GEMINI: integrative exploration of genetic variation and genome annotations

Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical genetics. We have developed GEMINI (GEnome MINIng), a flexib...

Full description

Saved in:
Bibliographic Details
Published in:PLoS computational biology 2013-07, Vol.9 (7), p.e1003153-e1003153
Main Authors: Paila, Umadevi, Chapman, Brad A, Kirchner, Rory, Quinlan, Aaron R
Format: Article
Language:English
Subjects:
Biology
Computational biology
Data Mining
Databases, Genetic
DNA methylation
Genes
Genetic Variation
Genome, Human
Genomics
Genomics - methods
Genotype
Humans
Medical research
Software
Studies
Technology application
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical genetics. We have developed GEMINI (GEnome MINIng), a flexible software package for exploring all forms of human genetic variation. Unlike existing tools, GEMINI integrates genetic variation with a diverse and adaptable set of genome annotations (e.g., dbSNP, ENCODE, UCSC, ClinVar, KEGG) into a unified database to facilitate interpretation and data exploration. Whereas other methods provide an inflexible set of variant filters or prioritization methods, GEMINI allows researchers to compose complex queries based on sample genotypes, inheritance patterns, and both pre-installed and custom genome annotations. GEMINI also provides methods for ad hoc queries and data exploration, a simple programming interface for custom analyses that leverage the underlying database, and both command line and graphical tools for common analyses. We demonstrate GEMINI's utility for exploring variation in personal genomes and family based genetic studies, and illustrate its ability to scale to studies involving thousands of human samples. GEMINI is designed for reproducibility and flexibility and our goal is to provide researchers with a standard framework for medical genomics.
ISSN:1553-7358
1553-734X
1553-7358
DOI:10.1371/journal.pcbi.1003153