What is PhenoMatcher
PhenoMatcher is developed as part of the exome reanalysis pipeline for the paper Post-reporting reanalysis of exome sequencing data – molecular diagnostic and clinical genomic outcomes, by Liu et al. The code used in this program is a re-implementation and extension of the algorithm from a previous publication by James et al, A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics. (2016) Genome Med. 8:13. The algorithm was used in the publication by Posey and Harel et al, Resolution of disease phenotypes sesulting from multilocus genomic variation (2017) N Engl J Med 376: 21-31.
PhenoMatcher takes human phenotype ontology (HPO) term sets as inputs, and calculates semantic similarity scores
between the input term sets and all disease genes reported in OMIM https://www.omim.org/.
How to interpret the results
PhenoMatcher annotates each disease-associated gene with:
1. entrez_gene_symbol: gene symbols of Entrez genes
2. disease_id_max: the OMIM disease identifier corresponding to the disease gene. When the same gene is associated with multiple diseases, the best matching disease ID is shown.
3. PhenoMatcher_score_max: semantic similarity score between the input HPO term set and the disease term set. When the same gene is associated with multiple diseases, the highest matching score is shown.
4. dz_ID_all: similar to # 2, with all disease identifiers listed
5. scores: similar to # 3, with all matching scores listed
6. ID: patient identification
7. Patient_HPO: input HPO terms
Additional documentation
The source codes and documentation can be found in the GitHub link:
https://github.com/liu-lab/exome_reanalysis
Contact us
Please contact us at [email protected];[email protected];[email protected]