|Title||SNPpy--database management for SNP data from genome wide association studies.|
|Publication Type||Journal Article|
|Year of Publication||2011|
|Authors||Mitha, Faheem, Herodotos Herodotou, Nedyalko Borisov, Chen Jiang, Josh Yoder, and Kouros Owzar|
|Keywords||Databases, Genetic, Genome-Wide Association Study, Humans, Polymorphism, Single Nucleotide, Software|
BACKGROUND: We describe SNPpy, a hybrid script database system using the Python SQLAlchemy library coupled with the PostgreSQL database to manage genotype data from Genome-Wide Association Studies (GWAS). This system makes it possible to merge study data with HapMap data and merge across studies for meta-analyses, including data filtering based on the values of phenotype and Single-Nucleotide Polymorphism (SNP) data. SNPpy and its dependencies are open source software.RESULTS: The current version of SNPpy offers utility functions to import genotype and annotation data from two commercial platforms. We use these to import data from two GWAS studies and the HapMap Project. We then export these individual datasets to standard data format files that can be imported into statistical software for downstream analyses.CONCLUSIONS: By leveraging the power of relational databases, SNPpy offers integrated management and manipulation of genotype and phenotype data from GWAS studies. The analysis of these studies requires merging across GWAS datasets as well as patient and marker selection. To this end, SNPpy enables the user to filter the data and output the results as standardized GWAS file formats. It does low level and flexible data validation, including validation of patient data. SNPpy is a practical and extensible solution for investigators who seek to deploy central management of their GWAS data.
|Alternate Journal||PLoS One|
|Original Publication||SNPpy--database management for SNP data from genome wide association studies.|
|PubMed Central ID||PMC3198468|
|Grant List||CA33601 / CA / NCI NIH HHS / United States |
U01 GM061393 / GM / NIGMS NIH HHS / United States
U10 CA033601 / CA / NCI NIH HHS / United States
P01CA142538 / CA / NCI NIH HHS / United States
P01 CA142538 / CA / NCI NIH HHS / United States
U01GM061393 / GM / NIGMS NIH HHS / United States
SNPpy--database management for SNP data from genome wide association studies.