Navigating the Phenotype Frontier: The Monarch Initiative

McMurry, Julie A.; Köhler, Sebastian; Washington, Nicole; Balhoff, James P.; Borromeo, Charles; Brush, Matthew; Carbon, Seth; Conlin, Tom; Dunn, Nathan; Engelstad, Mark; Foster, Erin D.; Gourdine, Jean-Philippe; Jacobsen, Julius O. B.; Keith, Daniel; Laraway, Bryan; Xuan, Jeremy Nguyen; Shefchek, Kent; Vasilevsky, Nicole; Zhou, Yuan; Lewis, Suzanna; Hochheiser, Harry; Groza, Tudor; Smedley, Damian; Robinson, Peter N.; Mungall, Christopher J.; Haendel, Melissa

doi:10.1534/genetics.116.188870

Cited by 70 publications

(58 citation statements)

References 17 publications

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“…The GIST is thus intended to be used in conjunction with all relevant species- or tissue-specific phenotype ontologies such that the type of genetic interaction is curated as a separate entity from the specific phenotype that is scored. This approach allows BioGRID to take full advantage of rigorous phenotype ontologies across model systems and humans, including Uberon, the Monarch Initiative, the Human Phenotype Ontology, and others (57,58). For yeast genetic interactions, 11 of the current BioGRID GI terms map to seven of the new GIST terms that will be used for curation going forward in 2017.…”

Section: Genetic Interaction Curationmentioning

confidence: 99%

The BioGRID interaction database: 2017 update

et al. 2016

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The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the annotation and archival of protein, genetic and chemical interactions for all major model organism species and humans. As of September 2016 (build 3.4.140), the BioGRID contains 1 072 173 genetic and protein interactions, and 38 559 post-translational modifications, as manually annotated from 48 114 publications. This dataset represents interaction records for 66 model organisms and represents a 30% increase compared to the previous 2015 BioGRID update. BioGRID curates the biomedical literature for major model organism species, including humans, with a recent emphasis on central biological processes and specific human diseases. To facilitate network-based approaches to drug discovery, BioGRID now incorporates 27 501 chemical–protein interactions for human drug targets, as drawn from the DrugBank database. A new dynamic interaction network viewer allows the easy navigation and filtering of all genetic and protein interaction data, as well as for bioactive compounds and their established targets. BioGRID data are directly downloadable without restriction in a variety of standardized formats and are freely distributed through partner model organism databases and meta-databases.

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Section: Genetic Interaction Curationmentioning

confidence: 99%

The BioGRID interaction database: 2017 update

et al. 2016

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“…Patient Archive (PA) (2) is a clinical-grade phenotype-oriented platform for managing patient data; PA combines the richness of the HPO with highly intuitive user interfaces to aid the discovery and decision-making process in the context of clinical genomics. PA enables clinicians to use free text clinical notes as the starting point for structured HPO-centric patient phenotyping to support clinical diagnostics and care.…”

Section: Clinical Utilitymentioning

confidence: 99%

“…The HPO was initially published in 2008 (1) with the goal of enabling the integration of phenotype information across scientific fields and databases. Since then, the project has grown in terms of coverage, scope and sophistication, and has become a core component of the Monarch Initiative, allowing computational cross-species analysis (2). …”

Section: Introductionmentioning

confidence: 99%

The Human Phenotype Ontology in 2017

et al. 2016

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Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.

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“…Tracking these individuals might also identify information regarding the progression of the disease and any shared, or individual, phenotypes that might be relevant to study in the future. Of course, we look forward to the day when there is a comprehensive and interactive database that incorporates extensive phenotypic and whole-genome information while maintaining acceptable privacy standards, but no such database currently exists, although there are certainly efforts along these lines (Kibbe et al 2015; McMurry et al 2016). …”

Section: Discussionmentioning

confidence: 99%

KBG syndrome involving a single-nucleotide duplication in ANKRD11

Kleyner

Malcolmson

Tegay

et al. 2016

Cold Spring Harb Mol Case Stud

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KBG syndrome is a rare autosomal dominant genetic condition characterized by neurological involvement and distinct facial, hand, and skeletal features. More than 70 cases have been reported; however, it is likely that KBG syndrome is underdiagnosed because of lack of comprehensive characterization of the heterogeneous phenotypic features. We describe the clinical manifestations in a male currently 13 years of age, who exhibited symptoms including epilepsy, severe developmental delay, distinct facial features, and hand anomalies, without a positive genetic diagnosis. Subsequent exome sequencing identified a novel de novo heterozygous single base pair duplication (c.6015dupA) in ANKRD11, which was validated by Sanger sequencing. This single-nucleotide duplication is predicted to lead to a premature stop codon and loss of function in ANKRD11, thereby implicating it as contributing to the proband's symptoms and yielding a molecular diagnosis of KBG syndrome. Before molecular diagnosis, this syndrome was not recognized in the proband, as several key features of the disorder were mild and were not recognized by clinicians, further supporting the concept of variable expressivity in many disorders. Although a diagnosis of cerebral folate deficiency has also been given, its significance for the proband's condition remains uncertain.

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Navigating the Phenotype Frontier: The Monarch Initiative

Cited by 70 publications

References 17 publications

The BioGRID interaction database: 2017 update

The BioGRID interaction database: 2017 update

The Human Phenotype Ontology in 2017

KBG syndrome involving a single-nucleotide duplication in ANKRD11

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