retardation, and tumor predisposition. NS was first clinically described decades ago, and several genes have since been identified, providing a molecular foundation to understand their physiopathology and identify targets for therapeutic strategies. These genes encode proteins that participate in, or regulate, RAS/MAPK signalling. The RAS pathway regulates cellular metabolism by controlling mitochondrial homeostasis, dynamics, and energy production; however, little is known about the role of mitochondrial metabolism in NS and NSML. This manuscript comprehensively reviews the most frequently mutated genes responsible for NS and NSML, covering their role in the current knowledge of cellular signalling pathways, and focuses on the pathophysiological outcomes on mitochondria and energy metabolism.

Automated Facial Recognition for Noonan Syndrome Using Novel Deep Convolutional Neural Network With Additive Angular Margin Loss

BACKGROUND

Noonan syndrome (NS), a genetically heterogeneous disorder, presents with hypertelorism, ptosis, dysplastic pulmonary valve stenosis, hypertrophic cardiomyopathy, and small stature. Early detection and assessment of NS are crucial to formulating an individualized treatment protocol. However, the diagnostic rate of pediatricians and pediatric cardiologists is limited. To overcome this challenge, we propose an automated facial recognition model to identify NS using a novel deep convolutional neural network (DCNN) with a loss function called additive angular margin loss (ArcFace).

METHODS

The proposed automated facial recognition models were trained on dataset that included 127 NS patients, 163 healthy children, and 130 children with several other dysmorphic syndromes. The photo dataset contained only one frontal face image from each participant. A novel DCNN framework with ArcFace loss function (DCNN-Arcface model) was constructed. Two traditional machine learning models and a DCNN model with cross-entropy loss function (DCNN-CE model) were also constructed. Transfer learning and data augmentation were applied in the training process. The identification performance of facial recognition models was assessed by five-fold cross-validation. Comparison of the DCNN-Arcface model to two traditional machine learning models, the DCNN-CE model, and six physicians were performed.

RESULTS

At distinguishing NS patients from healthy children, the DCNN-Arcface model achieved an accuracy of 0.9201 ± 0.0138 and an area under the receiver operator characteristic curve (AUC) of 0.9797 ± 0.0055. At distinguishing NS patients from children with several other genetic syndromes, it achieved an accuracy of 0.8171 ± 0.0074 and an AUC of 0.9274 ± 0.0062. In both cases, the DCNN-Arcface model outperformed the two traditional machine learning models, the DCNN-CE model, and six physicians.

CONCLUSION

This study shows that the proposed DCNN-Arcface model is a promising way to screen NS patients and can improve the NS diagnosis rate.

Molecular and phenotypic spectrum of Noonan syndrome in Chinese patients

Noonan syndrome (NS) is a common autosomal dominant/recessive disorder. No large-scale study has been conducted on NS in China, which is the most populous country in the world. Next-generation sequencing (NGS) was used to identify pathogenic variants in patients that exhibited NS-related phenotypes. We assessed the facial features and clinical manifestations of patients with pathogenic or likely pathogenic variants in the RAS-MAPK signaling pathway. Gene-related Chinese NS facial features were described using artificial intelligence (AI).NGS identified pathogenic variants in 103 Chinese patients in eight NS-related genes: PTPN11 (48.5%), SOS1 (12.6%), SHOC2 (11.7%), KRAS (9.71%), RAF1 (7.77%), RIT1 (6.8%), CBL (0.97%), NRAS (0.97%), and LZTR1 (0.97%). Gene-related facial representations showed that each gene was associated with different facial details. Eight novel pathogenic variants were detected and clinical features because of specific genetic variants were reported, including hearing loss, cancer risk due to a PTPN11 pathogenic variant, and ubiquitous abnormal intracranial structure due to SHOC2 pathogenic variants. NGS facilitates the diagnosis of NS, especially for patients with mild/moderate and atypical symptoms. Our study describes the genotypic and phenotypic spectra of NS in China, providing new insights into distinctive clinical features due to specific pathogenic variants.

Dermatological manifestations in Noonan syndrome: a prospective multicentric study of 129 patients positive for mutation

BACKGROUND

Data on dermatological manifestations of Noonan syndrome (NS) remain heterogeneous and are based on limited dermatological expertise.

OBJECTIVES

To describe the dermatological manifestations of NS, compare them with the literature findings, and test for dermatological phenotype-genotype correlations with or without the presence of PTPN11 mutations.

METHODS

We performed a large 4-year, prospective, multicentric, collaborative dermatological and genetic study.

RESULTS

Overall, 129 patients with NS were enrolled, including 65 patients with PTPN11-NS, 34 patients with PTPN11-NS with multiple lentigines (NSML), and 30 patients with NS who had a mutation other than PTPN11. Easy bruising was the most frequent dermatological finding in PTPN11-NS, present in 53·8% of patients. Multiple lentigines and café-au-lait macules (n ≥ 3) were present in 94% and 80% of cases of NSML linked to specific mutations of PTPN11, respectively. Atypical forms of NSML could be associated with NS with RAF1 or NRAS mutations. In univariate analysis, patients without a PTPN11 mutation showed (i) a significantly higher frequency of keratinization disorders (P = 0·001), including keratosis pilaris (P = 0·005), ulerythema ophryogenes (P = 0·0001) and palmar and/or plantar hyperkeratosis (P = 0·06, trend association), and (ii) a significantly higher frequency of scarce scalp hair (P = 0·035) and scarce or absent eyelashes (P = 0·06, trend association) than those with PTPN11 mutations.

CONCLUSIONS

The cutaneous phenotype of NS with a PTPN11 mutation is generally mild and nonspecific, whereas the absence of a PTPN11 mutation is associated with a high frequency of keratinization disorders and hair abnormalities.