The Human Phenotype Ontology in 2024: phenotypes around the world.

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs.

Buprenorphine dispensing before and after the April 2021 X-Waiver exemptions: An interrupted time series analysis.

BACKGROUND: Until the end of 2022, a special registration, known as the X-waiver, was required to prescribe buprenorphine in the US. Before its removal, US federal regulations trialed an X-waiver exemption, initiated on April 28, 2021, which permitted buprenorphine prescribing for up to 30 patients without additional training. We aimed to understand if these regulatory changes impacted buprenorphine dispensing. METHODS: We conducted an interrupted time series analysis to understand changes in buprenorphine dispensing during the 26 weeks after the X-waiver exemption compared to the expected baseline trend established in the 26 weeks before using the IQVIA Longitudinal Prescription claims database. The primary outcome was number of new buprenorphine prescribers nationwide (defined as no prior buprenorphine prescription dispensed in the last 26 weeks). Segmented regression estimated relative changes in buprenorphine dispensing at 1, 13, and 26 weeks post-X-waiver change. RESULTS: A total of 15,517,525 prescriptions filled for 1,328,172 patients (43.4 % female) ordered by 62,312 providers were included for analysis. At 26 weeks post-X-waiver change, there was no change in the number of new prescribers compared to the expected baseline trend (-2.7 % [95 % CI:-8.3,2.9]). The number of new (15.2 % [4.6,25.8]) and existing (1.7 % [0.9,2.4]) patients and patients per prescriber (4.3 % [3,5.6]) increased. Buprenorphine prescriptions reimbursed by Medicaid increased (7.5 % [6.6,8.4]) while commercial fills decreased (-3.4 % [-5.3,-1.5]). CONCLUSIONS: The number of new prescribers did not increase six months post-X-waiver exemption while new patients continued to enter treatment at higher-than-expected rates. These findings suggest that additional interventions beyond the recent X-waiver removal may be needed to increase access to buprenorphine.

Bent pinkies: Quantifying fifth finger clinodactyly in a sample of U.S. adults.

Mild curvature of the fifth finger (or clinodactyly) is a relatively common trait. While severe forms can cause functional impairment and are a feature of certain congenital syndromes, mild clinodactyly is considered a minor morphological variant. Despite exhibiting continuous variation, clinodactyly is rarely treated as a quantitative trait. Consequently, the degree of fifth finger curvature in the general population and the factors that impact this curvature are not well understood. In the present study, we measured fifth finger curvature in a sample of 1,295 U.S. adults and investigated the role of sex, age and body size. We found that clinodactyly exhibited a non-normal distribution. All participants displayed some degree of curvature, but it tended to be slight with an overall mean of 3.68 degrees (median: 3.58 degrees). In only 0.8% of cases did the curvature exceed the nominal 10-degree threshold for clinically meaningful clinodactyly. We did not find statically significant sex differences. Further, there was no meaningful relationship with height and only a weak positive relationship with age. We found that clinodactyly showed asymmetry; the curvature was greater on the left than on the right fifth finger (p < 2.2e-16), but this was not influenced by sex, age, or height. These results suggest the possibility that the kind of ubiquitous mild clinodactyly observed in the general population may be etiologically distinct from more rare and severe forms of the condition.

U.S. Adult Perspectives on Facial Images, DNA, and Other Biometrics.

Applications of biometrics in various societal contexts have been increasing in the United States, and policy debates about potential restrictions and expansions for specific biometrics (such as facial recognition and DNA identification) have been intensifying. Empirical data about public perspectives on different types of biometrics can inform these debates. We surveyed 4048 adults to explore perspectives regarding experience and comfort with six types of biometrics; comfort providing biometrics in distinct scenarios; trust in social actors to use two types of biometrics (facial images and DNA) responsibly; acceptability of facial images in eight scenarios; and perceived effectiveness of facial images for five tasks. Respondents were generally comfortable with biometrics. Trust in social actors to use biometrics responsibly appeared to be context specific rather than dependent on biometric type. Contrary to expectations given mounting attention to dataveillance concerns, we did not find sociodemographic factors to influence perspectives on biometrics in obvious ways. These findings underscore a need for qualitative approaches to understand the contextual factors that trigger strong opinions of comfort with and acceptability of biometrics in different settings, by different actors, and for different purposes and to identify the informational needs relevant to the development of appropriate policies and oversight.

A survey of U.S. public perspectives on facial recognition technology and facial imaging data practices in health and research contexts.

Facial imaging and facial recognition technologies, now common in our daily lives, also are increasingly incorporated into health care processes, enabling touch-free appointment check-in, matching patients accurately, and assisting with the diagnosis of certain medical conditions. The use, sharing, and storage of facial data is expected to expand in coming years, yet little is documented about the perspectives of patients and participants regarding these uses. We developed a pair of surveys to gather public perspectives on uses of facial images and facial recognition technologies in healthcare and in health-related research in the United States. We used Qualtrics Panels to collect responses from general public respondents using two complementary and overlapping survey instruments; one focused on six types of biometrics (including facial images and DNA) and their uses in a wide range of societal contexts (including healthcare and research) and the other focused on facial imaging, facial recognition technology, and related data practices in health and research contexts specifically. We collected responses from a diverse group of 4,048 adults in the United States (2,038 and 2,010, from each survey respectively). A majority of respondents (55.5%) indicated they were equally worried about the privacy of medical records, DNA, and facial images collected for precision health research. A vignette was used to gauge willingness to participate in a hypothetical precision health study, with respondents split as willing to (39.6%), unwilling to (30.1%), and unsure about (30.3%) participating. Nearly one-quarter of respondents (24.8%) reported they would prefer to opt out of the DNA component of a study, and 22.0% reported they would prefer to opt out of both the DNA and facial imaging component of the study. Few indicated willingness to pay a fee to opt-out of the collection of their research data. Finally, respondents were offered options for ideal governance design of their data, as "open science"; "gated science"; and "closed science." No option elicited a majority response. Our findings indicate that while a majority of research participants might be comfortable with facial images and facial recognition technologies in healthcare and health-related research, a significant fraction expressed concern for the privacy of their own face-based data, similar to the privacy concerns of DNA data and medical records. A nuanced approach to uses of face-based data in healthcare and health-related research is needed, taking into consideration storage protection plans and the contexts of use.

Prevalence of Torus Palatinus and association with dental arch shape in a multi-ethnic cohort.

Objectives: Torus Palatinus (TP) is a bony projection located on the oral surface of the hard palate. The trait is typically benign, has an unknown etiology, and varies widely in phenotypic expression. Prior studies suggest differences in TP prevalence by sex and ancestry, but the reported rates vary, even within a single ancestral group. We assessed the prevalence of TP and its association with palatal shape in a large multi-ethnic cohort of normal individuals. Methodology: 1102 adults were included (625 with European ancestry, 377 with West African anscestry, and 100 with East Asian ancestry). 3D digital dental casts were obtained and rated. TP frequencies were compared between sexes and/or ethnicities using Chi-squared tests. Dental cast models were then landmarked, and canonical variates analysis was performed to test for shape differences between those with and without TP. Results: Females had a significantly higher rate of TP than males across all three ancestral groups (p≤0.004). In males, no significant differences were found among ethnicities. Ancestral differences in TP frequency were driven by females, with East Asians having the highest rate (34.69%), followed by Europeans (24.88%) and West Africans (15.22%). Shape differences were found only in Asians and Africans, indicated a shorter and wider palate in presence of TP. Conclusions: Ethnic differences in TP frequency were present only in females. Further, females have considerably higher rates of TP than males in each population tested. Further studies of TP at earlier time-points and in connection to other aspects of craniofacial growth may shed light on these sex and ethnic differences.

GWAS reveals loci associated with velopharyngeal dysfunction.

Velopharyngeal dysfunction (VPD) occurs when the muscular soft palate (velum) and lateral pharyngeal walls are physically unable to separate the oral and nasal cavities during speech production leading to hypernasality and abnormal speech reduction. Because VPD is often associated with overt or submucous cleft palate, it could be present as a subclinical phenotype in families with a history of orofacial clefting. A key assumption to this model is that the overt and subclinical manifestations of the orofacial cleft phenotype exist on a continuum and therefore share common etiological factors. We performed a genome-wide association study in 976 unaffected relatives of isolated CP probands, 54 of whom had VPD. Five loci were significantly (p < 5 × 10-8) associated with VPD: 3q29, 9p21.1, 12q21.31, 16p12.3 and 16p13.3. An additional 15 loci showing suggestive evidence of association with VPD were observed. Several genes known to be involved in orofacial clefting and craniofacial development are located in these regions, such as TFRC, PCYT1A, BNC2 and FREM1. Although further research is necessary, this could be an indication for a potential shared genetic architecture between VPD and cleft palate, and supporting the hypothesis that VPD is a subclinical phenotype of orofacial clefting.

Adherence to escitalopram treatment in depression: a study of electronically compiled dosing histories in the 'Depression: the search for phenotypes' study.

Poor adherence to depression treatment is common. Understanding determinants of poor adherence to therapy is crucial to ensure optimal clinical outcomes. The aim of this study was to describe characteristics of dosing history in participants with depression receiving once daily escitalopram. Participants were randomly assigned to interpersonal psychotherapy (IPT) or pharmacotherapy. Participants assigned to IPT who did not evidence a response or remission had escitalopram added to their treatment. Adherence to pharmacotherapy was assessed using an electronically monitored pill cap (MEMS). Fifty-four participants on escitalopram alone and 32 on escitalopram+IPT were monitored. After 200 days, 71.7% of the participants in the escitalopram group and 54.8% of those in the escitalopram+IPT group were still engaged with the dosing regimen. Of those engaged in the dosing regimen, 17.9% (average over 210 days) of the participants did not take their medication (nonexecution). In 69% of the days participants took the correct dosage required. On average, participants had three drug holidays and the mean length of a holiday was 7 days per patient. No difference in adherence patterns was observed between patients receiving escitalopram alone vs. IPT+escitalopram. Early discontinuation of treatment and suboptimal daily execution of the prescribed regimen are the most common facets of poor adherence in this study population.