Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

Köhler, Sebastian; Carmody, Leigh C.; Vasilevsky, Nicole; Jacobsen, Julius O. B.; Daniš, Daniel; Gourdine, Jean-Philippe; Gargano, Michael; Harris, Nomi L.; Matentzoglu, Nicolas; McMurry, Julie A.; Osumi-Sutherland, David; Cipriani, Valentina; Balhoff, James P.; Conlin, Tom; Blau, Hannah; Baynam, Gareth; Palmer, Richard L.; Gratian, Dylan; Dawkins, Hugh; Segal, Michael M.; Jansen, Anna; Muaz, Ahmed; Chang, W.; Bergerson, Jenna; Laulederkind, Stanley J. F.; Yüksel, Zafer; Beltrán, Sergi; Freeman, Alexandra F.; Sergouniotis, Panagiotis I.; Durkin, Daniel W.; Storm, Andrea L.; Hanauer, Marc; Brudno, Michael; Bello, Susan M.; Sincan, Murat; Rageth, Kayli; Wheeler, Matthew T.; Oegema, Renske; Lourghi, Halima; Rocca, Maria G. Della; Thompson, Rachel; Castellanos, Francisco; Priest, James R.; Cunningham‐Rundles, Charlotte; Hegde, Ayushi; Lovering, Ruth C.; Hajek, Catherine; Olry, Annie; Notarangelo, Luigi D.; Similuk, Morgan; Zhang, Xingmin Aaron; Gómez‐Andrés, David; Lochmüller, Hanns; Dollfus, Hélène; Rosenzweig, Sergio D.; Marwaha, Shruti; Rath, Ana; Sullivan, Kathleen E.; Smith, Cynthia L.; Milner, Joshua D.; Leroux, Dorothée; Boerkoel, Cornelius F.; Klion, Amy D.; Carter, Melody C.; Groza, Tudor; Smedley, Damian; Haendel, Melissa; Mungall, Chris; Robinson, Peter N.

doi:10.1093/nar/gky1105

Cited by 614 publications

(562 citation statements)

References 62 publications

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“…We have identified 97 different morphological variants in our study cohort. Differences in the number of morphological variants observed between studies is likely due to of the recent efforts to establish unequivocal terminology of dysmorphic features and a clear ontology (Allanson et al, ; Kohler et al, ). Dysmorphic features previously lumped together in big ontology branches can now be broken down into multiple distinctive features, thus extending the list of possible identifiable features.…”

Section: Discussionmentioning

confidence: 99%

“…We have identified 97 different morphological variants in our study cohort. Differences in the number of morphological variants observed between studies is likely due to of the recent efforts to establish unequivocal terminology of dysmorphic features and a clear ontology (Allanson et al, 2009;Kohler et al, 2019 Table 4, the threshold was set at 4%, both for continuous and discontinuous features. Hennekam et al (2013) recently suggested a 2.5% cut-off while acknowledging the broad use of 4%.…”

Section: General Characteristicsmentioning

confidence: 99%

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Morphological characterization of newborns in Kinshasa, DR Congo: Common variants, minor, and major anomalies

Mubungu

Lumaka

Mvuama³

et al. 2020

American J of Med Genetics Pt A

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The evaluation of minor physical variation is crucial in a dysmorphological examination. Currently, data on the spectrum and incidence of minor physical variants in Central African newborns is lacking. We therefore conducted a cross‐sectional descriptive study of 722 newborns recruited within the first 24 hr of life, in two large maternities in Kinshasa, DR Congo. Minor anomalies were defined according to the series of articles in AJMG Part A and coded as human phenotype ontology terms. A total of 97 different morphological variants were recorded of which 13 were common. About 34.8% of the newborn carried one minor anomaly, 11.6% had two, and 4.3% had three minor anomalies. No gender differences were observed, but the incidence of specific anomalies appeared to vary with the geographical origin of parents within the DR Congo. The results of this study will aid clinicians to interpret morphological variation in Central African newborns.

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Section: Discussionmentioning

confidence: 99%

“…We have identified 97 different morphological variants in our study cohort. Differences in the number of morphological variants observed between studies is likely due to of the recent efforts to establish unequivocal terminology of dysmorphic features and a clear ontology (Allanson et al, 2009;Kohler et al, 2019 Table 4, the threshold was set at 4%, both for continuous and discontinuous features. Hennekam et al (2013) recently suggested a 2.5% cut-off while acknowledging the broad use of 4%.…”

Section: General Characteristicsmentioning

confidence: 99%

Morphological characterization of newborns in Kinshasa, DR Congo: Common variants, minor, and major anomalies

Mubungu

Lumaka

Mvuama³

et al. 2020

American J of Med Genetics Pt A

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“…A specific checklist was designed to study MDS to assess the degree of severity for each case (Table S1). The features in the checklist were annotated according to the Human Phenotype Ontology (HPO) database …”

Section: Methodsmentioning

confidence: 99%

“…The features in the checklist were annotated according to the Human Phenotype Ontology (HPO) database. 14 The study was approved by the ethical committees of Hospital…”

Section: Patientsmentioning

confidence: 99%

Molecular characterization of Spanish patients with MECP2 duplication syndrome

Pascual‐Alonso¹,

Blasco²,

Vidal³

et al. 2020

Clinical Genetics

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MECP2 duplication syndrome (MDS) is an X‐linked neurodevelopmental disorder characterized by a severe to profound intellectual disability, early onset hypotonia and diverse psycho‐motor and behavioural features. To date, fewer than 200 cases have been published. We report the clinical and molecular characterization of a Spanish MDS cohort that included 19 boys and 2 girls. Clinical suspicions were confirmed by array comparative genomic hybridization and multiplex ligation‐dependent probe amplification (MLPA). Using, a custom in‐house MLPA assay, we performed a thorough study of the minimal duplicated region, from which we concluded a complete duplication of both MECP2 and IRAK1 was necessary for a correct MDS diagnosis, as patients with partial MECP2 duplications lacked some typical clinical traits present in other MDS patients. In addition, the duplication location may be related to phenotypic severity. This observation may provide a new approach for genotype‐phenotype correlations, and thus more personalized genetic counselling.

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“…The patient classifications were based on the criteria described in previous Registry publications (Kishnani et al, , ) to allow for meaningful analysis, interpretation, and explanation of results of the reported Registry data. Clinical features of phenotypes were described using available Human Phenotype Ontology (HPO) terms and identification numbers (Kohler et al, ; The Human Phenotype Ontology (HPO), ).…”

Section: Methodsmentioning

confidence: 99%

GAA variants and phenotypes among 1,079 patients with Pompe disease: Data from the Pompe Registry

et al. 2019

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Identification of variants in the acid α‐glucosidase (GAA) gene in Pompe disease provides valuable insights and systematic overviews are needed. We report on the number, nature, frequency, and geographic distribution of GAA sequence variants listed in the Pompe Registry, a long‐term, observational program and the largest global repository of Pompe disease data. Variant information was reviewed and compared with publicly available GAA databases/resources. Among 1,079 eligible patients, 2,075 GAA variants (80 unique novel) were reported. Variants were listed by groups representing Pompe disease phenotypes. Patients were classified as Group A: Symptom onset ≤ 12 months of age with cardiomyopathy; Group B: Symptom onset ≤ 12 years of age (includes patients with symptom onset ≤ 12 months of age without cardiomyopathy); or Group C: Symptom onset > 12 years of age. Likely impact of novel variants was predicted using bioinformatics algorithms. Variants were classified by pathogenicity using ACMG guidelines. Data reported from the Pompe Registry provide new information about the distribution of GAA variants globally and across the clinical spectrum, add to the number and diversity of GAA variants registered in public databases through published data sharing, provide a first indication of the severity of novel variants, and assist in diagnostic practice and outcome prediction.

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Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

Cited by 614 publications

References 62 publications

Morphological characterization of newborns in Kinshasa, DR Congo: Common variants, minor, and major anomalies

Morphological characterization of newborns in Kinshasa, DR Congo: Common variants, minor, and major anomalies

Molecular characterization of Spanish patients with MECP2 duplication syndrome

GAA variants and phenotypes among 1,079 patients with Pompe disease: Data from the Pompe Registry

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