GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

By Umadevi Paila, Brad A. Chapman, Rory D. Kirchner, Aaron R. Quinlan. PLoS Comput. Biol., 2013

412 citations recorded by the source corpus.

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.

Subfields: Artificial Intelligence, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/20fb7483a4cff6651bf0feb46e7b9aaa6277eede

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Artificial Intelligence

In Genetics

In Molecular Biology

Citations in the corpus

SpeedSeq: Ultra-fast personal genome analysis and interpretation (2014, methodology): “We have engineered SpeedSeq to seamlessly interface with GEMINI, a flexible software package for genome mining[21].”
FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer (2014, methodology): “A number of tools have been developed using these data to annotate potential regulatory variants or to suggest the most likely causal variants in linkage disequilibrium with GWAS SNPs, such as Haploreg [18], RegulomeDB [19], ANNOVAR [20], GEMINI [21], FunciSNP [22], and VEP [23].”
The Ensembl Variant Effect Predictor (2016, methodology): “VEP’s annotations are used as input to tools for deep exploration of variant annotation such as GEMINI [33].”
DGIdb 2.0: mining clinically relevant drug–gene interactions (2015, background): “In addition, a number of other bioinformatics tools have used DGIdb in developing their own platforms including PANDA (22), iCAGES (icages.usc.edu), BioGPS (23), OmicsPipe (24), GEMINI (25), StationX (www.stationxinc. com) and IHLDB.rf (www.lungcancerdatabase.com), highlighting the broad usefulness ”
Settling the score: variant prioritization and Mendelian disease (2017, neutral): “Genome Mining (GEMINI) 69 , seqr (see Further Information), Variant Association Tools 70 and ANNOVAR 49 , for example, use filtering approaches that prioritize variants only if they follow a specified mode of inheritance, are predicted to affect protein sequence or function and have a population…”
DGIdb 3.0: a redesign and expansion of the drug–gene interaction database (2017, neutral): “edu), BioGPS (23), Omics Pipe (24), GEMINI (25), StationX (www.”
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018, methodology): “Examples of new tools include: GEMINI for exploring genetic variation (12); mothur for analyzing rRNA gene sequences (13); QIIME for quantitative microbiome analysis from raw DNA sequencing data (14); deepTools for explorative analysis of deeply sequence data (15,16); HiCexplorer (17) for analysis a”
Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR (2015, methodology): “In general, these tools can be accessed either through command line (for example, VEP 15 , VAAST 17 , pVAAST 37 , AnnTools 18 , SnpEff 38 and GEMINI 39 ) or on the web (for example, VAT 40 , SeattleSeq 41 , AVIA 42 and VARIANT 43 ).”