The Human Phenotype Ontology in 2021 Köhler, Sebastian; Gargano, Michael; Matentzoglu, Nicolas ...
Nucleic acids research,
01/2021, Letnik:
49, Številka:
D1
Journal Article
Recenzirano
Odprti dostop
Abstract
The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities ...found in human disease. The HPO is now a worldwide standard for phenotype exchange. The HPO has grown steadily since its inception due to considerable contributions from clinical experts and researchers from a diverse range of disciplines. Here, we present recent major extensions of the HPO for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas. For example, the seizure subontology now reflects the International League Against Epilepsy (ILAE) guidelines and these enhancements have already shown clinical validity. We present new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease. These efforts will benefit software such as Exomiser by improving the accuracy and scope of cross-species phenotype matching. The computational modeling strategy used by the HPO to define disease entities and phenotypic features and distinguish between them is explained in detail.We also report on recent efforts to translate the HPO into indigenous languages. Finally, we summarize recent advances in the use of HPO in electronic health record systems.
Abstract
The Human Phenotype Ontology (HPO)—a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases—is used by thousands of researchers, clinicians, informaticians and ...electronic health record systems around the world. Its detailed descriptions of clinical abnormalities and computable disease definitions have made HPO the de facto standard for deep phenotyping in the field of rare disease. The HPO’s interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data. It also plays a key role in the popular Exomiser tool, which identifies potential disease-causing variants from whole-exome or whole-genome sequencing data. Since the HPO was first introduced in 2008, its users have become both more numerous and more diverse. To meet these emerging needs, the project has added new content, language translations, mappings and computational tooling, as well as integrations with external community data. The HPO continues to collaborate with clinical adopters to improve specific areas of the ontology and extend standardized disease descriptions. The newly redesigned HPO website (www.human-phenotype-ontology.org) simplifies browsing terms and exploring clinical features, diseases, and human genes.
Provision of a molecularly confirmed diagnosis in a timely manner for children and adults with rare genetic diseases shortens their “diagnostic odyssey,” improves disease management, and fosters ...genetic counseling with respect to recurrence risks while assuring reproductive choices. In a general clinical genetics setting, the current diagnostic rate is approximately 50%, but for those who do not receive a molecular diagnosis after the initial genetics evaluation, that rate is much lower. Diagnostic success for these more challenging affected individuals depends to a large extent on progress in the discovery of genes associated with, and mechanisms underlying, rare diseases. Thus, continued research is required for moving toward a more complete catalog of disease-related genes and variants. The International Rare Diseases Research Consortium (IRDiRC) was established in 2011 to bring together researchers and organizations invested in rare disease research to develop a means of achieving molecular diagnosis for all rare diseases. Here, we review the current and future bottlenecks to gene discovery and suggest strategies for enabling progress in this regard. Each successful discovery will define potential diagnostic, preventive, and therapeutic opportunities for the corresponding rare disease, enabling precision medicine for this patient population.
Addressing Indigenous rights and interests in genetic resources has become increasingly challenging in an open science environment that promotes unrestricted access to genomic data. Although ...Indigenous experiences with genetic research have been shaped by a series of negative interactions, there is increasing recognition that equitable benefits can only be realized through greater participation of Indigenous communities. Issues of trust, accountability and equity underpin Indigenous critiques of genetic research and the sharing of genomic data. This Perspectives article highlights identified issues for Indigenous communities around the sharing of genomic data and suggests principles and actions that genomic researchers can adopt to recognize community rights and interests in data.
Rare disease (RD) is a term used to describe numerous, heterogeneous diseases that are geographically disparate. Approximately 400 million people worldwide live with an RD equating to roughly 1 in 10 ...people, with 71.9% of RDs having a genetic origin. RDs present a distinctive set of challenges to people living with rare diseases (PLWRDs), their families, healthcare professionals (HCPs), healthcare system, and societies at large. The possibility of inheriting a genetic disease has a substantial social and psychological impact on affected families. In addition to other concerns, PLWRDs and their families may feel stigmatized, experience guilt, feel blamed, and stress about passing the disease to future generations. Stigma can affect all stages of the journey of PLWRDs and their families, from pre-diagnosis to treatment access, care and support, and compliance. It adversely impacts the quality of life of RD patients. To better explore the impact of stigma associated with genetic testing for RDs, we conducted a literature search on PubMed and Embase databases to identify articles published on stigma and RDs from January 2013 to February 2023. There is a dearth of literature investigating the dynamics of stigma and RD genetic testing. The authors observed that the research into the implications of stigma for patient outcomes in low- and middle-income countries (LMICs) and potential interventions is limited. Herein, the authors present a review of published literature on stigma with a focus on RD genetic testing, the associated challenges, and possible ways to address these.
MECP2 duplication syndrome (MDS) is a rare, X-linked, neurodevelopmental disorder caused by a duplication of the methyl-CpG-binding protein 2 (MECP2) gene-a gene in which loss-of-function mutations ...lead to Rett syndrome (RTT). MDS has an estimated live birth prevalence in males of 1/150,000. The key features of MDS include intellectual disability, developmental delay, hypotonia, seizures, recurrent respiratory infections, gastrointestinal problems, behavioural features of autism and dysmorphic features-although these comorbidities are not yet understood with sufficient granularity. This review has covered the past two decades of MDS case studies and series since the discovery of the disorder in 1999. After comprehensively reviewing the reported characteristics, this review has identified areas of limited knowledge that we recommend may be addressed by better phenotyping this disorder through an international data collection. This endeavour would also serve to delineate the clinical overlap between MDS and RTT.
Objective
To describe trends, age, and sex-specific patterns of population hospital admissions with a diagnosis of craniosynostosis (CS) in Australia.
Data Source
Population data for hospital ...separations (in-patient) from public and private hospitals (July 1996-June 2018) were obtained from the publicly available Australian Institute of Health and Welfare (AIHW) National Hospital Morbidity Database.
Main outcome measures
The outcome variables were hospital separation rates (HSR) (number of hospital separations divided by the estimated resident population ERP per year) and average length of stay (aLOS) (patient days divided by the number of hospital separations) with a diagnosis of CS. Trends in HSR and aLOS adjusted for age, sex, and type of CS were investigated by negative binomial regression presented as annual percent change (APC).
Results
In 8057 admissions identified, we observed no significant change in the annual trend for HSR for the 22-year period. However, a marginal annual decrease of 1.6% (95% CI: -0.7, -2.4) in the aLOS was identified for the same time period. HSR were higher for males, infants, and single suture synostosis. aLOS was 3.8 days (95% CI: 3.8, 3.9) per visit, longer for syndromic conditions.
Conclusion
There was a minor reduction in the average length of hospital stay for CS over the 22-year period potentially indicative of improved care. Population-level information on hospitalisations for rare craniofacial conditions can inform research, clinical, and surgical practice.
Protecting the rare during a rare pandemic Baynam, Gareth S; Wicking, Carol; Bhattacharya, Kaustuv ...
Medical journal of Australia,
July 2020, Letnik:
213, Številka:
2
Journal Article
Objective
To describe patterns and demographic characteristics of total-population hospital admissions with a diagnosis of Treacher Collins syndrome (TCS) in Australia.
Data Source
Population summary ...data for inpatient hospitals admissions (public and private) with a principal diagnosis of TCS (ICD10-AM-Q87.04) were obtained from the Australian Institute of Health and Welfare National Hospital Morbidity Database for a 11-year period (2002-2013).
Main Outcome Measures
The primary outcome was hospital separation rate (HSR), calculated by dividing the number of hospital separations by estimated resident population per year. Trends in HSR s adjusted for age and sex were investigated by negative binomial regression presented as annual percent change and the association of rates with age and sex was expressed as incidence rate ratio.
Results
In 244 admissions identified, we observed an increase of 4.55% (95% confidence interval CI −1.78, 11.29) in HSR's over the 11-year period. Rates were higher during infancy (1.87 95% CI 1.42, 2.42), declining markedly with increasing age. The average length of hospital stay was 6.09 days (95% CI 5.78, 6.40) per episode, but longer for females and infants.
Conclusions
Findings indicate an increase in hospitalization rates, especially among infants and females which potentially relates to early airway intervention procedures possibly influenced by sex specific-disease severity and phenotypic variability of TCS. Awareness of the TCS phenotype and improved access to genetic testing may support more personalized and efficient care. Total-population administrative data offers a potential to better understand the health burden of rare craniofacial diseases.
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