Prenatal phenotyping: A community effort to enhance the Human Phenotype Ontology

Human phenotype ontology; Prenatal diagnosis; Prenatal phenotypingOntología del fenotipo humano; Diagnóstico prenatal; Fenotipado prenatalOntologia del fenotip humà; Diagnòstic prenatal; Fenotipat prenatalTechnological advances in both genome sequencing and prenatal imaging are increasing our ability to accurately recognize and diagnose Mendelian conditions prenatally. Phenotype-driven early genetic diagnosis of fetal genetic disease can help to strategize treatment options and clinical preventive measures during the perinatal period, to plan in utero therapies, and to inform parental decision-making. Fetal phenotypes of genetic diseases are often unique and at present are not well understood; more comprehensive knowledge about prenatal phenotypes and computational resources have an enormous potential to improve diagnostics and translational research. The Human Phenotype Ontology (HPO) has been widely used to support diagnostics and translational research in human genetics. To better support prenatal usage, the HPO consortium conducted a series of workshops with a group of domain experts in a variety of medical specialties, diagnostic techniques, as well as diseases and phenotypes related to prenatal medicine, including perinatal pathology, musculoskeletal anomalies, neurology, medical genetics, hydrops fetalis, craniofacial malformations, cardiology, neonatal-perinatal medicine, fetal medicine, placental pathology, prenatal imaging, and bioinformatics. We expanded the representation of prenatal phenotypes in HPO by adding 95 new phenotype terms under the Abnormality of prenatal development or birth (HP:0001197) grouping term, and revised definitions, synonyms, and disease annotations for most of the 152 terms that existed before the beginning of this effort. The expansion of prenatal phenotypes in HPO will support phenotype-driven prenatal exome and genome sequencing for precision genetic diagnostics of rare diseases to support prenatal care.European Commission; National Human Genome Research Institute; NIH Office of the Director; The European Union's EIT-Health Innovation Program bp2020-2022, Grant/Award Numbers: #211015, #20062; NIH Office of the Director (OD), the European Union's Horizon 2020 research and innovation program, Grant/Award Number: 779257; NHGRI, Grant/Award Numbers: 2R24OD011883-05A1, 1U24HG011449-01A

External validation of models to estimate gestational age in the second and third trimester using ultrasound: A prospective multicentre observational study

Objectives: Accurate assessment of gestational age (GA) is important at both individual and population levels. The most accurate way to estimate GA in women who book late in pregnancy is unknown. The aim of this study was to externally validate the accuracy of equations for GA estimation in late pregnancy and to identify the best equation for estimating GA in women who do not receive an ultrasound scan until the second or third trimester. Design: This was a prospective, observational cross‐sectional study. Setting: 57 prenatal care centres, France. Participants: Women with a singleton pregnancy and a previous 11–14‐week dating scan that gave the observed GA were recruited over an 8‐week period. They underwent a standardised ultrasound examination at one time point during the pregnancy (15–43 weeks), measuring 12 foetal biometric parameters that have previously been identified as useful for GA estimation. Main Outcome Measures: A total of 189 equations that estimate GA based on foetal biometry were examined and compared with GA estimation based on foetal CRL. Comparisons between the observed GA and the estimated GA were made using R2, calibration slope and intercept. RMSE, mean difference and 95% range of error were also calculated. Results: A total of 2741 pregnant women were examined. After exclusions, 2339 participants were included. In the 20 best performing equations, the intercept ranged from −0.22 to 0.30, the calibration slope from 0.96 to 1.03 and the RSME from 0.67 to 0.87. Overall, multiparameter models outperformed single‐parameter models. Both the 95% range of error and mean difference increased with gestation. Commonly used models based on measurement of the head circumference alone were not amongst the best performing models and were associated with higher 95% error and mean difference. Conclusions: We provide strong evidence that GA‐specific equations based on multiparameter models should be used to estimate GA in late pregnancy. However, as all methods of GA assessment in late pregnancy are associated with large prediction intervals, efforts to improve access to early antenatal ultrasound must remain a priority. Trial Registration: The proposal for this study and the corresponding methodological review was registered on PROSPERO international register of systematic reviews (registration number: CRD4201913776)

Prenatal Diagnosis of Bilateral Ectrodactyly and Radial Agenesis Associated with Trisomy 10 Mosaicism

Ectrodactyly or split hand and foot malformations (SHFMs) are rare malformations of the limbs, characterized by median cles of the hands and feet, syndactyly, and aplasia and/or hypoplasia of the phalanges. ey represent a clinically and genetically heterogeneous disorder, with both sporadic and familial cases. Most of the genomic rearrangements identi�ed to date in some forms of SHFM are autosomal dominant traits, involving various chromosome regions. Bilateral radial ray defects comprise also a large heterogenous group of disorders, including trisomy 18, Fanconi anemia, and thrombocytopenia-absent-radius syndrome, not commonly associated with ectrodactyly. e present paper describes a case of ectrodactyly associated with bilateral radial ray defects, diagnosed in the �rst trimester of pregnancy, in a fetus affected by trisomy 10. Only four cases of sporadic and isolated ectrodactyly, diagnosed by ultrasonography between 14 and 22 weeks' gestation, have been reported. To our knowledge, the present case is the �rst report of mosaic trisomy 10 associated with SHFM and radial aplasia. Trisomy 10 is a rare lethal chromosomal abnormality, most frequently found in abortion products. Only six liveborn mosaic trisomy 10 infants, with severe malformations, dead in early infancy, have been reported. A severe clinical syndrome can be de�ned, comprising ear abnormalities, cle lip/palate, malformations of eyes, heart, and kidneys, and deformity of hands and feet and most oen associated with death neonatally or in early infancy

Prenatal phenotyping: A community effort to enhance the Human Phenotype Ontology.

Technological advances in both genome sequencing and prenatal imaging are increasing our ability to accurately recognize and diagnose Mendelian conditions prenatally. Phenotype-driven early genetic diagnosis of fetal genetic disease can help to strategize treatment options and clinical preventive measures during the perinatal period, to plan in utero therapies, and to inform parental decision-making. Fetal phenotypes of genetic diseases are often unique and at present are not well understood; more comprehensive knowledge about prenatal phenotypes and computational resources have an enormous potential to improve diagnostics and translational research. The Human Phenotype Ontology (HPO) has been widely used to support diagnostics and translational research in human genetics. To better support prenatal usage, the HPO consortium conducted a series of workshops with a group of domain experts in a variety of medical specialties, diagnostic techniques, as well as diseases and phenotypes related to prenatal medicine, including perinatal pathology, musculoskeletal anomalies, neurology, medical genetics, hydrops fetalis, craniofacial malformations, cardiology, neonatal-perinatal medicine, fetal medicine, placental pathology, prenatal imaging, and bioinformatics. We expanded the representation of prenatal phenotypes in HPO by adding 95 new phenotype terms under the Abnormality of prenatal development or birth (HP:0001197) grouping term, and revised definitions, synonyms, and disease annotations for most of the 152 terms that existed before the beginning of this effort. The expansion of prenatal phenotypes in HPO will support phenotype-driven prenatal exome and genome sequencing for precision genetic diagnostics of rare diseases to support prenatal care

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

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Aide à la décision à partir des connaissances, et des données (apprentissage automatique et réseaux de neurones) – exemple de l'aide au suivi de grossesse par échographie (Smart Ultrasound in Obstetrics and Gynecology - SUOG)

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