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GenoPheno: cataloging large-scale phenotypic and next-generation sequencing data within human datasets
- Source :
- Briefings in Bioinformatics
- Publication Year :
- 2020
- Publisher :
- Oxford University Press (OUP), 2020.
-
Abstract
- Precision medicine promises to revolutionize treatment, shifting therapeutic approaches from the classical one-size-fits-all to those more tailored to the patient’s individual genomic profile, lifestyle and environmental exposures. Yet, to advance precision medicine’s main objective—ensuring the optimum diagnosis, treatment and prognosis for each individual—investigators need access to large-scale clinical and genomic data repositories. Despite the vast proliferation of these datasets, locating and obtaining access to many remains a challenge. We sought to provide an overview of available patient-level datasets that contain both genotypic data, obtained by next-generation sequencing, and phenotypic data—and to create a dynamic, online catalog for consultation, contribution and revision by the research community. Datasets included in this review conform to six specific inclusion parameters that are: (i) contain data from more than 500 human subjects; (ii) contain both genotypic and phenotypic data from the same subjects; (iii) include whole genome sequencing or whole exome sequencing data; (iv) include at least 100 recorded phenotypic variables per subject; (v) accessible through a website or collaboration with investigators and (vi) make access information available in English. Using these criteria, we identified 30 datasets, reviewed them and provided results in the release version of a catalog, which is publicly available through a dynamic Web application and on GitHub. Users can review as well as contribute new datasets for inclusion (Web: https://avillachlab.shinyapps.io/genophenocatalog/; GitHub: https://github.com/hms-dbmi/GenoPheno-CatalogShiny).
- Subjects :
- catalog
AcademicSubjects/SCI01060
Computer science
precision medicine
Cataloging
Dynamic web page
03 medical and health sciences
0302 clinical medicine
Database Review
Databases, Genetic
Humans
Genetic Predisposition to Disease
Molecular Biology
Exome sequencing
030304 developmental biology
Whole genome sequencing
0303 health sciences
Whole Genome Sequencing
phenotypic data
High-Throughput Nucleotide Sequencing
Subject (documents)
Precision medicine
Data science
Biobank
Phenotype
next-generation sequencing data
Genomic Profile
biobanks
Large-scale datasets
030217 neurology & neurosurgery
Information Systems
Subjects
Details
- ISSN :
- 14774054
- Volume :
- 22
- Database :
- OpenAIRE
- Journal :
- Briefings in Bioinformatics
- Accession number :
- edsair.doi.dedup.....dbd00cd855fa4cad1745b07739fd9ffa