PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data.

TitlePhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data.
Publication TypeJournal Article
Year of Publication2021
AuthorsWohler, E, Martin, R, Griffith, S, Rodrigues, Eda S, Antonescu, C, Posey, JE, Coban-Akdemir, Z, Jhangiani, SN, Doheny, KF, Lupski, JR, Valle, D, Hamosh, A, Sobreira, N
JournalOrphanet J Rare Dis
Date Published2021 Aug 18
KeywordsComputational Biology, Databases, Genetic, Genomics, Humans, Phenotype, Software

BACKGROUND: With the advent of whole exome (ES) and genome sequencing (GS) as tools for disease gene discovery, rare variant filtering, prioritization and data sharing have become essential components of the search for disease genes and variants potentially contributing to disease phenotypes. The computational storage, data manipulation, and bioinformatic interpretation of thousands to millions of variants identified in ES and GS, respectively, is a challenging task. To aid in that endeavor, we constructed PhenoDB, GeneMatcher and VariantMatcher.

RESULTS: PhenoDB is an accessible, freely available, web-based platform that allows users to store, share, analyze and interpret their patients' phenotypes and variants from ES/GS data. GeneMatcher is accessible to all stakeholders as a web-based tool developed to connect individuals (researchers, clinicians, health care providers and patients) around the globe with interest in the same gene(s), variant(s) or phenotype(s). Finally, VariantMatcher was developed to enable public sharing of variant-level data and phenotypic information from individuals sequenced as part of multiple disease gene discovery projects. Here we provide updates on PhenoDB and GeneMatcher applications and implementation and introduce VariantMatcher.

CONCLUSION: Each of these tools has facilitated worldwide data sharing and data analysis and improved our ability to connect genes to phenotypic traits. Further development of these platforms will expand variant analysis, interpretation, novel disease-gene discovery and facilitate functional annotation of the human genome for clinical genomics implementation and the precision medicine initiative.

Alternate JournalOrphanet J Rare Dis
PubMed ID34407837
PubMed Central IDPMC8371856
Grant ListP50 HD103538 / HD / NICHD NIH HHS / United States
K08 HG008986 / HG / NHGRI NIH HHS / United States
UM1 HG006542 / NH / NIH HHS / United States

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