The Human Phenotype Ontology in 2021.

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.

Birth prevalence of congenital heart defects in Western Australia, 1990-2016.

AIM: To describe the birth prevalence and characteristics of congenital heart defects in a geographically defined Australian population. METHODS: This descriptive, population-based study examined congenital heart defects in live births, stillbirths and pregnancy terminations ascertained by the Western Australian Register of Developmental Anomalies, 1990-2016. Birth prevalence (per 1000 births) was stratified by severity, known cause, maternal and birth characteristics, and primary diagnosis; and prevalence ratios were calculated for Aboriginal versus non-Aboriginal births. Temporal trends in prevalence, diagnosis age and infant mortality were examined. RESULTS: For births 1990-2010 (allowing 6 years for complete case ascertainment by 2016), 6419 cases were identified; prevalence was 11.5 per 1000 births (95% confidence interval (CI), 11.2-11.8). Severe defects were ascertained in 2.5 per 1000 births (95% CI 2.4-2.7). Most cases were liveborn (5842, 91.0%), and 28.9% had other birth defects. Prevalence was slightly higher in Aboriginal births (prevalence ratio 1.1; 95% CI 1.0-1.2); and the infant mortality rate more than doubled (13.4% vs. 5.8%, P < 0.001). Prenatal diagnosis increased over time but, in remote areas, was significantly lower for Aboriginal versus non-Aboriginal cases (3.1% vs. 9.3%; P = 0.008). A cause was identified in 920 cases (14.3%), more often for severe defects (347, 24.4%); 63% of known causes were rare diseases. Congenital heart defects associated with fetal alcohol spectrum disorder were much more common in Aboriginal births (prevalence ratio 82; 95% CI 28-239). CONCLUSIONS: Earlier detection of congenital heart defects and improved survival has occurred over time, although discrepancies between ethnic groups and regions warrant further investigation and strategic action.

Closing the sepsis gap: an exploration of sepsis presentations at a remote north Australian emergency department.

INTRODUCTION: The objective of this study was to explore the demographic characteristics, disease specifics and outcomes of adult patients with suspected sepsis presenting to a remote Australian emergency department (ED). A retrospective, uninterrupted time series audit of ED patients presenting with suspected sepsis was conducted. A total of 189 remote presentations were reviewed based on the time of clinician identification of sepsis. METHODS: Retrospective cohort analysis was performed for all adult patients with suspected or confirmed sepsis. RESULTS: A majority of patients presenting with sepsis to a remote hospital were Indigenous (61.9%) with a large proportion (34.9%) presenting by ambulance. Median age was 50 years. Indigenous patients (44.7%, 95%CI 34.1-55.9) were more likely to meet the quick Sequential (sepsis-related) Organ Failure Assessment criteria compared to non-Indigenous patients (27.1% 95%CI 16.6-41.0) (p=0.05 95%CI -1.1-34.3) with higher rates of critical care admission (34.2% v 10.4%) (difference 23.8, p=0.003, 95%CI 7.7-37.5). Congruent with previous research, Indigenous status did not confer a difference in sepsis mortality (12.1% v 11.8%, p=0.91). CONCLUSION: Remote Indigenous patients have worse clinical sepsis scores, are more likely to present by ambulance and require skin and soft tissue source control. This cohort has higher lactate values and critical care requirements but similar mortality rates. Improving access to culturally safe medical care could address this disparity.

Indigenous-led precision public health: a new starting point.

Precision public healthcare has been applied to bring about positive change, narrowing the gap in healthcare inequity for Aboriginal peoples. Three such examples include the Mappa, Lyfe Languages, and Pilbra Faces projects, which were all developed through engagement and codesign with Indigenous Australians and each meet a distinct critical need. The Mappa project offers patients and healthcare providers with the necessary geographical information to navigate and maximally utilize available healthcare services. Lyfe Languages is a community driven translational tool that empowers indigenous languages in healthcare. The Pilbara Faces project aims to create a database of clinical measurements enabling better disease diagnosis and monitoring. These three projects have been integrated into a multi-faceted precision public health program, the Healthy Pilbara Project Initiative, acting synergistically to improve the lives of Aboriginal peoples living in Western Australia.

Barriers and Considerations for Diagnosing Rare Diseases in Indigenous Populations.

Advances in omics and specifically genomic technologies are increasingly transforming rare disease diagnosis. However, the benefits of these advances are disproportionately experienced within and between populations, with Indigenous populations frequently experiencing diagnostic and therapeutic inequities. The International Rare Disease Research Consortium (IRDiRC) multi-stakeholder partnership has been advancing toward the vision of all people living with a rare disease receiving an accurate diagnosis, care, and available therapy within 1 year of coming to medical attention. In order to further progress toward this vision, IRDiRC has created a taskforce to explore the access barriers to diagnosis of rare genetic diseases faced by Indigenous peoples, with a view of developing recommendations to overcome them. Herein, we provide an overview of the state of play of current barriers and considerations identified by the taskforce, to further stimulate awareness of these issues and the passage toward solutions. We focus on analyzing barriers to accessing genetic services, participating in genomic research, and other aspects such as concerns about data sharing, the handling of biospecimens, and the importance of capacity building.