Use of model organism and disease databases to support matchmaking for human disease gene discovery.
The Matchmaker Exchange application programming interface (API) allows searching a patient's genotypic or phenotypic profiles across clinical sites, for the purposes of cohort discovery and variant disease causal validation. This API can be used not only to search for matching patients, but also to match against public disease and model organism data. This public disease data enable matching known diseases and variant-phenotype associations using phenotype semantic similarity algorithms developed by the Monarch Initiative. The model data can provide additional evidence to aid diagnosis, suggest relevant models for disease mechanism and treatment exploration, and identify collaborators across the translational divide. The Monarch Initiative provides an implementation of this API for searching multiple integrated sources of data that contextualize the knowledge about any given patient or patient family into the greater biomedical knowledge landscape. While this corpus of data can aid diagnosis, it is also the beginning of research to improve understanding of rare human diseases.
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California.
Christopher J
CJ
Mungall
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California.
Nicole L
NL
Washington
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California.
Jeremy
J
Nguyen-Xuan
San Diego Supercomputing Center, UC San Diego, La Jolla, California.
Christopher
C
Condit
Wellcome Trust Sanger Institute, Mouse Informatics group, Hinxton, UK.
Damian
D
Smedley
Charité - Universitätsmedizin Berlin, Institute for Medical and Human Genetics, Berlin, Germany.
Sebastian
S
Köhler
Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia.
Tudor
T
Groza
Department of Biomedical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon.
Kent
K
Shefchek
Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania.
Harry
H
Hochheiser
Charité - Universitätsmedizin Berlin, Institute for Medical and Human Genetics, Berlin, Germany.
Peter N
PN
Robinson
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California.
Suzanna E
SE
Lewis
Department of Biomedical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon.
Melissa A
MA
Haendel
D000818:Animals; D030541:Databases, Genetic; D004194:Disease / Q000235:genetics*; D004195:Disease Models, Animal; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D014644:Genetic Variation; D006801:Humans; D033181:Information Dissemination; D010641:Phenotype; D014584:User-Computer Interface
Matchmaker Exchange; informatics; model systems; ontology; phenotype; rare disease