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.

The Medical Action Ontology: A tool for annotating and analyzing treatments and clinical management of human disease

BACKGROUND

Navigating the clinical literature to determine the optimal clinical management for rare diseases presents significant challenges. We introduce the Medical Action Ontology (MAxO), an ontology specifically designed to organize medical procedures, therapies, and interventions.

METHODS

MAxO incorporates logical structures that link MAxO terms to numerous other ontologies within the OBO Foundry. Term development involves a blend of manual and semi-automated processes. Additionally, we have generated annotations detailing diagnostic modalities for specific phenotypic abnormalities defined by the Human Phenotype Ontology (HPO). We introduce a web application, POET, that facilitates MAxO annotations for specific medical actions for diseases using the Mondo Disease Ontology.

FINDINGS

MAxO encompasses 1,757 terms spanning a wide range of biomedical domains, from human anatomy and investigations to the chemical and protein entities involved in biological processes. These terms annotate phenotypic features associated with specific disease (using HPO and Mondo). Presently, there are over 16,000 MAxO diagnostic annotations that target HPO terms. Through POET, we have created 413 MAxO annotations specifying treatments for 189 rare diseases.

CONCLUSIONS

MAxO offers a computational representation of treatments and other actions taken for the clinical management of patients. Its development is closely coupled to Mondo and HPO, broadening the scope of our computational modeling of diseases and phenotypic features. We invite the community to contribute disease annotations using POET (https://poet.jax.org/). MAxO is available under the open-source CC-BY 4.0 license (https://github.com/monarch-initiative/MAxO).

FUNDING

NHGRI 1U24HG011449-01A1 and NHGRI 5RM1HG010860-04.

De novo TRPM3 missense variant associated with neurodevelopmental delay and manifestations of cerebral palsy

We identified a de novo heterozygous transient receptor potential cation channel subfamily M (melastatin) member 3 (TRPM3) missense variant, p.(Asn1126Asp), in a patient with developmental delay and manifestations of cerebral palsy (CP) using phenotype-driven prioritization analysis of whole-genome sequencing data with Exomiser. The variant is localized in the functionally important ion transport domain of the TRPM3 protein and predicted to impact the protein structure. Our report adds TRPM3 to the list of Mendelian disease-associated genes that can be associated with CP and provides further evidence for the pathogenicity of the variant p.(Asn1126Asp).

The Medical Action Ontology: A Tool for Annotating and Analyzing Treatments and Clinical Management of Human Disease

Navigating the vast landscape of clinical literature to find optimal treatments and management strategies can be a challenging task, especially for rare diseases. To address this task, we introduce the Medical Action Ontology (MAxO), the first ontology specifically designed to organize medical procedures, therapies, and interventions in a structured way. Currently, MAxO contains 1757 medical action terms added through a combination of manual and semi-automated processes. MAxO was developed with logical structures that make it compatible with several other ontologies within the Open Biological and Biomedical Ontologies (OBO) Foundry. These cover a wide range of biomedical domains, from human anatomy and investigations to the chemical and protein entities involved in biological processes. We have created a database of over 16000 annotations that describe diagnostic modalities for specific phenotypic abnormalities as defined by the Human Phenotype Ontology (HPO). Additionally, 413 annotations are provided for medical actions for 189 rare diseases. We have developed a web application called POET (https://poet.jax.org/) for the community to use to contribute MAxO annotations. MAxO provides a computational representation of treatments and other actions taken for the clinical management of patients. The development of MAxO is closely coupled to the Mondo Disease Ontology (Mondo) and the Human Phenotype Ontology (HPO) and expands the scope of our computational modeling of diseases and phenotypic features to include diagnostics and therapeutic actions. MAxO is available under the open-source CC-BY 4.0 license (https://github.com/monarch-initiative/MAxO).

Interpretable prioritization of splice variants in diagnostic next-generation sequencing

A critical challenge in genetic diagnostics is the computational assessment of candidate splice variants, specifically the interpretation of nucleotide changes located outside of the highly conserved dinucleotide sequences at the 5' and 3' ends of introns. To address this gap, we developed the Super Quick Information-content Random-forest Learning of Splice variants (SQUIRLS) algorithm. SQUIRLS generates a small set of interpretable features for machine learning by calculating the information-content of wild-type and variant sequences of canonical and cryptic splice sites, assessing changes in candidate splicing regulatory sequences, and incorporating characteristics of the sequence such as exon length, disruptions of the AG exclusion zone, and conservation. We curated a comprehensive collection of disease-associated splice-altering variants at positions outside of the highly conserved AG/GT dinucleotides at the termini of introns. SQUIRLS trains two random-forest classifiers for the donor and for the acceptor and combines their outputs by logistic regression to yield a final score. We show that SQUIRLS transcends previous state-of-the-art accuracy in classifying splice variants as assessed by rank analysis in simulated exomes, and is significantly faster than competing methods. SQUIRLS provides tabular output files for incorporation into diagnostic pipelines for exome and genome analysis, as well as visualizations that contextualize predicted effects of variants on splicing to make it easier to interpret splice variants in diagnostic settings.

Interpretable Clinical Genomics with a Likelihood Ratio Paradigm

Human Phenotype Ontology (HPO)-based analysis has become standard for genomic diagnostics of rare diseases. Current algorithms use a variety of semantic and statistical approaches to prioritize the typically long lists of genes with candidate pathogenic variants. These algorithms do not provide robust estimates of the strength of the predictions beyond the placement in a ranked list, nor do they provide measures of how much any individual phenotypic observation has contributed to the prioritization result. However, given that the overall success rate of genomic diagnostics is only around 25%-50% or less in many cohorts, a good ranking cannot be taken to imply that the gene or disease at rank one is necessarily a good candidate. Here, we present an approach to genomic diagnostics that exploits the likelihood ratio (LR) framework to provide an estimate of (1) the posttest probability of candidate diagnoses, (2) the LR for each observed HPO phenotype, and (3) the predicted pathogenicity of observed genotypes. LIkelihood Ratio Interpretation of Clinical AbnormaLities (LIRICAL) placed the correct diagnosis within the first three ranks in 92.9% of 384 case reports comprising 262 Mendelian diseases, and the correct diagnosis had a mean posttest probability of 67.3%. Simulations show that LIRICAL is robust to many typically encountered forms of genomic and phenomic noise. In summary, LIRICAL provides accurate, clinically interpretable results for phenotype-driven genomic diagnostics.

Abstract OT1-01-04: A phase 2, open-label study of imprime PGG (Imprime), a novel beta glucan, with pembrolizumab (Pembro) in chemotherapy-resistant metastatic triple negative breast cancer (TNBC)

By blocking the interaction of PD-L1 with PD-1, immune checkpoint inhibitors (CPI) can unleash specific, anti-cancer killing function of activated cytotoxic T cells in patients (pts) for whom there is evidence of an ongoing anti-cancer immune response (PD-L1 expression and/or activated T cells within the tumor bed). Single agent CPI therapy has provided substantial clinical benefit to pts with multiple cancer types. Though effective, response rates are typically limited (˜15-30% of pts depending on tumor type) and therapy fails to benefit the majority of pts. For these pts there is often limited or no evidence of an ongoing T cell-based immune response. Agents that stimulate the anti-cancer immune response may be particularly promising in expanding the clinical responsiveness to CPI therapies. Imprime is a novel beta glucan derived from Saccharomyces acting mechanistically as a pathogen-associated molecular pattern (PAMP) or non-self danger signal, to awaken and activate the innate immune system. Imprime drives a cascade of immune activating events activating tumor-specific cytotoxic T cells. Imprime treatment elicits repolarization of the immunosuppressive microenvironment while activating the maturation of antigen presenting cells. Imprime has significantly enhanced the efficacy of CPI therapy in preclinical tumor models. In humans, Imprime-mediated innate immune activation requires the formation of an immune complex with naturally-occurring anti-beta glucan antibodies (ABA). Formation of this complex is dependent upon sufficient ABA levels. Imprime is now being studied in combination with pembro (KEYTRUDA®), a humanized mAb against PD-1 which has been previously studied in TNBC pts.This phase 2 study explores the treatment combination in pts with metastatic TNBC who progressed following at least one line of chemotherapy and pts with metastatic melanoma who progressed following CPI therapy with sufficient pre-treatment ABA levels (˜50% of screened patients). The study is a Simon 2-stage design. Specific to the TNBC tumor type, a sample size of 12 pts in Stage 1 is planned. Criteria to advance to Stage 2 are ≤4 GR 3/4 AEs and ≥2 objective responses in TNBC. An additional 30 TNBC pts may be enrolled in Stage 2. Main eligibility criteria are metastatic TNBC after chemotherapy in the metastatic setting and serum ABA ≥20 µg/mL. The primary endpoints are ORR and safety; secondary endpoints are TTR, CRR, DoR, PFS, and OS. Efficacy will be analyzed for ORR and CRR as point estimates with 95% CI and for PFS, OS, DoR and TTR as descriptive summaries. Safety parameters will be summarized. Exploratory endpoints include ORR and PFS based on irRECIST. This study aims to collect pre- and early on-treatment tumor (6 wks post-1st dose) biopsies and peripheral blood to assess the impact of the treatment combination on immune activating events in the periphery and at the tumor site. As of June 2017, 11 sites were open and 4 pts were in treatment. The trial is sponsored by Biothera Pharmaceuticals, Inc. in collaboration with Merck & Co. (ClinicalTrials.gov NCT02981303) For information, contact Richard D. Huhn, MD, Biothera Med Dir at rhuhn@biothera.com or 651-256-4657.

Citation Format: O'Day SJ, Stopeck AT, Huhn RD, Gargano MA, Prathikanti R, Ma B, Mattson PM, Lowe JR, Bose N, Ertelt KE, Ottoson NC, Uhlik MT, Graff JR, Chisamore MJ. A phase 2, open-label study of imprime PGG (Imprime), a novel beta glucan, with pembrolizumab (Pembro) in chemotherapy-resistant metastatic triple negative breast cancer (TNBC) [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr OT1-01-04.

shinyGEO: a web-based application for analyzing gene expression omnibus datasets

The Gene Expression Omnibus (GEO) is a public repository of gene expression data. Although GEO has its own tool, GEO2R, for data analysis, evaluation of single genes is not straightforward and survival analysis in specific GEO datasets is not possible without bioinformatics expertise. We describe a web application, shinyGEO, that allows a user to download gene expression data sets directly from GEO in order to perform differential expression and survival analysis for a gene of interest. In addition, shinyGEO supports customized graphics, sample selection, data export and R code generation so that all analyses are reproducible. The availability of shinyGEO makes GEO datasets more accessible to non-bioinformaticians, promising to lead to better understanding of biological processes and genetic diseases such as cancer.

AVAILABILITY AND IMPLEMENTATION

Web application and source code are available from http://gdancik.github.io/shinyGEO/ CONTACT: dancikg@easternct.eduSupplementary information: Supplementary data are available at Bioinformatics online.

Two randomized, double-blind, placebo-controlled, dose-escalation phase 1 studies evaluating BTH1677, a 1, 3-1,6 beta glucan pathogen associated molecular pattern, in healthy volunteer subjects

BACKGROUND

BTH1677 is a beta glucan pathogen associated molecular pattern (PAMP) currently being investigated as a novel cancer therapy. Here, the initial safety and pharmacokinetic (PK) results of BTH1677 in healthy subjects are reported.

SUBJECTS AND METHODS

In the Phase 1a single-dosing study, subjects were randomized (3:1 per cohort) to a single intravenous (i.v.) infusion of BTH1677 at 0.5, 1, 2, 4, or 6 mg/kg or placebo, respectively. In the Phase 1b multi-dosing study, subjects were randomized (3:1 per cohort) to 7 daily i.v. infusions of BTH1677 at 1, 2, or 4 mg/kg or placebo, respectively. Safety and PK non-compartmental analyses were performed.

RESULTS

Thirty-six subjects (N = 24 Phase 1a; N = 12 Phase 1b) were randomized to treatment. No deaths or serious adverse events occurred in either study. Mild or moderate adverse events (AEs) occurred in 67% of BTH1677-treated subjects in both studies. Treatment-related AEs (occurring in ≥10% of subjects) included dyspnea, flushing, headache, nausea, paraesthesia, and rash in Phase 1a and conjunctivitis and headache in Phase 1b. BTH1677 serum concentration was linear with dose. Clearance, serum elimination half-life (t1/2) and volume of distribution (Vss) were BTH1677 dose-independent. In Phase 1b, area under the curve, t1/2, and Vss values were larger at steady state on days 6-30 versus day 0.

CONCLUSIONS

BTH1677 was well tolerated after single doses up to 6 mg/kg and after 7 daily doses up to 4 mg/kg.

Determination by HPLC of adrenalin (E) and of noradrenalin (NE) in certain species of mesopelagic fish in the Strait of Messina

The presence of adrenalin (E) and noradrenalin (NE) was found by HPLC both in the photophores and at other tissue levels of numerous species of mesopelagic fish in The Strait of Messina, with the aim of determining the incidence of these catecholamines in photophores, in light transmission and the eventual presence at other tissue levels.

[Bencyclane in memory disorders. Treatment of memory disorders caused by electroshock in a group of depressed patients]

Subjects treated with electroshock and subjected simultaneously to bencyclan at a dose of 00 mg (2 ampoules) i.v. and 100 mg (1 pill) per os pro die did not present dysmnesia either during the intervals between one electroshock treatment and another, nor at the conclusion of treatment (on average 12 sessions in about 40 days), while a control group treated at the same rhythm and with the same number of sessions, but without bencyclan, presented considerable memory lapses which disappeared only after a lengthy period of this latter treatment. Memory disturbances have been evaluated with a memorization test to which all patients were subjected. This test belongs to the group of intellectual efficiency reactive tests used in the psychology laboratory of the Catholic University of Milan; it consists of a group of 12 figures of common objects which, once observed, have to be recalled exactly immediately and some time later by the patient, who has to indicate the name and position of the objects represented in the chart.